Patent Application
20250205357
The contents of the electronic sequence listing (H082470405WO00-SEQ-AZW.xml; Size: 115,494 bytes; and Date of Creation: Mar. 13, 2023) is herein incorporated by reference in its entirety.
Arrestin domain-containing protein 1 (ARRDC1)-mediated microvesicles (ARMMs) have been demonstrated to be able to package and deliver a myriad of therapeutic cargos such as proteins, RNAs, and genome-editors. However, there remains a need to deliver ARMMs and their cargo in a tissue or cell-specific manner.
This invention provides microvesicles with increased cell specificity. The present disclosure provides evidence that surface modification (i.e., pseudotyping) of ARMMs with the Nipah virus (NiV) envelope proteins (glycoprotein [G] and fusion protein [F]) allows targeted delivery into specific cells of cargos contained in the vesicles. For example, it is shown that ARMMs decorated with engineered NiV-G protein that contains a CD8-targeting single-chain variable fragment (scFv) can deliver proteins, as well as mRNAs, into CD8+-T cells. Because the NiV-G protein can be engineered to contain other targeting moieties, ARMMs may thus be pseudotyed with such NiV-G proteins to allow for specific targeting of many other cell or tissue types. In addition, the present disclosure provides for envelope proteins with similar recognition and fusion activities from other viruses, such as the Measles virus, that can be used to modify ARMMs for targeted delivery.
Thus, in one aspect, the present disclosure provides ARRDC1-mediated microvesicles (ARMMs), comprising: (i) a lipid bilayer and an ARRDC1 protein or a variant thereof, (ii) a Nipah virus (NiV) glycoprotein variant fused to an antibody or antigen-binding fragment, wherein the NiV glycoprotein variant does not recognize and/or bind to an ephrin receptor, and (iii) a NiV fusion protein. In certain embodiments, the ARRDC1 protein comprises an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 4. In certain embodiments, the NiV glycoprotein variant fused to an antibody or antigen binding fragment comprises an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 58. In certain embodiments, the NiV fusion protein comprises an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to the amino acid sequence SEQ ID NOs: 69.
In some embodiments, the antibody or antigen binding fragment comprises a CD8 targeting antibody or antigen binding fragment. In certain embodiments, the antigen-binding fragment comprises an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 60.
In another aspect, the present disclosure provides microvesicle-producing cells comprising: a first isolated nucleic acid encoding an ARRDC1 protein or a variant thereof, a second isolated nucleic acid encoding a Nipah virus (NiV) glycoprotein variant fused to an antibody or antigen-binding fragment, wherein the NiV glycoprotein variant does not recognize and/or bind to an ephrin receptor, and a third isolated nucleic acid encoding a NiV fusion protein. In some embodiments, the first isolated nucleic acid, the second isolated nucleic acid, and the third isolated nucleic acid are expressed on the same recombinant expression construct under the control of one or more heterologous promoters. In some embodiments, the first isolated nucleic acid, the second isolated nucleic acid, and the third isolated nucleic acid are expressed on more than one recombinant expression construct, wherein the one or more recombinant expression constructs are under the control of one or more heterologous promoters. In certain embodiments, the first isolated nucleic acid, the second isolated nucleic acid, and the third isolated nucleic acid are expressed on different recombinant expression constructs, wherein the different recombinant expression constructs are each under the control of a heterologous promoter.
In some embodiments, the antibody or antigen-binding fragment used in the microvesicles described herein comprises a single-chain variable fragment (scFv). In certain embodiments, the antibody or antigen-binding fragment comprises a nanobody. In certain embodiments, the antibody or antigen-binding fragment comprises an antibody mimetic protein, such as a designed ankyrin repeat protein (DARPin). The antibody or antigen-binding fragment of the microvesicles described herein may be modified to target specific cell types, or a single cell type. In some embodiments, the antibody or antigen-binding fragment targets a particular cell type (e.g., neurons, astrocytes, oligodendrocytes, microglial cells, T-cells, dendritic cells, B cells, NK cells, stem cells, progenitor cells, endothelial cells, muscle cells, myocardial cells, epithelial cells, or hepatic cells). In certain embodiments, the antibody or antigen-binding fragment targets T cells. In certain embodiments, the antibody or antigen-binding fragment targets neurons. In certain embodiments, the antibody or antigen-binding fragment binds selectively to an antigen expressed by target cell. In certain embodiments, the target cell is a CD8 expressing cell. In certain embodiments, the target cell is a T cell.
In various embodiments, the NiV glycoprotein variant and NiV fusion protein used in the microvesicles described herein may be modified (e.g., with amino acid mutations or truncations) relative to the wild-type NiV glycoprotein and fusion protein. In some embodiments, the NiV glycoprotein variant comprises one or more amino acid substitutions relative to a wild-type NiV glycoprotein of SEQ ID NO: 1. The sequence of wild-type NiV glycoprotein can also be found at https://www.uniprot.org/uniprot/Q9IH62. In some embodiments, the one or more amino acid substitutions are selected from the group consisting of Y389X, E501X, W504X, Q530X, E533X, and I588X, wherein X is any amino acid. In some embodiments, the one or more amino acid substitutions are selected from the group consisting of Y389A, E501A, W504A, Q530A, E533A, and I588A. In certain embodiments, the NiV glycoprotein variant comprises amino acid substitutions E501A, W504A, Q530A, and E533A relative to a wild-type NiV glycoprotein of SEQ ID NO: 1.
In addition to the amino acid substitutions described herein, both the NiV glycoprotein and NiV fusion protein may also be truncated for use in the presently described microvesicles. In some embodiments, the NiV glycoprotein variant further comprises a C-terminal truncation. In certain embodiments, the NiV glycoprotein variant further comprises a C-terminal truncation of about 33 or about 34 amino acids in length. In some embodiments, the NiV fusion protein comprises a C-terminal truncation. In certain embodiments, the NiV fusion protein comprises a C-terminal truncation of about 22 amino acids in length.
In various embodiments, the NiV glycoprotein variant comprises an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 63-68. In certain embodiments, the NiV glycoprotein variant comprises the amino acid sequence of any one of SEQ ID NOs: 63-68. In certain embodiments, the NiV fusion protein comprises an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the amino acid sequence of SEQ ID NO: 6. In certain embodiments, the NiV fusion protein comprises the amino acid sequence of SEQ ID NO: 6. In certain embodiments, the ARRDC1 protein comprises an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 3-5. In certain embodiments, the ARRDC1 protein comprises the amino acid sequence of any one of SEQ ID NOs: 3-5.
In various embodiments, the microvesicles described herein may further comprise an agent. In certain embodiments, the agent is fused to the ARRDC1 protein. In certain embodiments, the ARRDC1 protein is fused to TAR. In certain embodiments, TAR recruits an agent fused to Tat, optionally wherein the agent is an RNA. In certain embodiments, the agent is fused to a WW domain, optionally wherein the agent is a protein. In certain embodiments, the WW domain comprises an amino acid sequence of any one of SEQ ID NOs: 7-44, or an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 7-44.
In some embodiments, the agent is selected from the group consisting of a nucleic acid, a protein, and a small molecule. In some embodiments, the nucleic acid comprises an RNA. In certain embodiments, the nucleic acid comprises an RNAi agent (e.g., a coding RNA, a non-coding RNA, an antisense RNA, an mRNA, a small RNA, an siRNA, an shRNA, a microRNA, an snRNA, a snoRNA, a lincRNA, a structural RNA, a ribozyme, or a precursor thereof). In some embodiments, the nucleic acid comprises a DNA. In certain embodiments, the DNA comprises a retrotransposon sequence, a LINE sequence, a SINE sequence, a composite SINE sequence, or an LTR-retrotransposon sequence. In some embodiments, the nucleic acid encodes a protein.
In some embodiments, the agent comprises a detectable label. In some embodiments, the agent comprises a therapeutic agent. In certain embodiments, the agent is selected from the group consisting of an enzyme, an antibody, a Fab, a Fab′, a F(ab′)2, a Fd, a scFv, a Fv, a dsFv, a diabody, and an affibody. The agent may also comprise a protein. For example, in some embodiments, the agent comprises a transcription factor, a transcriptional repressor, a fluorescent protein, a kinase, a phosphatase, a protease, a ligase, or a recombinase. In certain embodiments, the agent comprises a cytotoxic agent. In some embodiments, the agent is covalently bound to the ARRDC1 protein or a variant thereof. For example, the agent may be conjugated to the ARRDC1 protein or a variant thereof via a linker (e.g., a cleavable linker). In some embodiments, the linker comprises a protease recognition site or a UV-cleavable moiety. In some embodiments, the agent is a fusion protein. In some embodiments, the agent comprises a nuclease. In some embodiments, the agent comprises a zinc finger nuclease (ZFN). In some embodiments, the agent comprises a TALEN. In some embodiments, the agent comprises a Cas protein (e.g., a Cas9 protein), or a variant thereof. In certain embodiments, the Cas9 protein is a Cas9 nickase (nCas9) or a nuclease-inactivated Cas9 (dCas9). In certain embodiments, the Cas9 protein or variant thereof is fused to at least one nuclear localization sequence (NLS). In certain embodiments, the microvesicle further comprises a guide RNA (gRNA).
In some embodiments, the fusion protein comprises a nuclease. In certain embodiments, the fusion protein comprises a ZFN. In certain embodiments, the fusion protein comprises a TALEN. In certain embodiments, the fusion protein comprises a Cas protein. In certain embodiments, In certain embodiments, In certain embodiments, In certain embodiments, the microvesicle further comprising a guide RNA (gRNA).
In some embodiments, the agent comprises a detectable label. In certain embodiments, the agent comprises a therapeutic agent. In certain embodiments, the agent comprises a cytotoxic agent.
In some embodiments, the present disclosure provides one or more isolated nucleic acids encoding the ARRDC1 protein, the NiV glycoprotein variant, and the NiV fusion protein of the microvesicle of the disclosure. In some embodiments, the present disclosure provides one or more vectors comprising the one or more isolated nucleic acids of the disclosure. In certain embodiments, the present disclosure provides a vector comprising the isolated nucleic acid of the disclosure.
In some embodiments, the present disclosure provides microvesicle-producing cell comprising a first isolated nucleic acid encoding an ARRDC1 protein or a variant thereof, a second isolated nucleic acid encoding a Nipah virus (NiV) glycoprotein variant fused to an antibody or antigen-binding fragment, wherein the NiV glycoprotein variant does not recognize and/or bind to an ephrin receptor, and a third isolated nucleic acid encoding a NiV fusion protein. In certain embodiments, the ARRDC1 protein comprises an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 4. In certain embodiments, the NiV glycoprotein variant fused to an antibody or antigen binding fragment comprises an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 58. In certain embodiments, the NiV fusion protein comprises an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 69. In certain embodiments, the antigen-binding fragment comprises an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 60.
In some embodiments, the first isolated nucleic acid, the second isolated nucleic acid, and the third isolated nucleic acid are expressed on the same recombinant expression construct under the control of one or more heterologous promoters. In certain embodiments, the first isolated nucleic acid, the second isolated nucleic acid, and the third isolated nucleic acid are expressed on more than one recombinant expression construct, wherein the more than one recombinant expression constructs are under the control of one or more heterologous promoters. the first isolated nucleic acid, the second isolated nucleic acid, and the third isolated nucleic acid are each expressed on different recombinant expression constructs, wherein the different recombinant expression constructs are each under the control of a heterologous promoter.
In some embodiments, the antibody or antigen-binding fragment used in the microvesicles described herein comprises a single-chain variable fragment (scFv). In certain embodiments, the antibody or antigen-binding fragment comprises a nanobody. In certain embodiments, the antibody or antigen-binding fragment comprises an antibody mimetic protein, such as a designed ankyrin repeat protein (DARPin). The antibody or antigen-binding fragment of the microvesicles described herein may be modified to target specific cell types, or a single cell type. In some embodiments, the antibody or antigen-binding fragment targets a particular cell type (e.g., neurons, astrocytes, oligodendrocytes, microglial cells, T-cells, dendritic cells, B cells, NK cells, stem cells, progenitor cells, endothelial cells, muscle cells, myocardial cells, epithelial cells, or hepatic cells). In certain embodiments, the antibody or antigen-binding fragment targets T cells. In certain embodiments, the antibody or antigen-binding fragment targets neurons. In certain embodiments, the antibody or antigen-binding fragment binds selectively to an antigen expressed by target cell. In certain embodiments, the target cell is a CD8 expressing cell. In certain embodiments, the target cell is a T cell.
In various embodiments, the NiV glycoprotein variant and NiV fusion protein used in the microvesicles described herein may be modified (e.g., with amino acid mutations or truncations) relative to the wild-type NiV glycoprotein and fusion protein. In some embodiments, the NiV glycoprotein variant comprises one or more amino acid substitutions relative to a wild-type NiV glycoprotein of SEQ ID NO: 1. The sequence of wild-type NiV glycoprotein can also be found at https://www.uniprot.org/uniprot/Q9IH62. In some embodiments, the one or more amino acid substitutions are selected from the group consisting of Y389X, E501X, W504X, Q530X, E533X, and I588X, wherein X is any amino acid. In some embodiments, the one or more amino acid substitutions are selected from the group consisting of Y389A, E501A, W504A, Q530A, E533A, and I588A. In certain embodiments, the NiV glycoprotein variant comprises amino acid substitutions E501A, W504A, Q530A, and E533A relative to a wild-type NiV glycoprotein of SEQ ID NO: 1.
In addition to the amino acid substitutions described herein, both the NiV glycoprotein and NiV fusion protein may also be truncated for use in the presently described microvesicles. In some embodiments, the NiV glycoprotein variant further comprises a C-terminal truncation. In certain embodiments, the NiV glycoprotein variant further comprises a C-terminal truncation of about 33 or about 34 amino acids in length. In some embodiments, the NiV fusion protein comprises a C-terminal truncation. In certain embodiments, the NiV fusion protein comprises a C-terminal truncation of about 22 amino acids in length.
In various embodiments, the NiV glycoprotein variant comprises an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOS: 63-68. In certain embodiments, the NiV glycoprotein variant comprises the amino acid sequence of any one of SEQ ID NOs: 63-68. In certain embodiments, the NiV fusion protein comprises an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the amino acid sequence of SEQ ID NO: 6. In certain embodiments, the NiV fusion protein comprises the amino acid sequence of SEQ ID NO: 6. In certain embodiments, the ARRDC1 protein comprises an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOs: 3-5. In certain embodiments, the ARRDC1 protein comprises the amino acid sequence of any one of SEQ ID NOs: 3-5.
In another aspect, the present disclosure provides methods of delivering a molecule to a target cell comprising contacting the target cell with any of the microvesicles described herein. In some embodiments, the target cells are T cells. In some embodiments, the methods described herein are performed in vitro. In some embodiments, the methods described herein are performed ex vivo. In some embodiments, the methods described herein are performed in vivo.
In another aspect, the present disclosure provides methods of treating a patient consisting of administering to the patient any of the microvesicles described herein.
In another aspect, the present disclosure provides methods of treating a patient consisting of administering to the patient any of the microvesicle-producing cells described herein.
In another aspect, the present disclosure provides methods of delivering ARMMs, comprising delivering any of the ARMMs described herein, or any of the microvesicle-producing cells described herein, to a subject. In some embodiments, the subject is mammalian. In certain embodiments, the subject is human.
In another aspect, the present disclosure provides kits comprising one or more of the ARMMs described herein, or one or more of the microvesicle-producing cells described herein.
Other advantages, features, and uses of the invention will be apparent from the detailed description of certain exemplary, non-limiting embodiments, the drawings, the non-limiting working examples, and the claims.
As used herein, the term “agent” refers to a substance that can be incorporated in an ARMM, for example, into the liquid phase of the ARMM or into the lipid bilayer of the ARMM. In some embodiments, the agent is an agent to be delivered to a target cell. In some embodiments, the agent is a biologically active agent, i.e., it has activity in a cell, biological system, and/or subject. For instance, a substance that, when administered to a subject, has a biological effect on that subject, is considered to be biologically active. In some embodiments, an agent is a therapeutic agent. As used herein, the term “therapeutic agent” refers to any agent that, when administered to a subject, has a therapeutic, diagnostic, and/or prophylactic effect and/or elicits a desired biological and/or pharmacological effect. As used herein, the term “therapeutic agent” may be a nucleic acid that is delivered to a cell via its association with or inclusion into an ARMM. In certain embodiments, the agent is a nucleic acid. In some embodiments, the nucleic acid encodes a protein. In certain embodiments, the agent is DNA (e.g., a retrotransposon sequence, a LINE sequence, a SINE sequence, a composite SINE sequence, or an LTR-retrotransposon sequence). In certain embodiments, the agent is RNA (e.g., an RNAi agent, a coding RNA, a non-coding RNA, an antisense RNA, an mRNA, a small RNA, an siRNA, an shRNA, a microRNA, an snRNA, a snoRNA, a lincRNA, a structural RNA, a ribozyme, or a precursor thereof). the agent is selected from the group consisting of an enzyme, an antibody, a Fab, a Fab′, a F(ab′)2, a Fd, a scFv, a Fv, a dsFv, a diabody, and an affibody. In certain embodiments, the agent is a peptide or protein. In some embodiments, the protein is a transcription factor, a transcriptional repressor, a fluorescent protein, a kinase, a phosphatase, a protease, a ligase, or a recombinase. In certain embodiments, the agent to be delivered is a small molecule. In some embodiments, the small molecule is an FDA-approved drug. In some embodiments, the agent is a fusion protein. In certain embodiments, the agent comprises a nuclease. In certain embodiments, the agent comprises a zinc finger nuclease. In certain embodiments, the agent comprises a TALEN. In certain embodiments, the agent comprises a Cas protein. In certain embodiments, the agent comprises a Cas9 protein, or a variant thereof (e.g., nCas9 or dCas9). In some embodiments, the agent to be delivered is a diagnostic agent. In some embodiments, the agent to be delivered is useful as an imaging agent. In some embodiments, the agent comprises a detectable label.
An “antibody” refers to a glycoprotein belonging to the immunoglobulin superfamily. With some exceptions, mammalian antibodies are typically made of basic structural units each with two large heavy chains and two small light chains. There are several different types of antibody heavy chains, and several different kinds of antibodies, which are grouped together into different isotypes based on which heavy chain they possess. Five different antibody isotypes are known in mammals (IgG, IgA, IgE, IgD, and IgM), which perform different roles, and help direct the appropriate immune response for each different type of foreign object they encounter. Antibodies (and antigen-binding fragments) may be used in the present disclosure to target ARMMs to a particular cell type. The term “antibody” as used herein also encompasses antibody fragments and nanobodies, as well as variants of antibodies and variants of antibody fragments and nanobodies. In some embodiments, an antibody is a nanobody. In some embodiments, an antibody is a single chain variable fragment (scFv).
As used herein, the terms “approximately” and “about,” as applied to one or more values of interest, refer to a value that is similar to a stated reference value. In certain embodiments, the term “approximately” or “about” refers to a range of values that fall within 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, or less in either direction (greater than or less than) of the stated reference value unless otherwise stated or otherwise evident from the context (for example, when such number would exceed 100% of a possible value).
As used herein, the terms “Arrestin domain-containing protein 1” and “ARRDC1” or variants thereof refer to a protein that comprises a PSAP (SEQ ID NO: 2) and a PPXY motif, also referred to herein as a PSAP (SEQ ID NO: 2) and PPXY motif, respectively, in its C-terminus, and interacts with TSG101. Exemplary, non-limiting ARRDC1 protein sequences are provided herein, and additional, suitable ARRDC1 protein variants according to aspects of this invention are known in the art. For example, ARRDC1 variants are described in detail in PCT Publication WO2021/062196; the entire contents of which are hereby incorporated by reference in its entirety. It will be appreciated by those of skill in the art that this invention is not limited in this respect. Exemplary ARRDC1 sequences include the following (PSAP (SEQ ID NO: 2) and PPXY motifs are marked):
The terms “ARRDC1-mediated microvesicle” or “ARMM,” as used herein, refer to a microvesicle comprising an ARRDC1 protein or variant thereof, and/or TSG101 protein, or variant thereof. ARMMs have been described in detail, for example, in PCT application number PCT/US2013/024839, filed Feb. 6, 2013 (published as WO 2013/119602 A1 on Aug. 15, 2013) by Lu et al., and entitled “Arrdc1-Mediated Microvesicles (ARMMs) and Uses Thereof,” as well as in U.S. Pat. Nos. 9,737,480; 9,816,080; 10,260,055, 10,945,954, 11,001,817, and PCT Publications WO2018/067546, WO2021/062196, and WO2021/252924; the entire contents of which are hereby incorporated by reference in their entirety. In some embodiments, the ARMM is shed from a cell, and comprises an agent, for example, a nucleic acid, protein, or small molecule, present in the cytoplasm or associated with the membrane of the cell. In some embodiments, the ARMM is shed from a transgenic cell comprising a recombinant expression construct that includes a transgene, and the ARMM comprises a gene product, for example, an RNA transcript and/or a protein (e.g., an ARRDC1-Tat fusion protein and a TAR-payload RNA) encoded by the expression construct. In some embodiments, the ARMM is produced synthetically, for example, by contacting a lipid bilayer with an ARRDC1 protein or a variant thereof, or a variant thereof, in a cell-free system in the presence of TSG101, or a variant thereof. In other embodiments, the ARMM is synthetically produced by contacting a lipid bilayer with HECT domain ligase, and VPS4a. In some embodiments, an ARMM lacks a late endosomal marker. Some of the ARMMs provided herein do not include, or are negative for, one or more exosomal biomarkers. Exosomal biomarkers are known to those of skill in the art and include, but are not limited to, CD63, Lamp-1, Lamp-2, CD9, HSPA8, GAPDH, CD81, SDCBP, PDCD6IP, ENO1, ANXA2, ACTB, YWHAZ, HSP90AA1, ANXA5, EEF1A1, YWHAE, PPIA, MSN, CFL1, ALDOA, PGK1, EEF2, ANXA1, PKM2, HLA-DRA, and YWHAB. Certain ARMMs provided herein may include an exosomal biomarker. Accordingly, some ARMMs may be negative for one or more other exosomal biomarkers, but positive for one or more different exosomal biomarkers. For example, such an ARMM may be negative for CD63 and Lamp-1 but may include PGK1 or GAPDH; or may be negative for CD63, Lamp-1, CD9, and CD81, but may be positive for HLA-DRA. In some embodiments, ARMMs include an exosomal biomarker, but at a lower level than the level found in exosomes. For example, some ARMMs include one or more exosomal biomarkers at a level of less than about 1%, less than about 5%, less than about 10%, less than about 20%, less than about 30%, less than about 40%, or less than about 50% of the level of that biomarker found in exosomes. To give a non-limiting example, in some embodiments, an ARMM may be negative for CD63 and Lamp-1, include CD9 at a level of less than about 5% of the level of CD9 typically found in exosomes, and be positive for ACTB. Exosomal biomarkers in addition to those listed above are known to those of skill in the art, and the invention is not limited in this regard. In some embodiments, ARMMs provided by the present disclosure may comprise a NiV glycoprotein (or a variant thereof) and a NiV fusion protein (or a variant thereof).
As used herein, the terms “associated with,” “conjugated,” “linked,” “attached,” and “tethered,” when used with respect to two or more entities, for example, moieties, molecules, and/or ARMMs, means that the entities are physically associated or connected with one another, either directly or via one or more additional moieties that serve as a linker, to form a structure that is sufficiently stable so that the entities remain physically associated under the conditions in which the structure is used, e.g., physiological conditions. An ARMM is typically associated with an agent, for example, a nucleic acid, protein, or small molecule, by a mechanism that involves a covalent or non-covalent association. In certain embodiments, the agent is covalently bound to a molecule that is part of the ARMM, for example, an ARRCD1 protein or fragment thereof, a TSG101 protein or fragment thereof, or a lipid or protein that forms part of the lipid bilayer of the ARMM. In some embodiments, a peptide or protein is associated with an ARRCD1 protein or fragment thereof, a TSG101 protein or fragment thereof, or a lipid bilayer-associated protein by a covalent bond (e.g., an amide bond). In some embodiments, the association is via a linker, for example, a cleavable linker. In some embodiments, an entity is associated with an ARMM by inclusion in the ARMM, for example, by encapsulation of an entity (e.g., an agent) within the ARMM. For example, in some embodiments, an agent present in the cytoplasm of an ARMM-producing cell is associated with an ARMM by encapsulation of agent-comprising cytoplasm in the ARMM upon ARMM budding. Similarly, a membrane protein, or other molecule associated with the cell membrane of an ARMM producing cell, may be associated with an ARMM produced by the cell by inclusion into the ARMM membrane upon budding.
The term “Cas9” or “Cas9 protein” refers to an RNA-guided nuclease comprising a Cas9 protein, or a variant thereof (e.g., a protein comprising an active, inactive, or altered DNA cleavage domain of Cas9, and/or the gRNA binding domain of Cas9). A Cas9 nuclease is also referred to sometimes as a casn1 nuclease or a CRISPR (clustered regularly interspaced short palindromic repeat)-associated nuclease. CRISPR is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements, and conjugative plasmids). CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). In type II CRISPR systems, correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc), and a Cas9 protein. The tracrRNA serves as a guide for ribonuclease 3-aided processing of pre-crRNA. Subsequently, Cas9/crRNA/tracrRNA endonucleolytically cleaves a linear or circular dsDNA target complementary to the spacer. The target strand not complementary to crRNA is first cut endonucleolytically, then trimmed 3′-5′ exonucleolytically. In nature, DNA-binding and cleavage typically requires protein and both RNAs. However, single guide RNAs (“sgRNA”, or simply “gRNA”) can be engineered so as to incorporate aspects of both the crRNA and tracrRNA into a single RNA species. See, e.g., Jinek M., Chylinski K., Fonfara I., Hauer M., Doudna J. A., Charpentier E. Science 337:816-821 (2012), the entire contents of which is hereby incorporated by reference. Cas9 recognizes a short motif in the CRISPR repeat sequences (the PAM or protospacer adjacent motif) to help distinguish self versus non-self. Cas9 nuclease sequences and structures are well known to those of skill in the art (see, e.g., “Complete genome sequence of an M1 strain of Streptococcus pyogenes.” Ferretti et al., J. J., McShan W. M., Ajdic D. J., Savic D. J., Savic G., Lyon K., Primeaux C., Sezate S., Suvorov A. N., Kenton S., Lai H. S., Lin S. P., Qian Y., Jia H. G., Najar F. Z., Ren Q., Zhu H., Song L., White J., Yuan X., Clifton S. W., Roe B. A., Mclaughlin R. E., Proc. Natl. Acad. Sci. U.S.A. 98:4658-4663 (2001); “CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III.” Deltcheva E., Chylinski K., Sharma C. M., Gonzales K., Chao Y., Pirzada Z. A., Eckert M. R., Vogel J., Charpentier E., Nature 471:602-607 (2011); and “A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.” Jinek M., Chylinski K., Fonfara I., Hauer M., Doudna J. A., Charpentier E. Science 337:816-821 (2012), the entire contents of each of which are incorporated herein by reference). Cas9 orthologs have been described in various species, including, but not limited to, S. pyogenes and S. thermophilus. Additional suitable Cas9 nucleases and sequences are disclosed in Chylinski, Rhun, and Charpentier, “The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems” (2013) RNA Biology 10:5, 726-737; the entire contents of which are incorporated herein by reference. In some embodiments, a Cas9 nuclease has an inactive (e.g., an inactivated) DNA cleavage domain. In some embodiments, a Cas9 protein, or a variant thereof, is delivered to a target cell using any of the microvesicles disclosed herein. In certain embodiments, the microvesicle further comprises a gRNA.
In some embodiments, a Cas9 protein comprises Streptococcus pyogenes Cas9 of SEQ ID NO: 70, or a variant having at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity with SEQ ID NO: 70:
In some embodiments, a Cas9 protein is a Cas9 nickase in which the nuclease activity of either the RuvC or the HNH domain has been inactivated. In some embodiments, a Cas9 nickase comprises a D10A or an H840A mutation relative to a wild type Streptococcus pyogenes Cas9 of SEQ ID NO: 70, or a variant having at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity with SEQ ID NO: 70.
In some embodiments, a Cas9 protein is a nuclease-inactivated Cas9 protein (also referred to herein as a “dead Cas9” or “dCas9.” In some embodiments, a dCas9 comprises both a D10A and an H840A mutation relative to a wild type Streptococcus pyogenes Cas9 of SEQ ID NO: 70, or a variant having at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity with SEQ ID NO: 70.
In some embodiments, Cas9 refers to Cas9 from: Corynebacterium ulcerans (NCBI Refs: NC_015683.1, NC_017317.1); Corynebacterium diphtheria (NCBI Refs: NC_016782.1, NC_016786.1); Spiroplasma syrphidicola (NCBI Ref: NC_021284.1); Prevotella intermedia (NCBI Ref: NC_017861.1); Spiroplasma taiwanense (NCBI Ref: NC_021846.1); Streptococcus iniae (NCBI Ref: NC_021314.1); Belliella baltica (NCBI Ref: NC_018010.1); Psychroflexus torquisI (NCBI Ref: NC_018721.1); Streptococcus thermophilus (NCBI Ref: YP_820832.1); Listeria innocua (NCBI Ref: NP_472073.1); Campylobacter jejuni (NCBI Ref: YP_002344900.1); or Neisseria. meningitidis (NCBI Ref: YP_002342100.1). Mutations at positions corresponding to D10 and H840 in SEQ ID NO: 70 may also be made at corresponding positions in any of these Cas9 proteins to produce nickase or dead variants.
A “cell type” refers to a classification of cells that share common morphological and/or phenotypical features. Multicellular organisms may be composed of cells of multiple different, specialized cell types (e.g., nervous system cells, immune cells, muscle cells, skin cells, etc.). The ARMMs disclosed herein may, in some embodiments, target one or more than one particular cell type through, for example, the antibody or antigen-binding fragment that is fused to the NiV glycoprotein of the microvesicle. Cell types contemplated for use in the present disclosure include, but are not limited to, stem and progenitor cells (e.g., embryonic stem cells, hematopoietic stem cells, mesenchymal stem cells, neural crest cells, etc.), endothelial cells, muscle cells, myocardial cells, smooth and skeletal muscle cells, mesenchymal cells, epithelial cells, hematopoietic cells, lymphocytes such as T-cells (e.g., Th1 T cells, Th2 T cells, ThO T cells, cytotoxic T cells) and B cells (e.g., pre-B cells), monocytes, dendritic cells, neutrophils, macrophages, natural killer cells, mast cells, adipocytes, immune cells, neurons, hepatocytes, and cells involved with particular organs (e.g., thymus, endocrine glands, pancreas, brain, neurons, glia, astrocytes, dendrocytes, and genetically modified cells thereof). The cells may also be transformed or neoplastic cells of different types (e.g., carcinomas of different cell origins, lymphomas of different cell types, etc.) or cancerous cells of any kind. Cells of different origins (e.g., ectodermal, mesodermal, and endodermal) are also contemplated for use in the present disclosure. In some embodiments, the antibody or antigen-binding fragment of the ARMMs disclosed herein targets a particular cell type. In some embodiments, the cell type is selected from the group consisting of neurons, astrocytes, oligodendrocytes, microglial cells, T-cells, dendritic cells, B cells, NK cells, stem cells, progenitor cells, endothelial cells, muscle cells, myocardial cells, epithelial cells, and hepatic cells. In certain embodiments, the antibody or antigen-binding fragment of the ARMMs disclosed herein targets T-cells. In certain embodiments, the antibody or antigen-binding fragment of the ARMMs disclosed herein targets neurons. Other cell types besides those disclosed herein may be targeted using the presently described ARMMs, and a person of ordinary skill in the art would be able to select antibodies or antigen-binding fragments to target additional cell types besides those specifically listed herein.
A “designed ankyrin repeat protein” or “DARPin” refers to a genetically engineered antibody mimetic protein. DARPins typically exhibit high specificity and high-affinity target protein binding. They are derived from natural ankyrin repeat proteins, which are one of the most common classes of binding proteins in nature and play diverse roles in cell signaling, regulation, and structural integrity. DARPins typically comprise at least three ankyrin repeat motifs. In some embodiments, the antibody or antigen-binding fragment of the microvesicles disclosed herein comprises a DARPin.
As used herein, “expression” of a nucleic acid sequence refers to one or more of the following events: (1) production of an RNA transcript from a DNA sequence (e.g., by transcription); (2) processing of an RNA transcript (e.g., by splicing, editing, 5′ cap formation, and/or 3′ end processing); (3) translation of an RNA transcript into a polypeptide or protein; and (4) post-translational modification of a polypeptide or protein.
As used herein, a “fusion protein” includes a first protein moiety, e.g., an ARRCD1 protein or variant thereof, or a TSG101 protein or variant thereof, associated with a second protein moiety, for example, a protein to be delivered to a target cell through a peptide linkage. In certain embodiments, the fusion protein is encoded by a single fusion gene. It should be noted that the term “fusion protein” can, but need to necessarily, refer to a “NiV fusion protein,” which refers to the Nipah virus surface protein that facilitates viral entry into a target cell and is described further herein. As such, unless used in this context, the term “fusion protein” is distinct from the term “NiV fusion protein.”
As used herein, the term “gene” has its meaning as understood in the art. It will be appreciated by those of ordinary skill in the art that the term “gene” may include gene regulatory sequences (e.g., promoters, enhancers, etc.) and/or intron sequences. It will further be appreciated that the definition of gene includes references to nucleic acids that do not encode proteins but rather encode functional RNA molecules, such as gRNAs, RNAi agents, ribozymes, tRNAs, etc. For the purpose of clarity, it should be noted that, as used in the present application, the term “gene” generally refers to a portion of a nucleic acid that encodes a protein; the term may optionally encompass regulatory sequences, as will be clear from context to those of ordinary skill in the art. This definition is not intended to exclude application of the term “gene” to non-protein-coding expression units but rather to clarify that, in most cases, the term as used herein refers to a protein-coding nucleic acid.
As used herein, the term “gene product” or “expression product” generally refers to an RNA transcribed from the gene (pre-and/or post-processing) or a polypeptide (pre-and/or post-modification) encoded by an RNA transcribed from the gene.
The term “linker,” as used herein, refers to a chemical moiety linking two molecules or moieties, e.g., an ARRDC1 protein and a Tat protein, a WW domain and a Tat protein, or an ARRDC1 protein and a Cas9 nuclease, nickase, or dCas9 or other protein or peptide agent as described herein. Typically, the linker is positioned between, or flanked by, two groups, molecules, or other moieties and connected to each one via a covalent bond, thus connecting the two. In some embodiments, the linker comprises an amino acid or a plurality of amino acids (e.g., a peptide or protein). In some embodiments, the linker comprises a nucleotide (e.g., DNA or RNA) or a plurality of nucleotides (e.g., a nucleic acid). In some embodiments, the linker is an organic molecule, functional group, polymer, or other chemical moiety. In some embodiments, the linker is a cleavable linker, e.g., the linker comprises a bond that can be cleaved upon exposure to, for example, UV light or a hydrolytic enzyme, such as a protease or esterase. In some embodiments, the linker is any stretch of amino acids having at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, at least 40, at least 50, or more amino acids (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 amino acids). In other embodiments, the linker is a chemical bond (e.g., a covalent bond, amide bond, disulfide bond, ester bond, carbon-carbon bond, carbon heteroatom bond).
As used herein, the term “microRNA” or “miRNA” refers to an RNAi agent that is approximately 21 nucleotides (nt)-23 nt in length. miRNAs can range between 18 nt-26 nt in length. Typically, miRNAs are single-stranded. However, in some embodiments, miRNAs may be at least partially double-stranded. In certain embodiments, miRNAs may comprise an RNA duplex (referred to herein as a “duplex region”) and may optionally further comprises one to three single-stranded overhangs. In some embodiments, an RNAi agent comprises a duplex region ranging from 15 bp to 29 bp in length and optionally further comprises one or two single-stranded overhangs. A miRNA may be formed from two RNA molecules that hybridize together, or may alternatively be generated from a single RNA molecule that includes a self-hybridizing portion. In general, free 5′ ends of miRNA molecules have phosphate groups, and free 3′ ends have hydroxyl groups. The duplex portion of a miRNA usually, but does not necessarily, comprise one or more bulges consisting of one or more unpaired nucleotides. One strand of a miRNA includes a portion that hybridizes with a target RNA. In certain embodiments, one strand of the miRNA is not precisely complementary with a region of the target RNA, meaning that the miRNA hybridizes to the target RNA with one or more mismatches. In some embodiments, one strand of the miRNA is precisely complementary with a region of the target RNA, meaning that the miRNA hybridizes to the target RNA with no mismatches. Typically, miRNAs are thought to mediate inhibition of gene expression by inhibiting translation of target transcripts. However, in some embodiments, miRNAs may mediate inhibition of gene expression by causing degradation of target transcripts.
The term “microvesicle,” as used herein, refers to a droplet of liquid surrounded by a lipid bilayer. In some embodiments, a microvesicle has a diameter of about 10 nm to about 1000 nm. In some embodiments, a microvesicle has a diameter of at least about 10 nm, at least about 20 nm, at least about 30 nm, at least about 40 nm, at least about 50 nm, at least about 60 nm, at least about 70 nm, at least about 80 nm, at least about 90 nm, at least about 100 nm, at least about 125 nm, at least about 150 nm, at least about 175 nm, at least about 200 nm, at least about 250 nm, at least about 300 nm, at least about 400 nm, or at least about 500 nm. In some embodiments, a microvesicle has a diameter of less than about 1000 nm, less than about 900 nm, less than about 800 nm, less than about 700 nm, less than about 600 nm, less than about 500 nm, less than about 400 nm, less than about 300 nm, less than about 250 nm, less than about 200 nm, less than about 150 nm, less than about 100 nm, less than about 90 nm, less than about 80 nm, less than about 70 nm, less than about 60 nm, or less than about 50 nm. The term microvesicle includes microvesicles shed from cells as well as synthetically produced microvesicles. Microvesicles shed from cells typically comprise the antigenic content of the cells from which they originate. Microvesicles shed from cells also typically comprise an asymmetric distribution of phospholipids, reflecting the phospholipid distribution of the cells from which they originate. In some embodiments, the inner membrane of microvesicles provided herein, e.g., of some ARMMs, comprises the majority of aminophospholipids, phosphatidylserine, and/or phosphatidylethanolamine within the lipid bilayer.
A “NiV fusion protein” or “NiV-F protein,” as used herein, refers to the fusion protein of the Nipah virus that facilitates fusion of the viral particle to a cell. The wild-type NiV fusion protein comprises the following amino acid sequence:
The sequence of wild-type NiV fusion protein can also be found at https://www.uniprot.org/uniprot/Q9IH63.
In some embodiments, the ARMMs described herein comprise a NiV fusion protein variant that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a wild-type NiV fusion protein of SEQ ID NO: 6. In some embodiments, the ARMMs described herein comprise a NiV fusion protein variant comprising amino acid truncations relative to a wild-type NiV fusion protein of SEQ ID NO: 6.
A “NiV glycoprotein” or “NiV-G protein,” as used herein, refers to the glycoprotein of the Nipah virus that facilitates recognition, binding, and attachment of the virus to a cell. The endogenous targets of the NiV glycoprotein are ephrin receptors (erythropoietin-producing human hepatocellular receptors, the largest known subfamily of receptor tyrosine kinases). The wild-type NiV glycoprotein comprises the following amino acid sequence:
In some embodiments, the ARMMs described herein comprise a NiV glycoprotein variant that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a wild-type NiV glycoprotein of SEQ ID NO: 1. In some embodiments, the ARMMs described herein comprise a NiV glycoprotein variant comprising amino acid substitutions or truncations as described herein. In some embodiments, the ARMMs described herein comprise a NiV glycoprotein variant that does not recognize and/or bind to its natural target (i.e., an ephrin receptor) and that is fused to an antibody or antigen-binding fragment such that the NiV glycoprotein targets the ARMM to a particular cell type.
As used herein, the term “nucleic acid,” in its broadest sense, refers to a compound and/or substance that is or can be incorporated into an oligonucleotide chain via a phosphodiester linkage. In some embodiments, “nucleic acid” refers to individual nucleic acid residues (e.g., nucleotides and/or nucleosides). In some embodiments, “nucleic acid” refers to an oligonucleotide chain comprising individual nucleotides. As used herein, the terms “oligonucleotide” and “polynucleotide” can be used interchangeably to refer to a polymer of nucleotides (e.g., a string of at least two nucleotides). In some embodiments, “nucleic acid” encompasses RNA as well as single and/or double-stranded DNA and/or complementary DNA (cDNA). Furthermore, the terms “nucleic acid,” “DNA,” “RNA,” and/or similar terms include nucleic acid analogs, i.e., analogs having other than a phosphodiester backbone. For example, the so-called “peptide nucleic acids,” which are known in the art and have peptide bonds instead of phosphodiester bonds in the backbone, are considered within the scope of the present invention. The term “nucleotide sequence encoding an amino acid sequence” includes all nucleotide sequences that are degenerate versions of each other and/or encode the same amino acid sequence. Nucleotide sequences that encode proteins and/or RNA may include introns. Nucleic acids can be purified from natural sources, produced using recombinant expression systems and optionally purified, chemically synthesized, etc. Where appropriate, e.g., in the case of chemically synthesized molecules, nucleic acids can comprise nucleoside analogs such as analogs having chemically modified bases or sugars, backbone modifications, etc. A nucleic acid sequence is presented in the 5′ to 3′ direction unless otherwise indicated. The term “nucleic acid segment” is used herein to refer to a nucleic acid sequence that is a portion of a longer nucleic acid sequence. In many embodiments, a nucleic acid segment comprises at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, or more residues. In some embodiments, a nucleic acid is or comprises natural nucleosides (e.g., adenosine, thymidine, guanosine, cytidine, uridine, deoxyadenosine, deoxythymidine, deoxyguanosine, and deoxycytidine); nucleoside analogs (e.g., 2-aminoadenosine, 2-thiothymidine, inosine, pyrrolo-pyrimidine, 3-methyl adenosine, 5-methylcytidine, 2-aminoadenosine, C5-bromouridine, C5-fluorouridine, C5-iodouridine, C5-propynyl-uridine, C5-propynyl-cytidine, C5-methylcytidine, 2-aminoadenosine, 7-deazaadenosine, 7-deazaguanosine, 8-oxoadenosine, 8-oxoguanosine, O(6)-methylguanine, and 2-thiocytidine); chemically modified bases; biologically modified bases (e.g., methylated bases); intercalated bases; modified sugars (e.g., 2′-fluororibose, ribose, 2′-deoxyribose, arabinose, and hexose); and/or modified phosphate groups (e.g., phosphorothioates and 5′-N-phosphoramidite linkages). In some embodiments, the present invention is specifically directed to “unmodified nucleic acids,” meaning nucleic acids (e.g., polynucleotides and residues, including nucleotides and/or nucleosides) that have not been chemically modified in order to facilitate or achieve delivery.
As used herein, the term “protein” refers to a string of at least two amino acids linked to one another by one or more peptide bonds. Proteins may include moieties other than amino acids (e.g., may be glycoproteins) and/or may be otherwise processed or modified. Those of ordinary skill in the art will appreciate that a “protein” can be a complete protein chain as produced by a cell (with or without a signal sequence), or can be a functional portion thereof. Those of ordinary skill will further appreciate that a protein can sometimes include more than one protein chain, for example linked by one or more disulfide bonds or associated by other means. Proteins may contain L-amino acids, D-amino acids, or both and may contain any of a variety of amino acid modifications or analogs known in the art. Useful modifications include, e.g., addition of a chemical entity such as a carbohydrate group, a phosphate group, a farnesyl group, an isofarnesyl group, a fatty acid group, an amide group, a terminal acetyl group, a linker for conjugation, functionalization, or other modification (e.g., alpha amidation), etc. In certain embodiments, the modifications of the protein lead to a more stable protein (e.g., greater half-life in vivo). These modifications may include cyclization of the protein, the incorporation of D-amino acids, etc. None of the modifications should substantially interfere with the desired biological activity of the protein. In certain embodiments, the modifications of the protein lead to a more biologically active protein. In some embodiments, proteins may comprise natural amino acids, non-natural amino acids, synthetic amino acids, amino acid analogs, and combinations thereof.
As used herein, the term “RNA interference” or “RNAi” refers to sequence-specific inhibition of gene expression and/or reduction in target RNA levels mediated by an RNA, which RNA comprises a portion that is substantially complementary to a target RNA. Typically, at least part of the substantially complementary portion is within the double stranded region of the RNA. In some embodiments, RNAi can occur via selective intracellular degradation of RNA. In some embodiments, RNAi can occur by translational repression.
As used herein, the term “RNAi agent” or “RNAi” refers to an RNA, optionally including one or more nucleotide analogs or modifications, having a structure characteristic of molecules that can mediate inhibition of gene expression through an RNAi mechanism. In some embodiments, RNAi agents mediate inhibition of gene expression by causing degradation of target transcripts. In some embodiments, RNAi agents mediate inhibition of gene expression by inhibiting translation of target transcripts. Generally, an RNAi agent includes a portion that is substantially complementary to a target RNA. In some embodiments, RNAi agents are at least partly double-stranded. In some embodiments, RNAi agents are single-stranded. In some embodiments, exemplary RNAi agents can include siRNA, shRNA, and/or miRNA. In some embodiments, RNAi agents may be composed entirely of natural RNA nucleotides (i.e., adenine, guanine, cytosine, and uracil). In some embodiments, RNAi agents may include one or more non-natural RNA nucleotides (e.g., nucleotide analogs, DNA nucleotides, etc.). Inclusion of non-natural RNA nucleic acid residues may be used to make the RNAi agent more resistant to cellular degradation than RNA. In some embodiments, the term “RNAi agent” may refer to any RNA, RNA derivative, and/or nucleic acid encoding an RNA that induces an RNAi effect (e.g., degradation of target RNA and/or inhibition of translation). In some embodiments, an RNAi agent may comprise a blunt-ended (i.e., without overhangs) dsRNA that can act as a Dicer substrate. For example, such an RNAi agent may comprise a blunt-ended dsRNA which is ≥25 base pairs length, which may optionally be chemically modified to abrogate an immune response.
As used herein, the term “short, interfering RNA” or “siRNA” refers to an RNAi agent comprising an RNA duplex (referred to herein as a “duplex region”) that is approximately 19 base pairs (bp) in length and optionally further comprises one to three single-stranded overhangs. In some embodiments, an RNAi agent comprises a duplex region ranging from 15 bp to 29 bp in length and optionally further comprising one or two single-stranded overhangs. An siRNA may be formed from two RNA molecules that hybridize together, or may alternatively be generated from a single RNA molecule that includes a self-hybridizing portion. In general, free 5′-ends of siRNA molecules have phosphate groups, and free 3′-ends have hydroxyl groups. The duplex portion of an siRNA may, but typically does not, comprise one or more bulges consisting of one or more unpaired nucleotides. One strand of an siRNA includes a portion that hybridizes with a target transcript. In certain embodiments, one strand of the siRNA is precisely complementary with a region of the target transcript, meaning that the siRNA hybridizes to the target transcript without a single mismatch. In some embodiments, one or more mismatches between the siRNA and the targeted portion of the target transcript may exist. In some embodiments in which perfect complementarity is not achieved, any mismatches are generally located at or near the siRNA termini. In some embodiments, siRNAs mediate inhibition of gene expression by causing degradation of target transcripts.
As used herein, the term “short hairpin RNA” or “shRNA” refers to an RNAi agent comprising an RNA having at least two complementary portions hybridized or capable of hybridizing to form a double-stranded (duplex) structure sufficiently long to mediate RNAi (typically at least approximately 19 bp in length), and at least one single-stranded portion, typically ranging between approximately 1 nucleotide (nt) and approximately 10 nt in length that forms a loop. In some embodiments, an shRNA comprises a duplex portion ranging from 15 bp to 29 bp in length and at least one single-stranded portion, typically ranging between approximately 1 nt and approximately 10 nt in length that forms a loop. The duplex portion may, but typically does not, comprise one or more bulges consisting of one or more unpaired nucleotides. In some embodiments, siRNAs mediate inhibition of gene expression by causing degradation of target transcripts, shRNAs are thought to be processed into siRNAs by the conserved cellular RNAi machinery. Thus, shRNAs may be precursors of siRNAs. Regardless, siRNAs in general are capable of inhibiting expression of a target RNA, similar to siRNAs.
In general, a “small molecule” refers to a substantially non-peptidic, non-oligomeric organic compound either prepared in the laboratory or found in nature. Small molecules, as used herein, can refer to compounds that are “natural product-like,” however, the term “small molecule” is not limited to “natural product-like” compounds. Rather, a small molecule is typically characterized in that it contains several carbon-carbon bonds and has a molecular weight of less than 2000 g/mol, less than 1500 g/mol, less than 1250 g/mol, less than 1000 g/mol, less than 750 g/mol, less than 500 g/mol, or less than 250 g/mol, although this characterization is not intended to be limiting for the purposes of the present invention. In certain other embodiments, natural-product-like small molecules are utilized.
As used herein, the term “subject” or “patient” refers to any organism to which a composition in accordance with the invention may be administered, e.g., for experimental, diagnostic, prophylactic, and/or therapeutic purposes. Typical subjects include animals (e.g., mammals, such as mice, rats, rabbits, non-human primates, and humans) and/or plants. In some embodiments, the subject is a patient having or suspected of having a disease or disorder. In other embodiments, the subject is a healthy volunteer.
As used herein, the term “therapeutic agent” refers to any agent that, when administered to a subject, has a beneficial effect. In some embodiments, the agent is a small molecule, or a protein or nucleic acid, such as DNA or RNA, that is associated with a small molecule. In some embodiments, the agent to be delivered by the ARMMs described herein is a diagnostic agent. In some embodiments, the agent to be delivered is a prophylactic agent. In some embodiments, the agent to be delivered is useful as an imaging agent. In some of these embodiments, the diagnostic or imaging agent is, and in others it is not, biologically active.
As used herein, the term “therapeutically effective amount” means an amount of an agent to be delivered (e.g., nucleic acid, protein, drug, therapeutic agent, diagnostic agent, prophylactic agent, ARMM, or ARMM comprising a protein agent or RNA agent) that is sufficient, when administered to a subject suffering from or susceptible to a disease, disorder, and/or condition, to treat, improve symptoms of, diagnose, prevent, and/or delay the onset of the disease, disorder, and/or condition. Use of the term “therapeutically effective amount” does not necessarily mean that the amount needs to be, or needs to be shown to be, clinically effective.
As used herein, the term “transcription factor” refers to a DNA-binding protein that regulates transcription of DNA into RNA, for example, by activation or repression of transcription. Some transcription factors effect regulation of transcription alone, while others act in concert with other proteins. Some transcription factor can both activate and repress transcription under certain conditions. In general, transcription factors bind a specific target sequence or sequences highly similar to a specific consensus sequence in a regulatory region of a target gene. Transcription factors may regulate transcription of a target gene alone or in a complex with other molecules. Examples of transcription factors include, but are not limited to, Sp1, NF1, CCAAT, GATA, HNF, PIT-1, MyoD, Myf5, Hox, Winged Helix, SREBP, p53, CREB, AP-1, Mef2, STAT, R-SMAD, NF-κB, Notch, TUBBY, and NFAT.
As used herein, the term “treating” refers to partially or completely preventing, and/or reducing the incidence of one or more symptoms or features of a particular disease or condition. For example, “treating” cancer may refer to inhibiting survival, growth, and/or spread of the cancer. Treatment may be administered to a subject who does not exhibit signs or symptoms of a disease, disorder, and/or condition and/or to a subject who exhibits only early signs or symptoms of a disease, or condition for the purpose of decreasing the risk of developing more severe effects associated with the disease, disorder, or condition. Use of the term “treating” or “treatment” does not necessarily needs to be, or needs to be shown to be, demonstrated clinically.
As used herein, a “vector” means any nucleic acid or nucleic acid-bearing particle, cell, or organism capable of being used to transfer a nucleic acid into a host cell. The term “vector” includes both viral and nonviral products and means for introducing the nucleic acid into a cell. A “vector” can be used in vitro, ex vivo, or in vivo. Vectors capable of directing the expression of operatively linked genes are referred to herein as “expression vectors.” Non-viral vectors include plasmids, cosmids, artificial chromosomes (e.g., bacterial artificial chromosomes or yeast artificial chromosomes) and can comprise liposomes, electrically charged lipids (cytofectins), DNA-protein complexes, and biopolymers, for example. Viral vectors include retroviruses, lentiviruses, adeno-associated virus, pox viruses, baculovirus, reoviruses, vaccinia viruses, herpes simplex viruses, Epstein-Barr viruses, and adenovirus vectors, for example. Vectors can also comprise the entire genome sequence or recombinant genome sequence of a virus. A vector can also comprise a portion of the genome that comprises the functional sequences for production of a virus capable of infecting, entering, or being introduced to a cell to deliver nucleic acid therein.
The term “WW domain,” as used herein, refers to a protein domain having two basic residues at the C-terminus that mediates protein-protein interactions with short proline-rich or proline-containing motifs. It should be appreciated that the two basic residues (e.g., any two of: H, R, and K) of the WW domain are not required to be at the absolute C-terminal end of the WW protein domain. Rather, the two basic residues may be at a C-terminal portion of the WW protein domain (e.g., the C-terminal half of the WW protein domain). In some embodiments, the WW domain contains at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 tryptophan (W) residues. In some embodiments, the WW domain contains at least two W residues. In some embodiments, the at least two W residues are spaced apart by from 15-25 amino acids. In some embodiments, the at least two W residues are spaced apart by from 19-23 amino acids. In some embodiments, the at least two W residues are spaced apart by from 20-22 amino acids. The WW domain possessing the two basic C-terminal amino acid residues may have the ability to associate with short proline-rich or proline-containing motifs (e.g., a PPXY motif). WW domains bind a variety of distinct peptide ligands including motifs with core proline-rich sequences, such as PPXY, which is found in AARDC1. A WW domain may be a 30-40 amino acid protein interaction domain with two signature tryptophan residues spaced by 20-22 amino acids. The three-dimensional structure of WW domains shows that they generally fold into a three-stranded, antiparallel β sheet with two ligand-binding grooves.
WW domains are found in many eukaryotes and are present in approximately 50 human proteins (Bork, P. & Sudol, M. The WW domain: a signaling site in dystrophin? Trends Biochem Sci 19, 531-533 (1994)). WW domains may be present together with several other interaction domains, including membrane targeting domains, such as C2 in the NEDD4 family proteins, the phosphotyrosine-binding (PTB) domain in FE65 protein, FF domains in CA150 and FBPII, and pleckstrin homology (PH) domains in PLEKHA5. WW domains are also linked to a variety of catalytic domains, including HECT E3 protein-ubiquitin ligase domains in NEDD4 family proteins, rotomerase or peptidyl prolyisomerase domains in Pin1, and Rho GAP domains in ArhGAP9 and ArhGAP12.
In the instant disclosure, the WW domain may be a WW domain that naturally possesses two basic amino acids at the C-terminus. In some embodiments, a WW domain or WW domain variant may be from the human ubiquitin ligase WWP1, WWP2, Nedd4-1, Nedd4-2, Smurf1, Smurf2, ITCH, NEDL1, or NEDL2. Exemplary amino acid sequences of WW domain containing proteins (WW domains underlined) are listed below. It should be appreciated that any of the WW domains or WW domain variants of the exemplary proteins may be used in the microvesicles described herein, and the particular WW domains described herein are not meant to be limiting.
Human WWP1 amino acid sequence (uniprot.org/uniprot/Q9H0M0). The four underlined WW domains correspond to amino acids 349-382 (WW1), 381-414 (WW2), 456-489 (WW3), and 496-529 (WW4).
LPSGWEQRKD PHGRTYYVDH NTRTTTWERP QPLPPGWERR VDDRRRVYYV 400
DHNTRTTTWQ RPTMESVRNF EQWQSQRNQL QGAMQQFNQR YLYSASMLAA 450
GWEIRYTREG VRYFVDHNTR TTTEKDPRNG KSSVTKGGPQ IAYERGFRWK 550
Human WWP2 amino acid sequence (uniprot.org/uniprot/O00308). The four underlined WW domains correspond to amino acids 300-333 (WW1), 330-363 (WW2), 405-437 (WW3), and 444-547 (WW4).
ALPAGWEQRE LPNGRVYYVD HNTKTTTWER PLPPGWEKRT DPRGRFYYVD 350
HNTRTTTWQR PTAEYVRNYE QWQSQRNQLQ GAMQHFSQRF LYQSSSASTD 400
EMKYTSEGVR YFVDHNTRTT TFKDPRPGFE SGTKQGSPGA YDRSFRWKYH 500
Human Nedd4-1 amino acid sequence (uniprot.org/uniprot/P46934). The four underlined WW domains correspond to amino acids 610-643 (WW1), 767-800 (WW2), 840-873 (WW3), and 892-925 (WW4).
APNGRPFFID HNTKTTTWED PRLKIPAHLR GKTSLDTSND LGPLPPGWEE 900
RTHTDGRIFY INHNIKRTQW EDPRLENVAI TGPAVPYSRD YKRKYEFFRR 950
Human Nedd4-2 amino acid sequence (>gi|21361472|ref|NP_056092.2|E3 ubiquitin-protein ligase NEDD4-like isoform 3 [Homo sapiens]). The four underlined WW domains correspond to amino acids 198-224 (WW1), 368-396 (WW2), 480-510 (WW3), and 531-561 (WW4).
DGRTFYIDHNSKITQWEDPRLQNPAITGPAVPYSREFKQKYDYFR
Human Smurf1 amino acid sequence (uniprot.org/uniprot/Q9HCE7). The two underlined WW domains correspond to amino acids 234-267 (WW1) and 306-339 (WW2).
Human Smurf2 amino acid sequence (uniprot.org/uniprot/Q9HAU4). The three underlined WW domains correspond to amino acids 157-190 (WW1), 251-284 (WW2), and 297-330 (WW3).
PDLPEGYEQR TTQQGQVYFL HTQTGVSTWH DPRVPRDLSN INCEELGPLP 300
PGWEIRNTAT GRVYFVDHNN RTTQFTDPRL SANLHLVLNR QNQLKDQQQQ 350
Human ITCH amino acid sequence (uniprot.org/uniprot/Q96J02). The four underlined WW domains correspond to amino acids 326-359 (WW1), 358-391 (WW2), 438-471 (WW3), and 478-511 (WW4).
RTTWDRPEPL PPGWERRVDN MGRIYYVDHF TRTTTWQRPT LESVRNYEQW 400
NGRVYFVNHN TRITQWEDPR SQGQLNEKPL PEGWEMRFTV DGIPYFVDHN 500
RRTTTYIDPR TGKSALDNGP QIAYVRDFKA KVQYFRFWCQ QLAMPQHIKI 550
Human NEDL1 amino acid sequence (uniprot.org/uniprot/Q76N89). The two underlined WW domains correspond to amino acids 829-862 (WW1), and 1018-1051 (WW2).
VNRTTTWQRP TAAATPDGMR RSGSIQQMEQ LNRRYQNIQR TIATERSEED 900
Human NEDL2 amino acid sequence (uniprot.org/uniprot/Q9P2P5). The two underlined WW domains correspond to amino acids 807-840 (WW1) and 985-1018 (WW2).
AFFVDHNSRT TTFIDPRLPL QSSRPTSALV HRQHLTRQRS HSAGEVGEDS 1050
In some embodiments, the WW domain consists essentially of a WW domain or WW domain variant. Consists essentially of means that a domain, peptide, or polypeptide consists essentially of an amino acid sequence when such an amino acid sequence is present with only a few additional amino acid residues, for example, from about 1 to about 10 or so additional residues, typically from 1 to about 5 additional residues in the domain, peptide, or polypeptide.
Alternatively, the WW domain may be a WW domain that has been modified to include two basic amino acids at the C-terminus of the domain. Techniques are known in the art and are described in the art, for example, in Sambrook et al., ((2001) Molecular Cloning: a Laboratory Manual, 3rd ed., Cold Spring Harbour Laboratory Press). Thus, a skilled person could readily modify an existing WW domain that does not normally have two C-terminal basic residues so as to include two basic residues at the C-terminus.
Basic amino acids are amino acids that possess a side-chain functional group that has a pKa of greater than 7 and include lysine, arginine, and histidine, as well as basic amino acids that are not included in the twenty α-amino acids commonly included in proteins. The two basic amino acids at the C-terminus of the WW domain may be the same basic amino acid or may be different basic amino acids. In one embodiment, the two basic amino acids are two arginines.
The term WW domain also includes variants of a WW domain, provided that any such variant possesses two basic amino acids at its C-terminus and maintains the ability of the WW domain to associate with the PPXY motif. A variant of such a WW domain refers to a WW domain that retains the ability of the variant to associate with the PPXY motif (i.e., the PPXY motif of ARRDC1 and that has been mutated at one or more amino acids, including point, insertion, and/or deletion mutations, but still retains the ability to associate with the PPXY motif. A variant or derivative therefore includes deletions, including truncations and fragments; insertions and additions, for example conservative substitutions, site-directed mutants, and allelic variants; and modifications, including one or more non-amino acyl groups (e.g., sugar, lipid, etc.) covalently linked to the peptide and post-translational modifications. In making such changes, substitutions of like amino acid residues can be made on the basis of relative similarity of side-chain substituents, for example, their size, charge, hydrophobicity, hydrophilicity, and the like, and such substitutions may be assayed for their effect on the function of the peptide by routine testing.
The WW domain may be part of a longer protein. Thus, the protein, in various different embodiments, comprises the WW domain, consists of the WW domain, or consists essentially of the WW domain, as defined herein. The polypeptide may be a protein that includes a WW domain as a functional domain within the protein sequence.
The instant disclosure relates, at least in part, to the discovery that an agent (e.g., a therapeutic agent, or any of the agents described herein) can be delivered to a particular target cell type using an ARMM that has been modified with a NiV glycoprotein and NiV fusion protein. Such modifications allow for the targeted delivery of agents contained in the microvesicles into specific cells. ARMMs modified with a NiV glycoprotein that has been fused to an antibody or antigen-binding fragment, such as an scFv or antibody mimetic protein, can deliver agents such as proteins and RNAs to cells in a targeted manner. NiV glycoproteins can also be fused to other proteins that can deliver the ARMMs to cells in a targeted manner. Various agents, including proteins such as Cas9 and/or nucleic acids such as DNA and/or RNA, can be loaded in such ARMMs for targeted delivery. Various types of protein agents, nucleic acid agents, and other agents are known in the art and include those described in U.S. Pat. Nos. 9,737,480; 9,816,080; 10,260,055; and PCT Application Publication WO2018/067546; the entire contents of each of which are incorporated by reference herein.
Thus, in various aspects, the present disclosure provides arrestin domain-containing protein 1 (ARRDC1)-mediated microvesicles (ARMMs) modified with Nipah virus (NiV) glycoproteins fused to antibodies or antigen-binding fragments and NiV fusion proteins, and variants thereof. The ARMMs of the present disclosure may be targeted to particular cell types and used to deliver agents (e.g., therapeutic agents) to target cells. Microvesicle-producing cells are also provided by the present disclosure. The present disclosure also provides methods of delivering molecules to target cells using the ARMMs described herein, and methods of treating a patient using any of the ARMMs or microvesicle-producing cells provided herein. Kits comprising any of the ARMMs or microvesicle-producing cells described herein are also provided by the present disclosure.
In some aspects, the present disclosure relates to arrestin domain-containing protein 1 (ARRDC1)-mediated microvesicles (ARMMs). Such ARMMs typically include a lipid bilayer and an ARRDC1 protein or a variant thereof. ARMMs are extracellular vesicles (EVs) that are distinct from exosomes. The budding of ARMMs requires Arrestin domain containing protein 1 (ARRDC1), which is localized to the cytosolic side of the plasma membrane and, through a tetrapeptide motif, recruits the ESCRT-I complex protein TSG101 to the cell surface to initiate the outward membrane budding. Thus, in contrast to exosomes, the biogenesis of ARMMs occurs at the plasma membrane. ARMMs exhibit several additional features that make them potentially ideal vehicles for therapeutic delivery. ARRDC1 is not only necessary, but also sufficient to drive ARMMs budding. Indeed, simple overexpression of the ARRDC1 protein increases the production of ARMMs in cells. This allows controlled production of ARMMs using modern biological manufacturing methods. Moreover, endogenous proteins such as cell surface receptors are actively recruited into ARMMs and can be delivered into recipient cells to initiate intercellular communication, and exogenous agents (e.g., any of the agents described herein, including therapeutic agents) may similarly be delivered via ARMMs.
In particular, the present disclosure relates to ARMMs comprising: (i) a lipid bilayer and an ARRDC1 protein, (ii) a Nipah virus (NiV) glycoprotein variant fused to an antibody or antigen-binding fragment, wherein the NiV glycoprotein variant does not recognize and/or bind to an ephrin receptor, and (iii) a NiV fusion protein. As described herein, surface modification of ARMMs with the NiV glycoprotein and fusion protein allows targeted delivery of agents encapsulated in the vesicles into specific cells.
ARRDC1 is a protein that comprises a PSAP (SEQ ID NO: 2) motif and a PPXY motif in its C-terminus and interacts with TSG101. It should be appreciated that the PSAP (SEQ ID NO: 2) motif and the PPXY motif are not required to be at the absolute C-terminal end of the ARRDC1. Rather, they may be at a C-terminal portion of the ARRDC1 protein (e.g., the C-terminal half of the ARRDC1). The disclosure also contemplates variants of ARRDC1, such as fragments of ARRDC1 and/or ARRDC1 proteins that have a degree of identity (e.g., 60%, 70%, 80%, 85%, 90%, 95%, 98%, or 99% identity) to an ARRDC1 protein and are capable if interacting with TSG101. Accordingly, an ARRDC1 protein or a variant thereof may be a protein that comprises a PSAP (SEQ ID NO: 2) motif and a PPXY motif and interacts with TSG101. In some embodiments, the ARRDC1 protein is at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identical to the amino acid sequence of any one of SEQ ID NOs: 3-5, comprises a PSAP (SEQ ID NO: 2) motif and a PPXY motif, and interacts with TSG101. In some embodiments, the ARRDC1 protein has at least 10, at least 20, at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 110, at least 120, at least 130, at least 140, at least 150, at least 160, at least 170, at least 180, at least 190, at least 200, at least 210, at least 220, at least 230, at least 240, at least 250, at least 260, at least 270, at least 280, at least 290, at least 300, at least 310, at least 320, at least 330, at least 340, at least 350, at least 360, at least 370, at least 380, at least 390, at least 400, at least 410, at least 420, or at least 430 identical contiguous amino acids of any one of SEQ ID NOs: 3-5, comprises a PSAP (SEQ ID NO: 2) motif and a PPXY motif, and interacts with TSG101. In some embodiments, the ARRDC1 protein has 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or more mutations compared to any one of the amino acid sequences set forth in SEQ ID NOs: 3-5, comprises a PSAP (SEQ ID NO: 2) motif and a PPXY motif, and interacts with TSG101. In some embodiments, the ARRDC1 protein comprises any one of the amino acid sequences set forth in SEQ ID NOs: 3-5. Exemplary, non-limiting ARRDC1 protein sequences are provided herein, and additional, suitable ARRDC1 protein variants according to aspects of this invention are known in the art. It will be appreciated by those of skill in the art that this invention is not limited in this respect. Exemplary ARRDC1 sequences include the following (PSAP (SEQ ID NO: 2) and PPXY motifs are marked):
In certain embodiments, the inventive microvesicles further comprise TSG101 (tumor susceptibility gene 101). TSG101 belongs to a group of apparently inactive homologs of ubiquitin-conjugating enzymes. The protein contains a coiled-coil domain that interacts with stathmin, a cytosolic phosphoprotein implicated in tumorigenesis. TSG101 is a protein that comprises a UEV domain and interacts with an ARRDC1 protein or a variant thereof. As referred to herein, UEV refers to the Ubiquitin E2 variant domain of approximately 145 amino acids. The structure of the domain contains a α/β fold similar to the canonical E2 enzyme but has an additional N-terminal helix and further lacks the two C-terminal helices. Often found in TSG101/Vps23 proteins, the UEV interacts with a ubiquitin molecule and is essential for the trafficking of a number of ubiquitylated payloads to multivesicular bodies (MVBs). Furthermore, the UEV domain can bind to Pro-Thr/Ser-Ala-Pro peptide ligands, a fact exploited by viruses such as HIV. Thus, the TSG101 UEV domain binds to the PTAP tetrapeptide motif in the viral Gag protein that is involved in viral budding. The disclosure also contemplates variants of TSG101, such as fragments of TSG101 and/or TSG101 proteins that have a degree of identity (e.g., 60%, 70%, 80%, 85%, 90%, 95%, 98%, or 99% identity) to a TSG101 protein and are capable if interacting with ARRDC1. Accordingly, a TSG101 protein may be a protein that comprises a UEV domain and interacts with ARRDC1. In some embodiments, the TSG101 protein is at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identical to the amino acid sequence of any one of SEQ ID NOs: 45-47, comprises a UEV domain, and interacts with ARRDC1. In some embodiments, the TSG101 protein has at least 10, at least 20, at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 110, at least 120, at least 130, at least 140, at least 150, at least 160, at least 170, at least 180, at least 190, at least 200, at least 210, at least 220, at least 230, at least 240, at least 250, at least 260, at least 270, at least 280, at least 290, at least 300, at least 310, at least 320, at least 330, at least 340, at least 350, at least 360, at least 370, at least 380, or at least 390 identical contiguous amino acids of any one of SEQ ID NOS: 45-47, comprises a UEV domain, and interacts with ARRDC1. In some embodiments, the TSG101 protein has 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, or more mutations compared to any one of the amino acid sequences set forth in SEQ ID NOs: 45-47 and comprises a UEV domain. In some embodiments, the ARRDC1 protein comprises any one of the amino acid sequences set forth in SEQ ID NOs: 3-5. Exemplary, non-limiting TSG101 protein sequences are provided herein, and additional, suitable TSG101 protein sequences, isoforms, and variants are known in the art. It will be appreciated by those of skill in the art that this invention is not limited in this respect. Exemplary TSG101 sequences include the following sequences (the UEV domain in these sequences includes amino acids 1-145 and is underlined in the sequences below):
MAVSESQLKKMVSKYKYRDLTVRETVNVITLYKDLKPVLDSYVFNDGSSR
ELMNLTGTIPVPYRGNTYNIPICLWLLDTYPYNPPICFVKPTSSMTIKTG
KHVDANGKIYLPYLHEWKHPQSDLLGLIQVMIVVFGDEPPVFSRPISASY
MAVSESQLKKMMSKYKYRDLTVRQTVNVIAMYKDLKPVLDSYVFNDGSSR
ELVNLTGTIPVRYRGNIYNIPICLWLLDTYPYNPPICFVKPTSSMTIKTG
KHVDANGKIYLPYLHDWKHPRSELLELIQIMIVIFGEEPPVFSRPTVSAS
MAVSESQLKKMMSKYKYRDLTVRQTVNVIAMYKDLKPVLDSYVFNDGSSR
ELVNLTGTIPVRYRGNIYNIPICLWLLDTYPYNPPICFVKPTSSMTIKTG
KHVDANGKIYLPYLHDWKHPRSELLELIQIMIVIFGEEPPVFSRPTVSAS
The structure of UEV domains is known to those of skill in the art (see, e.g., Owen Pornillos et al., Structure and functional interactions of the Tsg101 UEV domain, EMBO J. 2002 May 15; 21 (10): 2397-2406, the entire contents of which are incorporated herein by reference).
In some aspects, the present disclosure provides ARMMs modified with NiV glycoproteins and fusion proteins. In some embodiments, the ARMMs disclosed herein comprise a NiV glycoprotein variant fused to an antibody or antigen-binding fragment, wherein the NiV glycoprotein variant does not recognize and/or bind to an ephrin receptor, and a NiV fusion protein. Such modification of ARMMs allows them to be targeted for delivery to a particular cell type, as described herein, and the NiV glycoprotein variant may be fused to various antibodies or antigen-binding fragments that target different cell types.
Viral glycoproteins typically have two important functions: binding and attachment to a target cell, and fusion to the cell membrane. Typically, a single viral glycoprotein is responsible for performing both of these functions. In NiV, however, these functions are split between two different proteins (i.e., the NiV glycoprotein and the NiV fusion protein as described herein). Use of the NiV glycoprotein and fusion protein in the ARMMs described herein therefore allows the NiV glycoprotein to be modified and engineered (e.g., fused to an antibody or antigen-binding fragment to target the ARMMs to particular cell types) without adversely affecting or impacting the function of the fusion protein and the ability of the ARMMs to enter a target cell. The glycoprotein can thus be engineered to eliminate its endogenous binding to ephrin receptors, and a targeting domain (i.e., the antibodies and antigen-binding fragments described herein) can be fused to the glycoprotein. Such a targeting domain can target essentially any protein or other motif on the surface of a target cell.
The wild-type NiV glycoprotein comprises the following amino acid sequence:
In some embodiments, the ARMMs described herein comprise a NiV glycoprotein variant that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a wild-type NiV glycoprotein of SEQ ID NO: 1.
The wild-type NiV fusion protein comprises the following amino acid sequence:
In some embodiments, the ARMMs described herein comprise a NiV fusion protein variant that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a wild-type NiV fusion protein of SEQ ID NO: 6.
In various embodiments, the NiV glycoprotein variant and NiV fusion protein used in the microvesicles described herein may be modified (e.g., with amino acid substitutions or truncations) relative to the wild-type NiV glycoprotein and fusion protein. For example, the NiV glycoprotein and NiV fusion protein may be modified in any way described in U.S. Pat. App. No. US2019144885A1 and Bender, R. R. et al. Receptor-Targeted Nipah Virus Glycoproteins Improve Cell-Type Selective Gene Delivery and Reveal a Preference for Membrane-Proximal Cell Attachment. PLOS Pathogens 2016, 12 (6): e1005641, both of which are incorporated herein by reference.
In some embodiments, the NiV glycoprotein variant comprises one or more amino acid substitutions relative to a wild-type NiV glycoprotein of SEQ ID NO: 1. Such amino acid substitutions may be introduced, for example, to partially reduce or completely eliminate the ability of the NiV glycoprotein to bind its endogenous target (i.e., ephrin receptors). In some embodiments, the one or more amino acid substitutions are selected from the group consisting of Y389X, E501X, W504X, Q530X, E533X, and I588X, wherein X is any amino acid. In some embodiments, the one or more amino acid substitutions are selected from the group consisting of Y389A, E501A, W504A, Q530A, E533A, and I588A. In certain embodiments, the NiV glycoprotein variant comprises amino acid substitutions E501A, W504A, Q530A, and E533A relative to a wild-type NiV glycoprotein of SEQ ID NO: 1.
In addition to the amino acid substitutions described herein, both the NiV glycoprotein and NiV fusion protein may also be truncated for use in the presently described microvesicles. In some embodiments, the NiV glycoprotein variant further comprises a C-terminal truncation. In some embodiments, the NiV glycoprotein variant further comprises a C-terminal truncation of about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, about 25, about 26, about 27, about 28, about 29, about 30, about 31, about 32, about 33, about 34, about 35, about 36, about 37, about 38, about 39, about 40, about 41, about 42, about 43, about 44, about 45, about 46, about 47, about 48, about 49, about 50, or more than about 50 amino acids in length. In certain embodiments, the NiV glycoprotein variant further comprises a C-terminal truncation of about 33 or about 34 amino acids in length.
In some embodiments, the NiV glycoprotein used in the ARMMs of the present disclosure comprises the amino acid sequence of any one of SEO ID NOs: 63-68:
In some embodiments, the NiV fusion protein comprises a C-terminal truncation. In some embodiments, the NiV fusion protein comprises a C-terminal truncation of about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, about 25, about 26, about 27, about 28, about 29, about 30, about 31, about 32, about 33, about 34, about 35, about 36, about 37, about 38, about 39, about 40, about 41, about 42, about 43, about 44, about 45, about 46, about 47, about 48, about 49, about 50, or more than about 50 amino acids in length. In certain embodiments, the NiV fusion protein comprises a C-terminal truncation of about 22 amino acids in length.
In some embodiments, the NiV fusion protein used in the ARMMs of the present disclosure comprises the amino acid sequence of SEQ ID NO: 69:
The NiV glycoprotein variants used in the ARMMs of the present disclosure may also be fused to an antibody or antigen-binding fragment to target the ARMMs to particular cell types as described herein. In some embodiments, the NiV glycoproteins used in the microvesicles described herein are fused to a single-chain variable fragment (scFv). In certain embodiments, the NiV glycoproteins used in the microvesicles described herein are fused to a nanobody. In certain embodiments, the NiV glycoproteins used in the microvesicles described herein are fused to a DARPin.
Some aspects of this invention provide expression constructs for encoding a gene product or gene products that induce or facilitate the generation of ARMMs in cells harboring such a construct. In some embodiments, the expression constructs described herein encode a fusion proteins as described herein, such as ARRDC1 fusion proteins and TSG101 fusion proteins. In some embodiments, the expression constructs encode an ARRDC1 protein, or variant thereof, and/or a TSG101 protein, or variant thereof. In some embodiments, overexpression of either or both of these gene products in a cell increase the production of ARMMs in the cell, thus turning the cell into a microvesicle producing cell. In some embodiments, such an expression construct comprises at least one restriction or recombination site that allows in-frame cloning of a protein sequence to be fused, either at the C-terminus, or at the N-terminus of the encoded ARRDC1, or variant thereof. As another example, an expression construct comprises at least one restriction or recombination site that allows in-frame cloning of a protein sequence to be fused either at the C-terminus, or at the N-terminus of one or more encoded WW domains.
In some embodiments, the expression construct comprises (a) a nucleotide sequence encoding an ARRDC1 protein, or variant thereof, operably linked to a heterologous promoter, and (b) a restriction site or a recombination site positioned adjacent to the ARRDC1-encoding nucleotide sequence allowing for the insertion of a nucleotide sequencing encoding a payload protein, or an RNA binding protein or RNA binding protein variant sequence, in frame with the ARRDC1-encoding nucleotide sequence. In some embodiments, the heterologous promoter may be a constitutive promoter. In some embodiments, the heterologous promoter may be an inducible promoter. Some aspects of this invention provide an expression construct comprising (a) a nucleotide sequence encoding a TSG101 protein, or variant thereof, operably linked to a heterologous promoter, and (b) a restriction site or a recombination site positioned adjacent to the TSG101-encoding nucleotide sequence allowing for the insertion of a nucleotide sequence encoding a protein agent, or an RNA binding protein, DNA binding protein, or variant sequence thereof, in frame with the TSG101-encoding nucleotide sequence. In some embodiments, the heterologous promoter may be a constitutive promoter. In some embodiments, the heterologous promoter may be an inducible promoter.
Some aspects of this invention provide an expression construct comprising (a) a nucleotide sequence encoding a WW domain, or variant thereof, operably linked to a heterologous promoter, and (b) a restriction site or a recombination site positioned adjacent to the WW domain-encoding nucleotide sequence allowing for the insertion of a protein agent or RNA binding protein, or a protein variant sequence thereof in frame with the WW domain-encoding nucleotide sequence. In some embodiments, the heterologous promoter may be a constitutive promoter. In some embodiments, the heterologous promoter may be an inducible promoter. The expression constructs may encode a payload protein, or an RNA binding protein fused to at least one WW domain. In some embodiments, the expression constructs encode a payload protein or an RNA binding protein, or a variant thereof, fused to at least one WW domain, or variant thereof. Any of the expression constructs, described herein, may encode any WW domain or variant thereof. In some embodiments, the heterologous promoter may be a constitutive promoter. In some embodiments, the heterologous promoter may be an inducible promoter.
The expression constructs, described herein, may comprise any nucleic acid sequence capable of encoding a WW domain or variant thereof. For example, a nucleic acid sequence encoding a WW domain or WW domain variant may be from the human ubiquitin ligase WWP1, WWP2, Nedd4-1, Nedd4-2, Smurf1, Smurf2, ITCH, NEDL1, or NEDL2. Exemplary nucleic acid sequences of WW domain-containing proteins are listed below. It should be appreciated that any of the nucleic acids encoding WW domains or WW domain variants of the exemplary proteins may be used in the invention, described herein, and are not meant to be limiting.
Human WWP1 nucleic acid sequence (uniprot.org/uniprot/Q9H0M0):
Human WWP2 nucleic acid sequence (uniprot.org/uniprot/O00308):
Human Nedd4-1 nucleic acid sequence (uniprot.org/uniprot/P46934):
Human Nedd4-2 nucleic acid sequence (>gi|345478679|ref|NM_015277.5|Homo sapiens neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase (NEDD4L), transcript variant d, mRNA):
Human Smurf1 nucleic acid sequence (uniprot.org/uniprot/Q9HCE7):
Human Smurf2 nucleic acid sequence (uniprot.org/uniprot/Q9HAU4):
Human ITCH nucleic acid sequence (uniprot.org/uniprot/Q96J02):
Human NEDL1 nucleic acid sequence (uniprot.org/uniprot/Q76N89):
Human NEDL2 nucleic acid sequence (uniprot.org/uniprot/Q9P2P5):
Some aspects of this invention provide expression constructs that encode any of the proteins, nucleic acids, such as RNAs, or fusions thereof described herein.
Nucleic acids encoding any of the proteins and/or nucleic acid (including RNA) described herein, may be in any number of nucleic acid “vectors” known in the art. As used herein, a “vector” means any nucleic acid or nucleic acid-bearing particle, cell, or organism capable of being used to transfer a nucleic acid into a host cell. The term “vector” includes both viral and nonviral products and means for introducing the nucleic acid into a cell. A “vector” can be used in vitro, ex vivo, or in vivo. Non-viral vectors include plasmids, cosmids, artificial chromosomes (e.g., bacterial artificial chromosomes or yeast artificial chromosomes) and can comprise liposomes, electrically charged lipids (cytofectins), DNA-protein complexes, and biopolymers, for example. Viral vectors include retroviruses, lentiviruses, adeno-associated virus, pox viruses, baculovirus, reoviruses, vaccinia viruses, herpes simplex viruses, Epstein-Barr viruses, and adenovirus vectors, for example. Vectors can also comprise the entire genome sequence or recombinant genome sequence of a virus. A vector can also comprise a portion of the genome that comprises the functional sequences for production of a virus capable of infecting, entering, or being introduced to a cell to deliver nucleic acid therein.
Expression of any of the proteins and/or nucleic acids (including RNA) described herein, may be controlled by any regulatory sequence (e.g., a promoter sequence) known in the art. Regulatory sequences, as described herein, are nucleic acid sequences that regulate the expression of a nucleic acid sequence. A regulatory or control sequence may include sequences that are responsible for expressing a particular nucleic acid or may include other sequences, such as heterologous, synthetic, or partially synthetic sequences. The sequences can be of eukaryotic, prokaryotic, or viral origin that stimulate or repress transcription of a gene in a specific or non-specific manner and in an inducible or non-inducible manner. Regulatory or control regions may include origins of replication, RNA splice sites, introns, chimeric or hybrid introns, promoters, enhancers, transcriptional termination sequences, poly A sites, locus control regions, signal sequences that direct the polypeptide into the secretory pathways of the target cell. A heterologous regulatory region is a regulatory region not naturally associated with the expressed nucleic acid it is linked to. Included among the heterologous regulatory regions are regulatory regions from a different species, regulatory regions from a different gene, hybrid regulatory sequences, and regulatory sequences that do not occur in nature, but which are designed by one of ordinary skill in the art.
The term operably linked refers to an arrangement of sequences or regions wherein the components are configured so as to perform their usual or intended function. Thus, a regulatory or control sequence operably linked to a coding sequence is capable of affecting the expression of the coding sequence. The regulatory or control sequences need not be contiguous with the coding sequence, so long as they function to direct the proper expression or polypeptide production. Thus, for example, intervening untranslated but transcribed sequences can be present between a promoter sequence and the coding sequence, and the promoter sequence can still be considered operably linked to the coding sequence. A promoter sequence, as described herein, is a DNA regulatory region a short distance from the 5′ end of a gene that acts as the binding site for RNA polymerase. The promoter sequence may bind RNA polymerase in a cell and/or initiate transcription of a downstream (3′ direction) coding sequence. The promoter sequence may be a promoter capable of initiating transcription in prokaryotes or eukaryotes. Some non-limiting examples of eukaryotic promoters include the cytomegalovirus (CMV) promoter, the chicken β-actin (CBA) promoter, and a hybrid form of the CBA promoter (CBh).
A microvesicle-producing cell of the present invention may be a cell containing any of the expression constructs, any of the fusion proteins, or any of the agents (e.g., small molecules, proteins, and nucleic acids (e.g., DNA, RNA), DNA plasmids, siRNA, mRNA, Cas9 and other Cas proteins, zinc finger nucleases, TALENs, etc.) described herein. For example, in some aspect, the present disclosure provides microvesicle-producing cells comprising: a first isolated nucleic acid encoding an ARRDC1 protein or a variant thereof, a second isolated nucleic acid encoding a Nipah virus (NiV) glycoprotein variant fused to an antibody or antigen-binding fragment, wherein the NiV glycoprotein variant does not recognize and/or bind to an ephrin receptor, and a third isolated nucleic acid encoding a NiV fusion protein. In some embodiments, the first isolated nucleic acid, the second isolated nucleic acid, and the third isolated nucleic acid are expressed on the same recombinant expression construct under the control of one or more heterologous promoters. In some embodiments, the first isolated nucleic acid, the second isolated nucleic acid, and the third isolated nucleic acid are expressed on more than one recombinant expression construct, wherein the one or more recombinant expression constructs are under the control of one or more heterologous promoters. In certain embodiments, the first isolated nucleic acid, the second isolated nucleic acid, and the third isolated nucleic acid are expressed on different recombinant expression constructs, wherein the different recombinant expression constructs are each under the control of a heterologous promoter.
Any of the expression constructs described herein may be stably inserted into the genome of the cell. In some embodiments, the expression construct is maintained in the cell, but not inserted into the genome of the cell. In some embodiments, the expression construct is in a vector, for example, a plasmid vector, a cosmid vector, a viral vector, or an artificial chromosome. In some embodiments, the expression construct further comprises additional sequences or elements that facilitate the maintenance and/or the replication of the expression construct in the microvesicle-producing cell, or that improve the expression of the fusion protein in the cell. Such additional sequences or elements may include, for example, an origin of replication, an antibiotic resistance cassette, a polyA sequence, and/or a transcriptional isolator. Some expression constructs suitable for the generation of microvesicle producing cells according to aspects of this invention are described elsewhere herein. Methods and reagents for the generation of additional expression constructs suitable for the generation of microvesicle producing cells according to aspects of this invention will be apparent to those of skill in the art based on the present disclosure. In some embodiments, the microvesicle producing cell is a mammalian cell, for example, a mouse cell, a rat cell, a hamster cell, a rodent cell, or a nonhuman primate cell. In some embodiments, the microvesicle producing cell is a human cell.
One skilled in the art may employ conventional techniques, such as molecular or cell biology, virology, microbiology, and recombinant DNA techniques. Exemplary techniques are explained fully in the literature. For example, one may rely on the following general texts to make and use the invention: Sambrook et al., Molecular Cloning: A Laboratory Manual, Second Edition (1989) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, and Sambrook et al., Third Edition (2001); DNA Cloning: A Practical Approach, Volumes I and II (D. N. Glover ed. 1985); Oligonucleotide Synthesis (M. J. Gaited. 1984); Nucleic Acid Hybridization (B. D. Hames & S. J. Higgins eds. (1985)); Transcription And Translation Hames & Higgins, eds. (1984); Animal Cell Culture (RI. Freshney, ed. (1986)); Immobilized Cells And Enzymes (IRL Press, (1986)); Gennaro et al., (eds.) Remington's Pharmaceutical Sciences, 18th edition; B. Perbal, A Practical Guide To Molecular Cloning (1984); F. M. Ausubel et al., (eds.), Current Protocols in Molecular Biology, John Wiley & Sons, Inc. (updates through 2001), Coligan et al., (eds.), Current Protocols in Immunology, John Wiley & Sons, Inc. (updates through 2001); W. Paul et al., (eds.) Fundamental Immunology, Raven Press; E. J. Murray et al., (ed.) Methods in Molecular Biology: Gene Transfer and Expression Protocols, The Humana Press Inc. (1991) (especially vol. 7); and J. E. Celis et al., Cell Biology: A Laboratory Handbook, Academic Press (1994).
The inventive microvesicles (e.g., ARMMs modified with NiV glycoproteins and fusion proteins and containing any of the agents described herein), comprise an antibody or antibody binding fragment, which may be used to target the delivery of ARMMs to specific cell types, resulting in the release of the contents of the ARMM into the cytoplasm of the specific targeted cell type. Antibodies or antigen-binding fragments contemplated for use in the present disclosure include, but are not limited to, single-chain variable fragments (scFvs) nanobodies and DARPins. The antibody or antigen-binding fragment may allow for the targeting of particular cell types (e.g., neurons, astrocytes, oligodendrocytes, microglial cells, T-cells, dendritic cells, B cells, NK cells, stem cells, progenitor cells, endothelial cells, muscle cells, myocardial cells, epithelial cells, and hepatic cells). In certain embodiments, the antibody or antigen-binding fragment targets T cells. In certain embodiments, the antibody or antigen-binding fragment targets neurons.
Some aspects of this invention relate to the recognition that ARMMs modified with engineered NiV glycoproteins and fusion proteins are taken up by target cells (e.g., T cell, neurons, or other specific cell types), and ARMM uptake results in the release of the contents of the ARMM (e.g., any of the agents described herein) into the cytoplasm of the target cells. In some embodiments, the payload is an agent that affects a desired change in the target cell, for example, a change in cell survival, proliferation rate, a change in differentiation stage, a change in a cell identity, a change in chromatin state, a change in the transcription rate of one or more genes, a change in the transcriptional profile, or a post-transcriptional change in gene compression of the target cell. It will be understood by those of skill in the art that the agent to be delivered will be chosen according to the desired effect in the target cell.
Thus, in some aspects, the present disclosure provides methods of delivering a molecule to a target cell comprising contacting the target cell with any of the microvesicles described herein. In some embodiments, the target cell is any of the cell types described herein (e.g., T cells or neurons). In some embodiments, the microvesicle is delivered to a target cell in a subject (e.g., a patient). In some aspects, the present disclosure provides methods of treating a patient comprising administering to the patient any of the microvesicles described herein, or any of the microvesicle-producing cells described herein. In some aspects, the present disclosure provides methods of delivering an ARMM comprising delivering any of the ARMMs or microvesicle-producing cells described herein to a subject. In some embodiments, the subject is mammalian. In certain embodiments, the subject is human.
In some embodiments, cells from a subject are obtained, and an agent is delivered to the cells by a microvesicle or method provided herein ex vivo. In some embodiments, the treated cells are selected for those cells in which a desired gene is expressed or repressed. In some embodiments, treated cells carrying a protein or RNA agent are returned to the subject they were obtained from.
Target cells can be contacted with an ARMM in different ways. For example, a target cell may be contacted directly with an ARMM as described herein, or with an isolated ARMM from a microvesicle-producing cell. The contacting can be done in vitro by administering the ARMM to the target cell in a culture dish, or in vivo by administering the ARMM to a subject (e.g., parenterally or non-parenterally). In some embodiments, an ARMM is produced from a cell obtained from a subject. In some embodiments, the ARMM that was produced from a cell that was obtained from the subject is administered to the subject from which the ARMM producing cell was obtained. In some embodiments, the ARMM that was produced from a cell that was obtained from the subject is administered to a subject different from the subject from which the ARMM producing cell was obtained. As one example, a cell may be obtained from a subject and engineered to express one or more of the constructs provided herein (e.g., any of the polynucleotides encoding the various components of the ARMMs described herein). The cell obtained from the subject and engineered to express one or more of the constructs provided herein may be administered to the same subject, or a different subject, from which the cell was obtained. Alternatively, the cell obtained from the subject and engineered to express one or more of the constructs provided herein produces ARMMs, which may be isolated and administered to the same subject from which the cell was obtained or administered to a different subject from which the cell was obtained.
Alternatively, a target cell can be contacted with a microvesicle producing cell as described herein, for example, in vitro by co-culturing the target cell and the microvesicle producing cell, or in vivo by administering a microvesicle producing cell to a subject harboring the target cell. Accordingly, the method may include contacting the target cell with a microvesicle, for example, an ARMM containing any of the agents described herein. The target cell may be contacted with a microvesicle-producing cell, as described herein, or with an isolated microvesicle that has a lipid bilayer, an ARRDC1 protein or variant thereof, and a NiV glycoprotein and NiV fusion protein.
It should be appreciated that the target cell may be of any origin, for example, from an organism. In some embodiments, the target cell is a mammalian cell. Some non-limiting examples of a mammalian cell include, without limitation, a mouse cell, a rat cell, a hamster cell, a rodent cell, and a nonhuman primate cell. In some embodiments, the target cell is a human cell. It should also be appreciated that the target cell may be of any cell type, such as a cell type of the nervous system. In other cases, the target cell may be any differentiated cell type found in a subject. In some embodiments, the target cell is a cell in vitro, and the method includes administering the microvesicle to the cell in vitro, or co-culturing the target cell with the microvesicle-producing cell in vitro. In some embodiments, the target cell is a cell in a subject, and the method comprises administering the microvesicle or the microvesicle-producing cell to the subject. In some embodiments, the subject is a mammalian subject, for example, a rodent, a mouse, a rat, a hamster, or a non-human primate. In some embodiments, the subject is a human subject.
In some embodiments, the target cell is a pathological cell. In some embodiments, the target cell is a cancer cell. In some embodiments, the microvesicle is associated with an antibody or antigen-binding fragment that selectively binds an antigen on the surface of the target cell. In some embodiments, the antigen of the target cell is a cell surface antigen. In some embodiments, the antibody or antigen-binding fragment is a single-chain variable fragment (scFv), a nanobody, or a DARPin. Suitable surface antigens of target cells, for example, of specific target cell types, e.g., T cells or neurons, are known to those of skill in the art, as are suitable antibodies or antigen-binding fragments that specifically bind such antigens. Methods for producing membrane-bound binding agents, for example, membrane-bound immunoglobulins, membrane-bound antibodies, or antibody fragments that specifically bind a surface antigen expressed on the surface of a target cell, are also known to those of skill in the art. The choice of the antibody or antigen-binding fragment will depend, of course, on the identity or the type of target cell. Cell surface antigens specifically expressed on various types of target cells that can be targeted by ARMMs comprising membrane-bound binding agents will be apparent to those of skill in the art. It will be appreciated that the present invention is not limited in this respect. In some embodiments, the target cells express the antigen that antibody or antigen-binding fragment binds to, for example that the antigen that antibody or antigen-binding fragment selectively binds to. In some embodiments, the target cells express the antigen that antibody or antigen-binding fragment on the surface of the target cell.
In some embodiments, any of the ARMMs described herein further include a detectable label. Such ARMMs allow for the labeling of a target cell without genetic manipulation. Detectable labels suitable for direct delivery to target cells are known in the art, and include, but are not limited to, fluorescent proteins, fluorescent dyes, membrane-bound dyes, and enzymes, for example, membrane-bound or cytosolic enzymes, catalyzing a reaction resulting in a detectable reaction product. Detectable labels suitable according to some aspects of this invention further include membrane-bound antigens, for example, membrane-bound ligands that can be detected with commonly available antibodies or antigen-binding agents.
In some embodiments, ARMMs are provided that comprise an RNA agent that encodes a transcription factor, a transcriptional repressor, a fluorescent protein, a kinase, a phosphatase, a protease, a ligase, a chromatin modulator, or a recombinase. In some embodiments, ARMMs are provided that comprise an RNA agent (e.g., an siRNA) that inhibits expression of a transcription factor, a transcriptional repressor, a fluorescent protein, a kinase, a phosphatase, a protease, a ligase, a chromatin modulator, or a recombinase. In some embodiments, the RNA agent is a therapeutic RNA. In some embodiments the RNA agent is an RNA that effects a change in the state or identity of a target cell. For example, in some embodiments, the RNA agent encodes a reprogramming factor. Suitable transcription factors, transcriptional repressors, fluorescent proteins, kinases, phosphatases, proteases, ligases, chromatin modulators, recombinases, and reprogramming factors may be encoded by an RNA agent that is associated with a binding RNA to facilitate their incorporation into ARMMs, and their function may be tested by any methods that are known to those skilled in the art, and the invention is not limited in this respect.
Methods for isolating the ARMMs described herein (i.e., ARMMs modified with NiV glycoproteins and fusion proteins) are also provided by the present disclosure. One exemplary method includes collecting the culture medium, or supernatant, of a cell culture comprising microvesicle-producing cells. In some embodiments, the cell culture comprises cells obtained from a subject, for example, cells suspected to exhibit a pathological phenotype, for example, a hyperproliferative phenotype. In some embodiments, the cell culture comprises genetically engineered cells producing ARMMs, for example, cells expressing a recombinant ARMM protein, for example, a recombinant ARRDC1 or TSG101 protein, such as an ARRDC1 or TSG101 protein fused to an RNA or protein agent as described herein. In some embodiments, the supernatant is pre-cleared of cellular debris by centrifugation, for example, by two consecutive centrifugations of increasing G value (e.g., 500G and 2000G). In some embodiments, the method comprises passing the supernatant through a 0.2 μm filter, eliminating all large pieces of cell debris and whole cells. In some embodiments, the supernatant is subjected to ultracentrifugation, for example, at 120,000G for 2 hours, depending on the volume of centrifugate. The pellet obtained comprises microvesicles. In some embodiments, exosomes are depleted from the microvesicle pellet by staining and/or sorting (e.g., by FACS or MACS) using an exosome marker as described herein. Isolated or enriched ARMMs can be suspended in culture media or a suitable buffer, as described herein.
Other aspects of the present disclosure relate to pharmaceutical compositions comprising any of the ARMMs or microvesicle-producing cells provided herein. The term “pharmaceutical composition”, as used herein, refers to a composition formulated for pharmaceutical use. In some embodiments, the pharmaceutical composition further comprises a pharmaceutically acceptable carrier. In some embodiments, the pharmaceutical composition comprises additional agents (e.g., for specific delivery, increasing half-life, or other therapeutic compounds as described herein).
As used herein, the term “pharmaceutically-acceptable carrier” means a pharmaceutically-acceptable material, composition, or vehicle, such as a liquid or solid filler, diluent, excipient, manufacturing aid (e.g., lubricant, talc magnesium, calcium or zinc stearate, or steric acid), or solvent encapsulating material, involved in carrying or transporting the compound from one site (e.g., the delivery site) of the body, to another site (e.g., organ, tissue, or portion of the body). A pharmaceutically acceptable carrier is “acceptable” in the sense of being compatible with the other ingredients of the formulation and not injurious to the tissue of the subject (e.g., physiologically compatible, sterile, physiologic pH, etc.). Some examples of materials that can serve as pharmaceutically-acceptable carriers include: (1) sugars, such as lactose, glucose and sucrose; (2) starches, such as corn starch and potato starch; (3) cellulose, and its derivatives, such as sodium carboxymethyl cellulose, methylcellulose, ethyl cellulose, microcrystalline cellulose and cellulose acetate; (4) powdered tragacanth; (5) malt; (6) gelatin; (7) lubricating agents, such as magnesium stearate, sodium lauryl sulfate and talc; (8) excipients, such as cocoa butter and suppository waxes; (9) oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; (10) glycols, such as propylene glycol; (11) polyols, such as glycerin, sorbitol, mannitol, and polyethylene glycol (PEG); (12) esters, such as ethyl oleate and ethyl laurate; (13) agar; (14) buffering agents, such as magnesium hydroxide and aluminum hydroxide; (15) alginic acid; (16) pyrogen-free water; (17) isotonic saline; (18) Ringer's solution; (19) ethyl alcohol; (20) pH buffered solutions; (21) polyesters, polycarbonates, and/or polyanhydrides; (22) bulking agents, such as polypeptides and amino acids (23) serum components, such as serum albumin, HDL, and LDL; (22) C2-C12 alcohols, such as ethanol; and (24) other non-toxic compatible substances employed in pharmaceutical formulations. Wetting agents, coloring agents, release agents, coating agents, sweetening agents, flavoring agents, perfuming agents, preservatives, and antioxidants can also be present in the formulation. The terms such as “excipient”, “carrier”, “pharmaceutically acceptable carrier,” or the like are used interchangeably herein.
In some embodiments, the pharmaceutical composition is formulated for delivery to a subject, e.g., for delivering an agent to a cell. Suitable routes of administrating the pharmaceutical composition described herein include, without limitation: topical, subcutaneous, transdermal, intradermal, intralesional, intraarticular, intraperitoneal, intravesical, transmucosal, gingival, intradental, intracochlear, transtympanic, intraorgan, epidural, intrathecal, intramuscular, intravenous, intravascular, intraosseus, periocular, intratumoral, intracerebral, and intracerebroventricular administration.
In some embodiments, the pharmaceutical composition described herein is administered locally to a diseased site. In some embodiments, the pharmaceutical composition described herein is administered to a subject by injection, by means of a catheter, by means of a suppository, or by means of an implant, the implant being of a porous, non-porous, or gelatinous material, including a membrane, such as a sialastic membrane, or a fiber.
In some embodiments, the pharmaceutical composition is formulated in accordance with routine procedures as a composition adapted for intravenous or subcutaneous administration to a subject, e.g., a human. In some embodiments, pharmaceutical compositions for administration by injection are solutions in sterile isotonic aqueous buffer. Where necessary, the pharmaceutical composition can also include a solubilizing agent and a local anesthetic such as lidocaine to ease pain at the site of the injection. Where the pharmaceutical is to be administered by infusion, it can be dispensed with an infusion bottle containing sterile pharmaceutical grade water or saline. Where the pharmaceutical composition is administered by injection, an ampoule of sterile water for injection or saline can be provided so that the ingredients can be mixed prior to administration.
A pharmaceutical composition for systemic administration may be a liquid, e.g., sterile saline, lactated Ringer's solution, or Hank's solution. In addition, the pharmaceutical composition can be in solid forms and re-dissolved or suspended immediately prior to use. Lyophilized forms are also contemplated.
The pharmaceutical composition described herein may be administered or packaged as a unit dose, for example. The term “unit dose” when used in reference to a pharmaceutical composition of the present disclosure refers to physically discrete units suitable as unitary dosage for the subject, each unit containing a predetermined quantity of active material calculated to produce the desired therapeutic effect in association with the required diluent, i.e., carrier, or vehicle.
Further, the pharmaceutical composition can be provided as a pharmaceutical kit comprising (a) a container containing any of the ARMMs or microvesicle-producing cells described herein and (b) a second container containing a pharmaceutically acceptable diluent (e.g., sterile water) for injection. The pharmaceutically acceptable diluent can be used, e.g., for reconstitution or dilution of the ARMM or microvesicle-producing cell. Optionally associated with such container(s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals or biological products, which notice reflects approval by the agency of manufacture, use, or sale for human administration.
In another aspect, an article of manufacture containing materials useful for the treatment of a disease or disorder is included. In some embodiments, the article of manufacture comprises a container and a label. Suitable containers include, for example, bottles, vials, syringes, and test tubes. The containers may be formed from a variety of materials such as glass or plastic. In some embodiments, the container holds a composition that is effective for treating a disease described herein and may have a sterile access port. For example, the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle. The active agent in the composition is an ARMM (or microvesicle-producing cell) of the invention. In some embodiments, the label on or associated with the container indicates that the composition is used for treating the disease of choice. The article of manufacture may further comprise a second container comprising a pharmaceutically-acceptable buffer, such as phosphate-buffered saline, Ringer's solution, or dextrose solution. It may further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, syringes, and package inserts with instructions for use.
Some aspects of this disclosure provide kits comprising a polynucleotide encoding any of the components of the ARMMs provided herein. In some embodiments, the polynucleotide encodes any of the proteins, fusion proteins, and/or RNAs provided herein. In some embodiments, the polynucleotide comprises a heterologous promoter that drives expression of any of the proteins, fusion proteins, and/or RNAs provided herein.
Some aspects of this disclosure provide microvesicle (e.g., ARMM) producing cells comprising any of the proteins, fusion proteins, and/or RNAs provided herein. In some embodiments, the cells comprise a polynucleotide that encodes any of the proteins, fusion proteins, and/or RNAs provided herein. In some embodiments, the cells comprise any of the polynucleotides or vectors provided herein. In some embodiments, the vector comprise viral targeting proteins.
It should be appreciated however, that additional proteins, fusion proteins, and RNAs would be apparent to the skilled artisan based on the present disclosure and knowledge in the art.
The function and advantage of these and other embodiments of the present invention will be more fully understood from the Examples below. The following Examples are intended to illustrate the benefits of the present invention and to describe particular embodiments but are not intended to exemplify the full scope of the invention. Accordingly, it will be understood that the Examples are not meant to limit the scope of the invention.
NiV-F and-G proteins can be used to pseudotype lentiviruses to allow specific cell targeting (R. Bender et al., PLOS Genetics, 2016). It was analyzed whether the NiV F/G system could be used to modify non-viral, lipid-bilayer-encapsulated particles such as ARMMs. First, it was tested whether NiV-F/G proteins can be recruited and packaged onto ARMMs. When co-expressed with ARRDC1 (which drives the formation and budding of ARMMs) and its associated cargos, NiV-F/G proteins can be incorporated onto ARMMs, thus allowing for targeting of the vesicles to specific cells or tissues (
It was next assessed whether ARMMs incorporated with NiV proteins mediate specific cell targeting. In particular, it was assessed whether NiV-G-CD8-containing ARMMs can specifically target CD8+ cells. PBMCs, which contain a population of CD8+ T cells, were used for this analysis. Primary PBMCs were incubated with either NiV-G-NT-ARMMs or NiV-G-CD8-ARMMs. Unmodified ARMMs and VSVG-pseudotyped ARMMs were used as controls. All ARMMs contained GFP protein as the cargo. After incubation with ARMMs, PBMCs were stained for CD8 and subjected to flow cytometry analysis to assess CD8 staining and cargo (GFP) uptake. As shown in
Positively charged peptides such as Vecotfusion-1 can be used to enhance the transduction efficiency of lentiviruses. It was next tested whether Vectofusin-1 can enhance ARMMs delivery into PBMCs. As shown in
The delivery of ARMMs in activated PBMCs was also tested. Activation of PBMCs by IL2, CD3, and CD28 antibodies leads to the expansion of T cells. Similar to what was observed in unstimulated PBMCs, there was a specific increase in the percentage of GFP-positive cells in the CD8+ cell population of activated PBMCs after incubation with NiV-CD8-ARMMs (
It was further tested whether NiV-ARMMs can mediate targeted delivery of mRNAs. GFP-mRNA was packaged into ARMMs using the published TAT-TAR system, which consists of a short TAT peptide fused directly to the C-terminus of ARRDC1 and TAR fused directly to the 5′ end of GFP mRNA. Binding of TAR to TAT-ARRDC1 allows the recruitment of the TAR-fused mRNA into ARMMs. PBMCs were incubated with either NiV-NT-ARMM (GFPmRNA) or NiV-CD8-ARMM (GFPmRNA), and then subjected to flow cytometry. As shown in
PBMC culturing and activation. Primary PBMCs were purchased from Lonza and cultured in RPMI 1640 supplemented with 10% FCS, 2 mM L-glutamine, 0.5% streptomycin/penicillin, 25 mM HEPES (Sigma-Aldrich, Munich, Germany), 100 U/ml interleukin-2 (R&D Systems, Minneapolis, USA). For activation, PBMCs were cultured for 72 h in RPMI 1640 supplemented with 10% FCS, 2 mM L-glutamine, 0.5% streptomycin/penicillin, 25 mM HEPES (Sigma-Aldrich, Munich, Germany), 100 U/ml interleukin-2 (R&D Systems, Minneapolis, USA), 1 μg/ml CD3 antibody (clone: OKT3, eBioscience, San Diego, USA) and 1 μg/ml CD28 antibody (clone: CD28.2, eBioscience, San Diego, USA). Following activation, cells were grown in the same medium without the CD3 and CD28 antibodies.
ARMMs production and purification. Briefly, HEK293T cells were transfected with different DNA constructs as indicated using the FuGene 6 reagent (Promega). 24 hours later, the medium was replaced with fresh DMEM supplemented with 10% exo-free FBS. 48 hours after transfection, a first cell culture supernatant was collected, and 72 hours after transfection, a second cell culture supernatant was collected. The collected supernatants were pooled and subjected to two consecutive rounds of centrifugation (500×g and 2000×g). The medium was then passed through a 200 nm filter (Acrodisc) and subjected to ultracentrifugation using the SW41Ti rotor in a L8-M or XE90 centrifuge (Beckman) at 166, 900×g for 2 h. The medium was then aspirated, and the pellets enriched with ARMMs were washed twice with ice-old PBS and resuspended in PBS. NanoSight Nanoparticle tracking analysis is done to determine the number of vesicles in the samples.
Western blotting analysis. Cells were lysed in NP-40 lysis buffer (0.5% NP-40, 50 mM Tris-HCl, and 150 mM NaCl) supplemented with a protease inhibitor mixture (Roche). Lysates or EVs resuspended in lithium dodecyl sulfate sampling buffer (Novex) were resolved on a 4-12% NuPAGE gel (Novex) and transferred onto a PVDF membrane (Bio-Rad). Blots were probed with primary antibodies in Tris-buffered saline containing 0.1% Tween 20 and 5% Nonfat milk, followed by HRP-conjugated anti-rabbit antibody (Cell Signaling, 7074S, at 1:5000 dilution) or anti-mouse antibodies (Cell Signaling, 7076S, at 1:5000 dilution). Primary antibodies used include anti-ARRDC1 rabbit polyclonal antibody (in house, 1:2000), anti-vinculin rabbit monoclonal antibody (Abcam, AB129002, at 1:1000 dilution), rabbit monoclonal GFP antibody (Cell Signaling, 2956S, 1:1000), CD9 antibody (Cell Signaling, 1:2000), monoclonal His antibody (Cell Signaling, 1:1000), and rabbit monoclonal AU1-Tag (Bethyl, 1:2000).
Flow cytometry. Primary PBMCs were transferred into FACS washing buffer and washed twice, and CD8 expression was detected by a human APC-conjugated anti-CD8 antibody (clone RPA-T8, 1:100, BD Biosciences, San Jose, USA). After two additional washing steps, cells were resuspended in 100 μl FACS washing buffer and analyzed by DXP11 flow cytometer. Data were analyzed using the FlowJo 10.0 software (BD Biosciences).
All publications, patents and sequence database entries mentioned herein, including those items listed above, are hereby incorporated by reference in their entirety as if each individual publication or patent was specifically and individually indicated to be incorporated by reference. In case of conflict, the present application, including any definitions herein, will control.
Those skilled in the art will recognize or be able to ascertain using no more than routine experimentation many equivalents to the specific embodiments of the invention described herein. The scope of the present invention is not intended to be limited to the above description, but rather is as set forth in the appended claims.
In the claims, articles such as “a,” “an,” and “the” may mean one or more than one unless indicated to the contrary or otherwise evident from the context. Claims or descriptions that include “or” between one or more members of a group are considered satisfied if one, more than one, or all of the group members are present in, employed in, or otherwise relevant to a given product or process unless indicated to the contrary or otherwise evident from the context. The invention includes embodiments in which exactly one member of the group is present in, employed in, or otherwise relevant to a given product or process. The invention also includes embodiments in which more than one, or all of the group members are present in, employed in, or otherwise relevant to a given product or process.
Furthermore, it is to be understood that the invention encompasses all variations, combinations, and permutations in which one or more limitations, elements, clauses, descriptive terms, etc., from one or more of the claims or from relevant portions of the description is introduced into another claim. For example, any claim that is dependent on another claim can be modified to include one or more limitations found in any other claim that is dependent on the same base claim. Furthermore, where the claims recite a composition, it is to be understood that methods of using the composition for any of the purposes disclosed herein are included, and methods of making the composition according to any of the methods of making disclosed herein or other methods known in the art are included, unless otherwise indicated or unless it would be evident to one of ordinary skill in the art that a contradiction or inconsistency would arise.
Where elements are presented as lists, e.g., in Markush group format, it is to be understood that each subgroup of the elements is also disclosed, and any element(s) can be removed from the group. It is also noted that the term “comprising” is intended to be open and permits the inclusion of additional elements or steps. It should be understood that, in general, where the invention, or aspects of the invention, is/are referred to as comprising particular elements, features, steps, etc., certain embodiments of the invention or aspects of the invention consist, or consist essentially of, such elements, features, steps, etc. For purposes of simplicity, those embodiments have not been specifically set forth in haec verba herein. Thus, for each embodiment of the invention that comprises one or more elements, features, steps, etc., the invention also provides embodiments that consist or consist essentially of those elements, features, steps, etc.
Where ranges are given, endpoints are included. Furthermore, it is to be understood that unless otherwise indicated or otherwise evident from the context and/or the understanding of one of ordinary skill in the art, values that are expressed as ranges can assume any specific value within the stated ranges in different embodiments of the invention, to the tenth of the unit of the lower limit of the range, unless the context clearly dictates otherwise. It is also to be understood that unless otherwise indicated or otherwise evident from the context and/or the understanding of one of ordinary skill in the art, values expressed as ranges can assume any subrange within the given range, wherein the endpoints of the subrange are expressed to the same degree of accuracy as the tenth of the unit of the lower limit of the range.
In addition, it is to be understood that any particular embodiment of the present invention may be explicitly excluded from any one or more of the claims. Where ranges are given, any value within the range may explicitly be excluded from any one or more of the claims. Any embodiment, element, feature, application, or aspect of the compositions and/or methods of the invention, can be excluded from any one or more claims. For purposes of brevity, all of the embodiments in which one or more elements, features, purposes, or aspects is excluded are not set forth explicitly herein.
This application claims priority under 35 U.S.C. § 119(e) to U.S. Provisional Application, U.S. Ser. No. 63/319,238, filed Mar. 11, 2022, which is incorporated by reference herein.
This invention was made with government support under ES030990 awarded by the National Institutes of Health. The government has certain rights in the invention.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2023/064262 | 3/13/2023 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 63319238 | Mar 2022 | US |
