Patent Application
20240124890
Compositions and methods are described for the delivery of a fully human post-translationally modified (HuPTM) therapeutic monoclonal antibody (“mAb”) that binds to CGRP or CGRPR or the HuPTM antigen-binding fragment of a therapeutic mAb that binds to CGRP or CGRPR—e.g., a fully human-glycosylated (HuGly) Fab of the therapeutic mAb—to a human subject diagnosed with a disease or condition indicated for treatment with the therapeutic mAb. Such diseases include migraine and cluster headaches. Co-delivery of two HuPTM therapeutic mAbs targeting anti-CGRP and anti-CGRPR HuPTM mAb is also disclosed.
Therapeutic mAbs have been shown to be effective in treating a number of diseases and conditions. However, because these agents are effective for only a short period of time, repeated injections for long durations are often required, thereby creating considerable treatment burden for patients. Treatments that interfere with the functioning of CGRP in the peripheral trigeminal system are effective against migraine. Blocking sensitization of the trigeminal nerve by attenuating CGRP activity in the periphery may be sufficient to block a migraine attack.
Therapeutic antibodies that bind to calcitonin gene-related peptide (CGRP) or its receptor (CGRPR) may be used for preventive treatment of migraine and cluster headaches. Currently, erenumab is approved for the treatment of migraine and three anti-CGRP antibodies, fremanezumab (AJOVY®), eptinezumab (VYETPI®), and galcanezumab (EMGALITY®), are also approved for the preventive treatment for migraine. Galcanezumab is also approved for the treatment of episodic cluster headaches. The recommended dosage of erenumab (AIMOVIG®) is 70 mg injected subcutaneously once monthly. Some patients can benefit from a dosage of 140 mg injected subcutaneously once monthly, which is administered as two consecutive subcutaneous injections of 70 mg each.
There is a need for more effective treatments that reduce the treatment burden on patients suffering from chronic or acute migraines and cluster headaches. Systemic (IV or IM) administration or intranasal (IN) administration of AAV9-based anti-CGRP/CGRPR gene therapy should allow maintenance of sufficient antibody levels at the appropriate location to treat and prevent migraines and cluster headaches. This increased level of antibodies in the CNS coupled with targeting both CGRP and the CGRP receptor may aid in increased efficacy of the treatment and increase the number of patients responsive to migraine treatment with a targeted CGRP therapy
Therapeutic antibodies delivered by gene therapy have several advantages over injected or infused therapeutic antibodies that dissipate over time resulting in peak and trough levels. Sustained expression of the transgene product antibody, as opposed to injecting an antibody repeatedly, allows for a more consistent level of antibody to be present at the site of action, and is less risky and more convenient for patients, since fewer injections need to be made. Furthermore, antibodies expressed from transgenes are post-translationally modified in a different manner than those that are directly injected because of the different microenvironment present during and after translation. Without being bound by any particular theory, this results in antibodies that have different diffusion, bioactivity, distribution, affinity, pharmacokinetic, and immunogenicity characteristics, such that the antibodies delivered to the site of action are “biobetters” in comparison with directly injected antibodies. Accordingly, provided herein are compositions and methods for anti-CGRP and anti-CGRPR gene therapy, particularly recombinant AAV gene therapy, designed to target the CNS, particularly arterial smooth muscle cells and/or the trigeminal ganglion (TG), and may also generate a depot in the liver, muscle, or liver and muscle, of transgenes for expression of anti-CGRP or anti-CGRPR antibodies that cross the blood-brain barrier, particularly erenumab, eptinezumab, fremanezumab, and galcanezumab, or an antigen binding fragment thereof, that result in a therapeutic or prophylactic serum levels of the antibody within 20 days, 30 days, 40 days, 50 days, 60 days, or 90 days of administration of the rAAV composition. Serum levels include 2 to 20 μg/ml antibody for an anti-CGRPR antibody, particularly, erenumab, or an antigen binding fragment thereof. The levels of antibody achieved are sufficient to lead to an at least 10%, 20%, 50%, 70% or 90% reduction in headache days per month from a baseline, or a reduction in at least 1, 2, 3, or 4 headache days per month from baseline.
Compositions and methods are described for the systemic delivery of an anti-CGRP or anti-CGRPR HuPTM mAb or an anti-CGRP or anti-CGRPR HuPTM antigen-binding fragment of a therapeutic mAb (for example, a fully human-glycosylated Fab (HuGlyFab) of a therapeutic mAb, to a patient (human subject) diagnosed with migraine, including episodic and chronic migraine, or cluster headaches or other conditions indicated for treatment with the therapeutic anti-CGRP or anti-CGRPR mAb. Such antigen-binding fragments of therapeutic mAbs include a Fab, F(ab′)2, or scFv (single-chain variable fragment) (collectively referred to herein as “antigen-binding fragment”). “HuPTM Fab” as used herein may include other antigen binding fragments of a mAb. In an alternative embodiment, full-length mAbs can be used. Provided are also compositions comprising and methods of administering a rAAV that encodes both an anti-CGRP antibody, particularly a Fab, and an anti-CGRPR antibody, particularly a Fab, particularly in which the anti-CGRP antibody and the anti-CGRPR antibody are under the control of different regulatory sequences that direct expression in different tissue types, or a combination of an rAAV encoding an anti-CGRP antibody and an rAAV encoding an anti-CGRP receptor antibody. Delivery may be advantageously accomplished via gene therapy—e.g., by administering a viral vector or other DNA expression construct encoding a therapeutic anti-CGRP and/or anti-CGRPR mAb or its antigen-binding fragment (or a hyperglycosylated derivative of either) diagnosed with a condition indicated for treatment with the therapeutic anti-CGRP or anti-CGRPR mAb—to create a permanent depot in CNS, PNS, arterial smooth muscle, muscle and/or liver cells, of the patient that continuously supplies the HuPTM mAb or antigen-binding fragment of the therapeutic mAb, e.g., a human-glycosylated transgene product, or peptide to dural vessels and/or the trigeminal ganglion, or generally to the circulation or CNS, of the subject where the mAb or antigen-binding fragment thereof or peptide exerts its therapeutic or prophylactic effect.
Provided are gene therapy vectors, particularly rAAV gene therapy vectors, which when administered to a human subject result in expression of an anti-CGRP or anti-CGRPR antibody to achieve a maximum or steady state serum concentration (for example, 20, 30, 40, 50, 60 or 90 days after administration) of 2 μg/ml to 20 μg/ml (or, 2 μg/ml to 10 μg/ml, or 5 μg/ml to 15 μg/ml, or 10 μg/ml to 20 μg/ml) anti-CGRP or anti-CGRPR antibody (including erenumab). Also provided are gene therapy vectors, particularly rAAV gene therapy vectors, which when administered to a human subject result in expression of an anti-CGRP or anti-CGRPR antibody to achieve a maximum or steady state serum concentration (for example, 20, 30, 40, 50, 60 or 90 days after administration) of 2 μg/ml to 20 μg/ml (or, 2 μg/ml to 10 μg/ml, or 5 μg/ml to 15 μg/ml, or 10 μg/ml to 20 μg/ml).
Methods include a method of treating migraine and/or cluster headaches in a human subject in need thereof, comprising intravenously or intramuscularly administering to the subject a dose of a composition comprising a recombinant AAV comprising a transgene encoding an antibody selected from fremanezumab, eptinezumab, galcanezumab or erenumab or an antigen binding protein comprising a heavy chain variable region, a light chain variable region and optionally an Fc domain of the antibody or an antigen binding fragment thereof, operably linked to one or more regulatory sequences that control expression of the transgene in liver and/or muscle cells, in an amount sufficient to result in expression from the transgene and secretion of the antibody, or the antigen binding protein or the antigen binding fragment thereof into the bloodstream of the human subject to produce antibody or the antigen binding protein or antigen binding fragment thereof, plasma levels of at least 1.5 μg/ml to 35 μg/ml antibody or the antigen binding protein or antigen binding fragment thereof, in said subject, or of at least 5 μg/ml to 35 μg/ml antibody or antigen binding protein or antigen binding fragment thereof, or of at least 1.5 μg/ml to 20 μg/ml antibody or antigen binding protein or antigen binding fragment thereof, of at least 1.5 μg/ml to 10 μg/ml antibody or antigen binding protein or antigen binding fragment thereof, or of at least 5 μg/ml to 20 μg/ml antibody or antigen binding protein or antigen binding fragment thereof, within at least 20, 30, 40 or 60 days of said administering.
In certain embodiments, administration of a therapeutically effective amount of the anti-CGRPR or anti-CGRP mAb, or antigen-binding fragment thereof, is determined to be sufficient to reduce nausea, light sensitivity, sound sensitivity, red eye, eyelid edema, forehead and facial sweating, tearing (lacrimation), abnormal small size of the pupil (miosis), nasal congestion, runny nose (rhinorrhea), and drooping eyelid (ptosis). Alternatively, administration of a therapeutically effective amount of the anti-CGRPR or anti-CGRP mAb, or antigen-binding fragment thereof, is determined to be sufficient to reduce the intensity or frequency of migraines or cluster headaches, or a reduction in the amount of acute migraine-specific medication used over a defined period of time.
The recombinant vector used for delivering the transgene includes non-replicating recombinant adeno-associated virus vectors (“rAAV”). In embodiments, the AAV type has a tropism for CNS, PNS, arterial smooth muscle, muscle and/or liver cells, for example an AAV8, AAV9, AAV.PHP.eB, AAVrh10, AAVhu.32, AAV3B, AAVrh46, AAVrh73, AAVS3, AAV-LK03, AAVhu.51, AAVhu.21, AAVhu.12 or AAVhu.26 serotype of AAV. However, other viral vectors may be used, including but not limited to lentiviral vectors; vaccinia viral vectors, or non-viral expression vectors referred to as “naked DNA” constructs. Expression of the transgene can be controlled by constitutive or tissue-specific expression control elements, particularly elements that are smooth muscle cell-specific control elements, for example one or more elements of Table 1. Regulatory elements include the CAG promoter, LMTP6 promoter or LMTP24 promoter.
In certain embodiments, the HuPTM mAb or HuPTM antigen-binding fragment encoded by the transgene can include, but is not limited to, a full-length or an antigen-binding fragment of a therapeutic antibody that binds to CGRP or CGRPR, particularly erenumab, eptinezumab, fremanezumab, and galcanezumab, see, for example
Gene therapy constructs for the therapeutic antibodies are designed such that both the heavy and light chains are expressed. The coding sequences for the heavy and light chains can be engineered in a single construct in which the heavy and light chains are separated by a cleavable linker or IRES so that separate heavy and light chain polypeptides are expressed. In particular embodiments, the linker is a Furin T2A linker (SEQ ID NOS:87 or 88). In certain embodiments, the coding sequences encode for a Fab or F(ab′)2 or an scFv. In certain embodiments the full length heavy and light chains of the antibody are expressed. Gene therapy constructs are also designed such that the construct encodes both an anti-CGRP antibody, particularly a Fab, and an anti-CGRPR antibody, particularly a Fab and, in particular, each operably linked and under the control of different tissue specific promoters such that the anti-CGRP antibody is expressed in a different set of cells from the ant-CGRPR antibody.
In addition, antibodies expressed from transgenes in vivo are not likely to contain degradation products associated with antibodies produced by recombinant technologies, such as protein aggregation and protein oxidation. Aggregation is an issue associated with protein production and storage due to high protein concentration, surface interaction with manufacturing equipment and containers, and purification with certain buffer systems. These conditions, which promote aggregation, do not exist in transgene expression in gene therapy. Oxidation, such as methionine, tryptophan, and histidine oxidation, is also associated with protein production and storage, and is caused by stressed cell culture conditions, metal and air contact, and impurities in buffers and excipients. The proteins expressed from transgenes in vivo may also oxidize in a stressed condition. However, humans, and many other organisms, are equipped with an antioxidation defense system, which not only reduces the oxidation stress, but sometimes also repairs and/or reverses the oxidation. Thus, proteins produced in vivo are not likely to be in an oxidized form. Both aggregation and oxidation could affect the potency, pharmacokinetics (clearance), and immunogenicity.
The production of HuPTM mAb or HuPTM Fab in the CNS, PNS, arterial smooth muscle cells, and/or liver cells, particularly smooth muscle cells of the dura, of the human subject should result in a “biobetter” molecule for the treatment of disease accomplished via gene therapy—e.g., by administering a viral vector or other DNA expression construct encoding a full-length HuPTM mAb or HuPTM Fab of a therapeutic mAb to a patient (human subject) diagnosed with a disease indication for that mAb, to create a permanent depot in the subject that continuously supplies the human-glycosylated, sulfated transgene product produced by the subject's transduced cells. The cDNA construct for the HuPTMmAb or HuPTM Fab should include a signal peptide that ensures proper co- and post-translational processing (glycosylation and protein sulfation) by the transduced human cells.
As an alternative, or an additional treatment to gene therapy, the full-length HuPTM mAb or HuPTM Fab can be produced in human cell lines by recombinant DNA technology, and the glycoprotein can be administered to patients.
Dual vector therapy involving systemic delivery of two viral vectors, wherein the first vector expresses as anti-CGRPR antibody or antigen-binding fragment thereof, and the second vector expresses an anti-CGRP antibody or antigen-binding fragment, to a patient in need thereof are encompassed by the methods provided herein. The viral vectors may be the same or different serotypes, for example, an AAV9 serotype and an AAV8 serotype.
Combination therapy involving systemic (including IV or IM) or intranasal delivery of the full-length HuPTM anti-CGRPR or anti-CGRP antibody, or an binding-fragment thereof, to the patient accompanied by administration of other available treatments are also encompassed by the methods provided herein. The additional treatments may be administered before, concurrently or subsequent to the gene therapy treatment. Such additional treatments can include but are not limited to co-therapy with the therapeutic mAb.
Also provided are methods of manufacturing the viral vectors, particularly the AAV based viral vectors. In specific embodiments, provided are methods of producing recombinant AAVs comprising culturing a host cell containing an artificial genome comprising a cis expression cassette flanked by AAV ITRs, wherein the cis expression cassette comprises a transgene encoding a therapeutic antibody operably linked to expression control elements that will control expression of the transgene in human cells; a trans expression cassette lacking AAV ITRs, wherein the trans expression cassette encodes an AAV rep and capsid protein operably linked to expression control elements that drive expression of the AAV rep and capsid proteins in the host cell in culture and supply the rep and cap proteins in trans; sufficient adenovirus helper functions to permit replication and packaging of the artificial genome by the AAV capsid proteins; and recovering recombinant AAV encapsidating the artificial genome from the cell culture.
Compositions and methods are described for the systemic delivery of a fully human post-translationally modified (HuPTM) therapeutic monoclonal antibody (mAb) or a HuPTM antigen-binding fragment of a therapeutic anti-CGRP or anti-CGRPR mAb (for example, a fully human-glycosylated Fab (HuGlyFab) of a therapeutic mAb) to a patient (human subject) diagnosed with an acute or chronic migraine or cluster headaches, including episodic cluster headaches, or other indications indicated for treatment with the therapeutic mAb. Provided are also compositions comprising and methods of administering a rAAV that encodes both an anti-CGRP antibody, particularly a Fab, and an anti-CGRPR antibody, particularly a Fab, or a combination of an rAAV encoding an anti-CGRP antibody and an rAAV encoding an anti-CGRP receptor antibody, each under the control of different promoter such that the anti-CGRP antibody is expressed in cell types that differ from the cell types where the anti-CGRPR antibody is expressed. Delivery may be advantageously accomplished via gene therapy—e.g., by administering a viral vector or other DNA expression construct encoding a therapeutic anti-CGRP and/or anti-CGRPR mAb or its antigen-binding fragment (or a hyperglycosylated derivative of either) diagnosed with a condition indicated for treatment with the therapeutic anti-CGRP or anti-CGRPR mAb—to create a permanent depot in CNS, PNS, arterial smooth muscles, and/or liver cells, of the patient that continuously supplies the HuPTM mAb or antigen-binding fragment of the therapeutic mAb, e.g., a human-glycosylated transgene product, or to dural vessels and/or the trigeminal ganglion of the subject where the mAb or antigen-binding fragment thereof or peptide exerts its therapeutic or prophylactic effect.
In certain embodiments, the HuPTM mAb or HuPTM antigen-binding fragment encoded by the transgene, but it not limited to, is a full-length or an antigen-binding fragment of a HuPTM mAb or HuPTM that binds CGRP, particularly erenumab, or CGRPR, particularly fremanezumab, eptinezumab, and galcanezumab (see
The compositions and methods provided herein systemically deliver anti-CGRP or anti-CGRPR antibodies, particularly, erenumab, fremanezumab, eptinezumab, and galcanezumab, from a depot of viral genomes, for example, in the subject's CNS, PNS, arterial smooth muscle, and/or liver cells at a level that is therapeutically or prophylactically effective to treat or ameliorate the symptoms of or to reduce the incidence of (for example, reducing the number of headache days per month) acute or chronic migraine or cluster headaches or other indication that may be treated with an anti-CGRP or anti-CGRPR antibody. Identified herein are viral vectors for delivery of transgenes encoding the therapeutic anti-CGRP or anti-CGRPR antibodies to cells in the human subject, including, in embodiments, CNS, PNS, arterial smooth muscle, and/or liver cells, and regulatory elements operably linked to the nucleotide sequence encoding the heavy and light chains of the anti-CGRP or anti-CGRPR antibody that promote the expression of the antibody in the cells, in embodiments, in CNS, PNS, arterial smooth muscle, and/or liver cells. Alternatively, identified herein are also viral vectors for delivery of a first and a second transgene, wherein the first transgene encodes a heavy chain and a light chain of an antigen-binding fragment of an anti-CGRP operably linked to a first regulatory sequence (e.g. a CAG promoter), and the second transgene encodes a heavy and light chain of an antigen binding fragment of an anti-CGRPR antibody, operably linked to a second regulatory sequence (e.g. sm22a promoter), wherein said first and second regulatory sequences promote expression of the first and second transgenes in different human cell types encoding the therapeutic anti-CGRP or anti-CGRPR antibodies to cells in the human subject, including, in embodiments, CNS, PNS, arterial smooth muscle, and/or liver cells, and regulatory elements operably linked to the nucleotide sequence encoding the heavy and light chains of the anti-CGRP or anti-CGRPR antibody that promote the expression of the antibody in the cells, in embodiments, in CNS, PNS, arterial smooth muscle, and/or liver cells. Such regulatory elements, including smooth muscle cell-specific promoters are provided in Table 1 herein. Accordingly, such viral vectors may be delivered to the human subject at appropriate dosages such that at least 20, 30, 40, 50 or 60 days after administration, the anti-CGRPR antibody or erenumab is present in the serum of said human subject at a level of at least 2 μg/ml to 20 μg/ml anti-CGRPR antibody or erenumab in said subject, or of at least 5 μg/ml to 35 μg/ml anti-CGRPR antibody or erenumab, or of at least 2 μg/ml to 10 μg/ml anti-CGRPR antibody or erenumab or of at least 2 μg/ml to 20 μg/ml anti-CGRPR antibody or erenumab or of at least 5 μg/ml to 20 μg/ml anti-CGRPR antibody or erenumab within at least 20, 30, 40, 50, or 60 days of said administering. Viral vectors may be delivered to the human subject at appropriate dosages such that at least 20, 30, 40, 50 or 60 days after administration, the anti-CGRP antibody or fremanezumab, eptinezumab, or galcanezumab is present in the serum of said human subject at a level of at least 5 μg/ml to 40 μg/ml anti-CGRP antibody or fremanezumab, eptinezumab, or galcanezumab in said subject, or of at least 5 μg/ml to 35 μg/ml anti-CGRP antibody or fremanezumab, eptinezumab, or galcanezumab, or of at least 5 μg/ml to 20 μg/ml anti-CGRPR antibody or erenumab or of at least 2 μg/ml to 20 μg/ml anti-CGRP antibody or fremanezumab, eptinezumab, or galcanezumab within at least 20, 30, 40, 50, or 60 days of said administering.
The HuPTM mAb or HuPTM antigen-binding fragment encoded by the transgene can include, but is not limited to, a full-length or an antigen-binding fragment of a therapeutic antibody that binds to CGRP or CGRPR, including but not limited to, erenumab, fremanezumab, eptinezumab, and galcanezumab. The amino acid sequences of the heavy and light chain of antigen binding fragments of the foregoing are provided in Table 8, infra. Heavy chain variable domain having an amino acid sequence of SEQ ID NO: 1, 3, 5, or 7 and light chain variable domain having an amino acid sequence of SEQ ID NO: 2, 4, 6, or 8 (encoded by nucleotide sequence SEQ ID NO: 9, 11, 13, or 15 and 10, 12, 14, or 16, respectively). The HuPTM mAb or HuPTM antigen-binding fragment encoded by the transgene can include, but is not limited to, a full-length or an antigen-binding fragment of a therapeutic antibody or antigen-binding fragments engineered to contain additional glycosylation sites on the Fab domain (e.g., see Courtois et al., 2016, mAbs 8: 99-112 which is incorporated by reference herein in its entirety for its description of derivatives of antibodies that are hyperglycosylated on the Fab domain of the full-length antibody).
The recombinant vector used for delivering the transgene includes non-replicating recombinant adeno-associated virus vectors (“rAAV”). rAAVs are particularly attractive vectors for a number of reasons—they can be modified to preferentially target a specific organ of choice; and there are hundreds of capsid serotypes to choose from to obtain the desired tissue specificity, and/or to avoid neutralization by pre-existing patient antibodies to some AAVs. “Throughout the specification, AAV “serotype” refers to an AAV having an immunologically distinct capsid, a naturally-occurring capsid, or an engineered capsid.” The AAV types for use here in preferentially target the liver, i.e., have a tropism for CNS cells, particularly vascular smooth muscle cells and the trigeminal ganglion. Such rAAVs include but are not limited to AAV based vectors comprising capsid components from one or more of AAV serotype 1 (AAV1), serotype 2 (AAV2), serotype 3 (AAV3), serotype 3B (AAV3B), serotype 4 (AAV4), serotype 5 (AAV5), serotype 6 (AAV6), serotype 7 (AAV7), serotype 8 (AAV8), serotype rh8 (AAVrh8), serotype 9 (AAV9), serotype 9e (AAV9e), serotype rh10 (AAVrh10), serotype rh20 (AAVrh20), serotype rh39 (AAVrh39), serotype rh34 (AAVrh34), serotype hu.32 (AAVhu.32), serotype hu.37 (AAVhu.37), serotype hu.60 (AAVrh73), serotype rh21 (AAVrh21), serotype rh15 (AAVrh15), serotype rh24 (AAVrh24), serotype hu5 (AAVhu.5), serotype hu.10 (AAVhu.10), serotype hu.46 (AAVhu.46), serotype rh73 (AAVrh73), or serotype rh74 (AAVrh74), or PHP.eB (AAV.PHP.eB). In certain embodiments, AAV based vectors provided herein comprise capsids from one or more of AAV8, AAV9, AAV.PHP.eB, or AAVrh10 serotypes.
However, other viral vectors may be used, including but not limited to lentiviral vectors; vaccinia viral vectors, or non-viral expression vectors referred to as “naked DNA” constructs. Expression of the transgene can be controlled by constitutive or tissue-specific expression control elements.
Gene therapy constructs are designed such that both the heavy and light chains are expressed. In certain embodiments, the full length heavy and light chains of the antibody are expressed. In certain embodiments, the coding sequences encode for a Fab or F(ab′)2 or an scFv. The heavy and light chains should be expressed at about equal amounts, in other words, the heavy and light chains are expressed at approximately a 1:1 ratio of heavy chains to light chains. The coding sequences for the heavy and light chains can be engineered in a single construct in which the heavy and light chains are separated by a cleavable linker or IRES so that separate heavy and light chain polypeptides are expressed. In specific embodiments, the linker separating the heavy and light chains is a Furin-2A linker, for example a Furin-F2A linker RKRR(GSG)APVKQTLNFDLLKLAGDVESNPGP (SEQ ID NOS:85 or 86) or a Furin-T2A linker RKRR(GSG)EGRGSLLTCGDVEENPGP (SEQ ID NOS: 87 or 88). In certain embodiments, the construct expresses, from the N-terminus to C-terminus, NH2-VL-linker-VH—COOH or NH2-VH-linker-VL-COOH. In other embodiments, the construct expresses, from the N-terminus to C-terminus, NH2-signal or localization sequence-VL-linker-VH—COOH or NH2-signal or localization sequence-VH-linker-VL-COOH. In other embodiments, the constructs express an scFv in which the heavy and light chain variable domains are connected via a flexible, non-cleavable linker.
Gene therapy constructs are designed such that both the heavy and light chains of an anti-CGRP antibody (first antibody), particularly a Fab, and the heavy and light chains of an anti-CGRPR antibody (second antibody), particularly a Fab, are expressed. The heavy and light chains of the first and second antibody should be expressed at about equal amounts, in other words, the heavy and light chains of the first and second antibody are expressed at approximately a 1:1 ratio of heavy chains to light chains. The coding sequences for both the heavy and light chains of the first and second antibody can be engineered in a single construct in which the heavy and light chains of the first and second antibody are separated by a cleavable linker or IRES so that separate heavy and light chain polypeptides are expressed. In specific embodiments, the linker separating the heavy and light chains is a Furin-2A linker, for example a Furin-F2A linker RKRR(GSG)APVKQTLNFDLLKLAGDVESNPGP (SEQ ID NOS:85 or 86) or a Furin-T2A linker RKRR(GSG)EGRGSLLTCGDVEENPGP (SEQ ID NOS: 87 or 88).
In certain embodiments, nucleic acids (e.g., polynucleotides) and nucleic acid sequences disclosed herein may be codon-optimized, for example, via any codon-optimization technique known to one of skill in the art (see, e.g., review by Quax et al., 2015, Mol Cell 59:149-161) and may also be optimized to reduce CpG dimers. Each heavy and light chain requires a signal sequence to ensure proper post-translation processing and secretion (unless expressed as an scFv, in which only the N-terminal chain requires a signal sequence sequence). Useful signal sequences for the expression of the heavy and light chains of the therapeutic antibodies in human cells are disclosed herein. Table 9 discloses optimized nucleotide sequences encoding the vectorized antibodies erenumab, fremanezumab, galcanezumab or eptinezumab (SEQ ID Nos 267, 274, 281, and 288, respectively, with leader sequence coding sequences underlined). Exemplary recombinant expression constructs are shown in
The production of HuPTM mAb or HuPTM Fab (including an HuPTM scFv) should result in a “biobetter” molecule for the treatment of disease accomplished via gene therapy—e.g., by administering a viral vector or other DNA expression construct encoding a full-length HuPTM mAb or HuPTM Fab or other antigen binding fragment, such as an scFv, of a therapeutic mAb to a patient (human subject) diagnosed with a disease indication for that mAb, to create a permanent depot in the subject that continuously supplies the human-glycosylated, sulfated transgene product produced by the subject's transduced cells. The cDNA construct for the HuPTM mAb or HuPTM Fab or HuPTM scFv should include a signal peptide that ensures proper co- and post-translational processing (glycosylation and protein sulfation) by the transduced human cells.
Pharmaceutical compositions suitable for administration to human subjects comprise a suspension of the recombinant vector in a formulation buffer comprising a physiologically compatible aqueous buffer, a surfactant and optional excipients. Such formulation buffer can comprise one or more of a polysaccharide, a surfactant, polymer, or oil. Provided are formulations adapted for intranasal administration.
As an alternative, or an additional treatment to gene therapy, the full-length HuPTM mAb or HuPTM Fab or other antigen binding fragment thereof can be produced in human cell lines by recombinant DNA technology, and the glycoprotein can be administered to patients. Human cell lines that can be used for such recombinant glycoprotein production include but are not limited to human embryonic kidney 293 cells (HEK293), fibrosarcoma HT-1080, HKB-11, CAP, HuH-7, and retinal cell lines, PER.C6, or RPE to name a few (e.g., see Dumont et al., 2015, Crit. Rev. Biotechnol. 36(6):1110-1122, which is incorporated by reference in its entirety for a review of the human cell lines that could be used for the recombinant production of the HuPTM mAb, HuPTM Fab or HuPTM scFv product, e.g., HuPTM Fab glycoprotein). To ensure complete glycosylation, especially sialylation, and tyrosine-sulfation, the cell line used for production can be enhanced by engineering the host cells to co-express α-2,6-sialyltransferase (or both α-2,3- and α-2,6-sialyltransferases) and/or TPST-1 and TPST-2 enzymes responsible for tyrosine-O-sulfation in human cells.
It is not essential that every molecule produced either in the gene therapy or protein therapy approach be fully glycosylated and sulfated. Rather, the population of glycoproteins produced should have sufficient glycosylation (including 2,6-sialylation) and sulfation to demonstrate efficacy. The goal of gene therapy treatment of the invention is to slow or arrest the progression of disease.
Combination therapies involving delivery of the full-length HuPTM mAb or HuPTM Fab or antigen binding fragment thereof to the patient accompanied by administration of other available treatments are encompassed by the methods of the invention. The additional treatments may be administered before, concurrently or subsequent to the gene therapy treatment. Such additional treatments can include but are not limited to co-therapy with the therapeutic mAb.
Also provided are methods of manufacturing the viral vectors, particularly the AAV based viral vectors. In specific embodiments, provided are methods of producing recombinant AAVs comprising culturing a host cell containing an artificial genome comprising a cis expression cassette flanked by AAV ITRs, wherein the cis expression cassette comprises a transgene encoding a therapeutic antibody operably linked to expression control elements that will control expression of the transgene in human cells; a trans expression cassette lacking AAV ITRs, wherein the trans expression cassette encodes an AAV rep and capsid protein operably linked to expression control elements that drive expression of the AAV rep and capsid proteins in the host cell in culture and supply the rep and cap proteins in trans; sufficient adenovirus helper functions to permit replication and packaging of the artificial genome by the AAV capsid proteins; and recovering recombinant AAV encapsidating the artificial genome from the cell culture.
Viral vectors or other DNA expression constructs encoding an anti-CGRP or anti-CGRPR HuPTM mAb or antigen-binding fragment thereof, particularly a HuGlyFab, or a hyperglycosylated derivative of a HuPTM mAb antigen-binding fragment are provided herein. The viral vectors and other DNA expression constructs provided herein include any suitable method for delivery of a transgene to a target cell. The means of delivery of a transgene include viral vectors, liposomes, other lipid-containing complexes, other macromolecular complexes, synthetic modified mRNA, unmodified mRNA, small molecules, non-biologically active molecules (e.g., gold particles), polymerized molecules (e.g., dendrimers), naked DNA, plasmids, phages, transposons, cosmids, or episomes. In some embodiments, the vector is a targeted vector, e.g., CNS, PNS, arterial smooth muscle, skeletal muscle, and/or liver cells, or a vector that has a tropism for CNS, PNS, arterial smooth muscle, skeletal muscle, and/or liver cells, particularly arterial smooth muscle cells.
In some aspects, the disclosure provides for a nucleic acid for use, wherein the nucleic acid comprises a nucleotide sequence that encodes a HuPTM mAb or HuGlyFab or other antigen-binding fragment thereof, as a transgene described herein, operatively linked to an ubiquitous promoter, a CNS-specific, skeletal muscle-specific, liver-specific and/or smooth muscle cell-specific promoter, or an inducible promoter, wherein the promoter is selected for expression in tissue targeted for expression of the transgene. Promoters may, for example, be a CAG promoter (SEQ ID NO: 25) and associated upstream regulatory sequences, cytomegalovirus (CMV) promoter, EF-1 alpha promoter (SEQ ID NO:27), mU1a (SEQ ID NO:26), UB6 promoter, chicken beta-actin (CBA) promoter, and liver-specific promoters, such as TBG (Thyroxine-binding Globulin) promoter (SEQ ID NO:183), APOA2 promoter, SERPINA1 (hAAT) promoter, ApoE.hAAT (SEQ ID NO:166), or muscle-specific promoters, such as a human desmin promoter, CK8 promoter (SEQ ID NO:182), LMTP6 promoter (SEQ ID NO: 169), LMTP24 promoter (SEQ ID NO: 263), or Pitx3 promoter, inducible promoters, such as a hypoxia-inducible promoter or a rapamycin-inducible promoter, or a combination thereof. In preferred embodiments, the promoter is a smooth muscle cell-specific promoter or a CNS-specific promoter. In preferred embodiments, the promoter is the sm22a (SEQ ID NO:184, 185, 186, 187, 188, 189, or 190) promoter. In other embodiments, the promoter is a hSyn promoter (SEQ ID NO:191-195).
In some aspects herein, transgene expression is controlled by engineered nucleic acid regulatory elements that have more than one regulatory element (promoter or enhancer), including regulatory elements that are arranged in tandem (two or three copies) that promote liver-specific expression, or both liver-specific expression and muscle-specific expression. These regulatory elements include for the liver-specific expression, LSPX1 (SEQ ID NO:154), LSPX2 (SEQ ID NO: 155), LTP1 (SEQ ID NO:156), LTP2 (SEQ ID NO:157), or LTP3 (SEQ ID NO:158), and for the liver and muscle expression, LMTP6 (SEQ ID NO:159), LMTP13 (SEQ ID NO:160), LMTP14 (SEQ ID NO:161), LMTP15 (SEQ ID NO:162), LMTP18 (SEQ ID NO:163), LMTP19 (SEQ ID NO:164), LMTP20 (SEQ ID NO:165), or LMTP24 (SEQ ID NO: 263), the sequences of which are provided in Table 1.
In some aspects, the disclosure provides for a nucleic acid for use, wherein the nucleic acid encodes a first and a second transgene encoding an CGRP antibody (particularly a Fab fragment thereof) and CGRPR antibody (particularly a Fab fragment thereof), respectively, including vice versa, wherein each transgene is operatively linked to an ubiquitous promoter, a CNS-specific and/or smooth muscle cell-specific promoter, or an inducible promoter, wherein the promoter is selected such that the promoters promote expression of the first and second transgenes in different human cell types. In some embodiments, the first transgene is operably linked to a smooth muscle cell-specific promoter and the second transgene is operably linked to a CNS specific promoter. In a specific embodiment, the first transgene is operably linked to the sm22a promoter (SEQ ID NOS:184, 185-190) and the second transgene to the hSyn promoter (SEQ ID NOS:191-195) or alternatively the first transgene is operably linked to the hSyn promoter (SEQ ID NOS:191-195) and the second transgene is operably linked to the sm22a promoter (SEQ ID NOS:184, 185-190).
In certain embodiments, provided herein are recombinant vectors that comprise one or more nucleic acids (e.g., polynucleotides). The nucleic acids may comprise DNA, RNA, or a combination of DNA and RNA. In certain embodiments, the DNA comprises one or more of the sequences selected from the group consisting of promoter sequences, the sequence of the gene of interest (the transgene, e.g., the nucleotide sequences encoding the heavy and light chains of the HuPTMmAb or HuGlyFab or other antigen-binding fragment), untranslated regions, and termination sequences. In certain embodiments, viral vectors provided herein comprise a promoter operably linked to the gene of interest.
In certain embodiments, nucleic acids (e.g., polynucleotides) and nucleic acid sequences disclosed herein may be codon-optimized, for example, via any codon-optimization technique known to one of skill in the art (see, e.g., review by Quax et al., 2015, Mol Cell 59:149-161).
In a specific embodiment, the constructs described herein comprise the following components: (1) AAV2 inverted terminal repeats that flank the expression cassette; (2) one or more control elements, b) optionally, a chicken β-actin or other intron (such as a VH4 intron), c) optionally, a Kozak sequence, and d) a rabbit β-globin poly A signal; and (3) nucleic acid sequences coding for the heavy and light chains of a mAb or Fab, separated by a self-cleaving furin (F)/(F/T)2A linker (SEQ ID NOS:85, 86, 87, or 88), ensuring expression of equal amounts of the heavy and the light chain polypeptides. An exemplary construct is shown in
In a specific embodiment, the constructs described herein comprise the following components: (1) AAV2 inverted terminal repeats that flank the expression cassette; (2) sm22a promoter, b) optionally, a chicken f-actin or other intron (such as a VH4 intron), c) optionally a Kozak sequence, d) a rabbit β-globin polyA signal; and (3) nucleic acid sequences coding for a full-length antibody comprising the heavy and light chain sequences using sequences that encode the Fab portion of the heavy chain, including the hinge region sequence, plus the Fc polypeptide of the heavy chain for the appropriate isotype and the light chain, wherein heavy and light chain nucleotide sequences are separated by a self-cleaving furin (FY(F/T)2A linker (SEQ ID NOS:85, 86, 87, or 88), ensuring expression of equal amounts of the heavy and the light chain polypeptides. An exemplary construct is shown in
In a specific embodiment, the constructs described herein comprise the following components: (1) AAV2 inverted terminal repeats that flank the expression cassette; (2) sm22a promoter, (3) a first nucleic acid sequences coding for the heavy and light chains of a first Fab (e.g. an anti-CGRP Fab), separated by a self-cleaving furin (FY(F/T)2A linker (SEQ ID NOS:85, 86, 87, or 88), (4) a rabbit β-globin polyA signal; (5) a hSyn promoter, (6) a second nucleic acid sequences coding for the heavy and light chains of a second Fab (e.g. an anti-CGRPR Fab), separated by a self-cleaving furin (F)/(F/T)2A linker (SEQ ID NOS:85, 86, 87, or 88), and (7) a rabbit β-globin polyA signal. An exemplary construct is shown in
5.1.1 mRNA Vectors
In certain embodiments, as an alternative to DNA vectors, the vectors provided herein are modified mRNA encoding for the gene of interest (e.g., the transgene, for example, HuPTMmAb or HuGlyFab or other antigen binding fragment thereof). The synthesis of modified and unmodified mRNA for delivery of a transgene to retinal pigment epithelial cells is taught, for example, in Hansson et al., J. Biol. Chem., 2015, 290(9):5661-5672, which is incorporated by reference herein in its entirety. In certain embodiments, provided herein is a modified mRNA encoding for a HuPTMmAb, HuPTM Fab, or HuPTM scFv.
5.1.2 Viral Vectors
Viral vectors include adenovirus, adeno-associated virus (AAV, e.g., AAV8, AAV9, AAVrh10, AAV.PHP.B), lentivirus, helper-dependent adenovirus, herpes simplex virus, poxvirus, hemagglutinin virus of Japan (HVJ), alphavirus, vaccinia virus, and retrovirus vectors. Retroviral vectors include murine leukemia virus (MLV) and human immunodeficiency virus (HIV)-based vectors. Alphavirus vectors include semliki forest virus (SFV) and sindbis virus (SIN). In certain embodiments, the viral vectors provided herein are recombinant viral vectors. In certain embodiments, the viral vectors provided herein are altered such that they are replication-deficient in humans. In certain embodiments, the viral vectors are hybrid vectors, e.g., an AAV vector placed into a “helpless” adenoviral vector. In certain embodiments, provided herein are viral vectors comprising a viral capsid from a first virus and viral envelope proteins from a second virus. In specific embodiments, the second virus is vesicular stomatitus virus (VSV). In more specific embodiments, the envelope protein is VSV-G protein.
In certain embodiments, the viral vectors provided herein are HIV based viral vectors. In certain embodiments, HIV-based vectors provided herein comprise at least two polynucleotides, wherein the gag and pol genes are from an HIV genome and the env gene is from another virus.
In certain embodiments, the viral vectors provided herein are herpes simplex virus-based viral vectors. In certain embodiments, herpes simplex virus-based vectors provided herein are modified such that they do not comprise one or more immediately early (IE) genes, rendering them non-cytotoxic.
In certain embodiments, the viral vectors provided herein are MLV based viral vectors. In certain embodiments, MLV-based vectors provided herein comprise up to 8 kb of heterologous DNA in place of the viral genes.
In certain embodiments, the viral vectors provided herein are lentivirus-based viral vectors. In certain embodiments, lentiviral vectors provided herein are derived from human lentiviruses. In certain embodiments, lentiviral vectors provided herein are derived from non-human lentiviruses. In certain embodiments, lentiviral vectors provided herein are packaged into a lentiviral capsid. In certain embodiments, lentiviral vectors provided herein comprise one or more of the following elements: long terminal repeats, a primer binding site, a polypurine tract, att sites, and an encapsidation site.
In certain embodiments, the viral vectors provided herein are alphavirus-based viral vectors. In certain embodiments, alphavirus vectors provided herein are recombinant, replication-defective alphaviruses. In certain embodiments, alphavirus replicons in the alphavirus vectors provided herein are targeted to specific cell types by displaying a functional heterologous ligand on their virion surface.
In certain embodiments, the viral vectors provided herein are AAV based viral vectors. In certain embodiments, the AAV-based vectors provided herein do not encode the AAV rep gene (required for replication) and/or the AAV cap gene (required for synthesis of the capsid proteins) (the rep and cap proteins may be provided by the packaging cells in trans). Multiple AAV serotypes have been identified. In certain embodiments, AAV-based vectors provided herein comprise components from one or more serotypes of AAV. In preferred embodiments, AAV-based vectors provided herein comprise components from one or more serotypes of AAV with tropism to CNS, liver and/or muscle. In certain embodiments, AAV based vectors provided herein comprise capsid components from one or more of AAV serotype 1 (AAV1), serotype 2 (AAV2), serotype 3 (AAV3), serotype 3B (AAV3B), serotype 4 (AAV4), serotype 5 (AAV5), serotype 6 (AAV6), serotype 7 (AAV7), serotype 8 (AAV8), serotype rh8 (AAVrh8), serotype 9 (AAV9), serotype 9e (AAV9e), serotype rh10 (AAVrh10), serotype rh20 (AAVrh20), serotype rh39 (AAVrh39), serotype rh34 (AAVrh34), serotype hu.37 (AAVhu.37), serotype hu.60 (AAVrh73), serotype rh21 (AAVrh21), serotype rh15 (AAVrh15), serotype rh24 (AAVrh24), serotype hu5 (AAVhu.5), serotype hu.10 (AAVhu.10), serotype rh73 (AAVrh73), or serotype rh74 (AAVrh74), or PHP.eB (AAV.PHP.eB). In certain embodiments, AAV based vectors provided herein are or comprise components from one or more of AAV serotype 1 (AAV1), serotype 2 (AAV2), serotype 3 (AAV3), serotype 3B (AAV3B), serotype 4 (AAV4), serotype 5 (AAV5), serotype 6 (AAV6), serotype 7 (AAV7), serotype 8 (AAV8), serotype rh8 (AAVrh8), serotype 9 (AAV9), serotype 9e (AAV9e), serotype rh10 (AAVrh10), serotype rh20 (AAVrh20), serotype rh39 (AAVrh39), serotype rh34 (AAVrh34), serotype hu.37 (AAVhu.37), serotype hu.60 (AAVhu.60), serotype rh21 (AAVrh21), serotype rh15 (AAVrh15), serotype rh24 (AAVrh24), serotype hu5 (AAVhu.5), serotype hu.10 (AAVhu.10), serotype rh73 (AAVrh73), or serotype rh74 (AAVrh74), or PHP.eB (AAV.PHP.eB). In certain embodiments, the encoded AAV capsid has the sequence of SEQ ID NO:139 with 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 or 30 amino acid substitutions and retaining the biological function of the AAV9 capsid.
Provided in particular embodiments are AAV9 vectors comprising a viral genome comprising an expression cassette for expression of the transgene, under the control of regulatory elements, and flanked by ITRs and an engineered viral capsid as described herein or is at least 95%, 96%, 97%, 98%, 99% or 99.9% identical to the amino acid sequence of the AAV9 capsid protein, while retaining the biological function of the engineered AAV9 capsid. In certain embodiments, the encoded AAV9 capsid has the sequence of wild type AAV9, with the peptide insertion as described herein, with, in addition, 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, or 30 amino acid substitutions with respect to the wild type AAV sequence and retains biological function of the AAV9 capsid. Also provided are engineered AAV vectors other than AAV9 vectors, such as engineered AAV1, AAV2 AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAVrh8, AAV9, AAVe9, AAVrh10, AAVrh20, AAVrh39, AAVrh34, AAVhu.37, AAV.hu60, AAVrh21, AAVrh15, AAVrh24, AAVhu.5, AAVhu.10, AAVrh73, AAVrh74, or AAV.PHP.eB vectors with the amino acid substitutions and/or peptide insert as described herein and 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, or 30 amino acid substitutions relative to the wild type or unengineered sequence for that AAV type and that retains its biological function.
The amino acid sequence of hu37 capsid can be found in international application PCT WO 2005/033321 (SEQ ID NO: 88 thereof) and the amino acid sequence for the rh8 capsid can be found in international application PCT WO 03/042397 (SEQ ID NO:97). The amino acid sequence for the rh64R1 sequence is found in WO2006/110689 (a R697W substitution of the Rh.64 sequence, which is SEQ ID NO: 43 of WO 2006/110689). The rh64R1 sequence is:
In some embodiments, AAV-based vectors comprise components from one or more serotypes of AAV. In some embodiments, AAV based vectors provided herein comprise capsid components from one or more of AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, AAV12, AAV13, AAV14, AAV15, AAV16, AAVS3, AAV.rh8, AAV.rh10, AAV.rh20, AAV.rh39, AAV.rh46, AAV.rh73, AAV.Rh74, AAV.RHM4-1, AAV.hu37, AAV.Anc80, AAV.Anc80L65, AAV.7m8, AAV.PHP.B, AAV.PHP.eB, AAV2.5, AAV2tYF, AAV3B, AAV.LK03, AAV.HSC1, AAV.HSC2, AAV.HSC3, AAV.HSC4, AAV.HSC5, AAV.HSC6, AAV.HSC7, AAV.HSC8, AAV.HSC9, AAV.HSC10, AAV.HSC11, AAV.HSC12, AAV.HSC13, AAV.HSC14, AAV.HSC15, or AAV.HSC16 or other rAAV particles, or combinations of two or more thereof. In some embodiments, AAV based vectors provided herein comprise components from one or more of AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, AAV12, AAV13, AAV14, AAV15, AAV16, AAVS3, AAV.rh8, AAV.rh10, AAV.rh20, AAV.rh39, AAV.rh46, AAV.rh73, AAV.Rh74, AAV.RHM4-1, AAV.hu37, AAV.Anc80, AAV.Anc80L65, AAV.7m8, AAV.PHP.B, AAV.PHP.eB, AAV2.5, AAV2tYF, AAV3B, AAV.LK03, AAV.HSC1, AAV.HSC2, AAV.HSC3, AAV.HSC4, AAV.HSC5, AAV.HSC6, AAV.HSC7, AAV.HSC8, AAV.HSC9, AAV.HSC10, AAV.HSC11, AAV.HSC12, AAV.HSC13, AAV.HSC14, AAV.HSC15, or AAV.HSC16 or other rAAV particles, or combinations of two or more thereof serotypes. In some embodiments, rAAV particles comprise a capsid protein at least 80% or more identical, e.g., 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, etc., i.e. up to 100% identical, to e.g., VP1, VP2 and/or VP3 sequence of an AAV capsid serotype selected from AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, AAV12, AAV13, AAV14, AAV15, AAV16, AAVS3, AAV.rh8, AAV.rh10, AAV.rh20, AAV.rh39, AAV.rh46, AAV.rh73, AAV.Rh74, AAV.RHM4-1, AAV.hu37, AAV.Anc80, rAAV.Anc80L65, AAV.7m8, AAV.PHP.B, AAV.PHP.eB, AAV2.5, AAV2tYF, AAV3B, AAV.LK03, AAV.HSC1, AAV.HSC2, AAV.HSC3, AAV.HSC4, AAV.HSC5, AAV.HSC6, AAV.HSC7, AAV.HSC8, AAV.HSC9, AAV.HSC10, AAV.HSC11, AAV.HSC12, AAV.HSC13, AAV.HSC14, AAV.HSC15, or AAV.HSC16, or a derivative, modification, or pseudotype thereof.
In particular embodiments, the recombinant AAV for us in compositions and methods herein is AAVS3 (including variants thereof) (see e.g., US Patent Application No. 20200079821, which is incorporated herein by reference in its entirety). In particular embodiments, rAAV particles comprise the capsids of AAV-LK03 or AAV3B, as described in Puzzo et al., 2017, Sci. Transl. Med. 29(9): 418, which is incorporated by reference in its entirety. In particular embodiments, the AAV for use in compositions and methods herein is any AAV disclosed in U.S. Pat. No. 10,301,648, such as AAV.rh46 or AAV.rh73. In some embodiments, the recombinant AAV for use in compositions and methods herein is Anc80 or Anc80L65 (see, e.g., Zinn et al., 2015, Cell Rep. 12(6): 1056-1068, which is incorporated by reference in its entirety). In particular embodiments, the AAV for use in compositions and methods herein is any AAV disclosed in U.S. Pat. No. 9,585,971, such as AAV-PHP.B. In particular embodiments, the AAV for use in compositions and methods herein is an AAV2/Rec2 or AAV2/Rec3 vector, which has hybrid capsid sequences derived from AAV8 and serotypes cy5, rh20 or rh39 (see, e.g., Issa et al., 2013, PLoS One 8(4): e60361, which is incorporated by reference herein for these vectors). In particular embodiments, the AAV for use in compositions and methods herein is an AAV disclosed in any of the following, each of which is incorporated herein by reference in its entirety: U.S. Pat. Nos. 7,282,199; 7,906,111; 8,524,446; 8,999,678; 8,628,966; 8,927,514; 8,734,809; 9,284,357; 9,409,953; 9,169,299; 9,193,956; 9,458,517; 9,587,282; US 2015/0374803; US 2015/0126588; US 2017/0067908; US 2013/0224836; US 2016/0215024; US 2017/0051257; PCT/US2015/034799; and PCT/EP2015/053335. In some embodiments, rAAV particles have a capsid protein at least 80% or more identical, e.g., 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, etc., i.e. up to 100% identical, to the VP1, VP2 and/or VP3 sequence of an AAV capsid disclosed in any of the following patents and patent applications, each of which is incorporated herein by reference in its entirety: U.S. Pat. Nos. 7,282,199; 7,906,111; 8,524,446; 8,999,678; 8,628,966; 8,927,514; 8,734,809; 9,284,357; 9,409,953; 9,169,299; 9,193,956; 9,458,517; and 9,587,282; US patent application publication nos. 2015/0374803; 2015/0126588; 2017/0067908; 2013/0224836; 2016/0215024; 2017/0051257; and International Patent Application Nos. PCT/US2015/034799; PCT/EP2015/053335.
In some embodiments, rAAV particles comprise any AAV capsid disclosed in U.S. Pat. No. 9,840,719 and WO 2015/013313, such as AAV.Rh74 and RHM4-1, each of which is incorporated herein by reference in its entirety. In some embodiments, rAAV particles comprise any AAV capsid disclosed in WO 2014/172669, such as AAV rh.74, which is incorporated herein by reference in its entirety. In some embodiments, rAAV particles comprise the capsid of AAV2/5, as described in Georgiadis et al., 2016, Gene Therapy 23: 857-862 and Georgiadis et al., 2018, Gene Therapy 25: 450, each of which is incorporated by reference in its entirety. In some embodiments, rAAV particles comprise any AAV capsid disclosed in WO 2017/070491, such as AAV2tYF, which is incorporated herein by reference in its entirety. In some embodiments, rAAV particles comprise any AAV capsid disclosed in U.S. Pat. Nos. 8,628,966; 8,927,514; 9,923,120 and WO 2016/049230, such as HSC1, HSC2, HSC3, HSC4, HSC5, HSC6, HSC7, HSC8, HSC9, HSC10, HSC11, HSC12, HSC13, HSC14, HSC15, or HSC16, each of which is incorporated by reference in its entirety.
In some embodiments, rAAV particles have a capsid protein disclosed in Intl. Appl. Publ. No. WO 2003/052051 (see, e.g., SEQ ID NO: 2 of '051 publication), WO 2005/033321 (see, e.g., SEQ ID NOs: 123 and 88 of '321 publication), WO 03/042397 (see, e.g., SEQ ID NOs: 2, 81, 85, and 97 of '397 publication), WO 2006/068888 (see, e.g., SEQ ID NOs: 1 and 3-6 of '888 publication), WO 2006/110689, (see, e.g., SEQ ID NOs: 5-38 of '689 publication) WO2009/104964 (see, e.g., SEQ ID NOs: 1-5, 7, 9, 20, 22, 24 and 31 of '964 publication), WO 2010/127097 (see, e.g., SEQ ID NOs: 5-38 of '097 publication), and WO 2015/191508 (see, e.g., SEQ ID NOs: 80-294 of '508 publication), and U.S. Appl. Publ. No. 20150023924 (see, e.g., SEQ ID NOs: 1, 5-10 of '924 publication), the contents of each of which is herein incorporated by reference in its entirety. In some embodiments, rAAV particles have a capsid protein at least 80% or more identical, e.g., 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, etc., i.e. up to 100% identical, to the VP1, VP2 and/or VP3 sequence of an AAV capsid disclosed in Intl. Appl. Publ. No. WO 2003/052051 (see, e.g., SEQ ID NO: 2 of '051 publication), WO 2005/033321 (see, e.g., SEQ ID NOs: 123 and 88 of '321 publication), WO 03/042397 (see, e.g., SEQ ID NOs: 2, 81, 85, and 97 of '397 publication), WO 2006/068888 (see, e.g., SEQ ID NOs: 1 and 3-6 of '888 publication), WO 2006/110689 (see, e.g., SEQ ID NOs: 5-38 of '689 publication) WO2009/104964 (see, e.g., SEQ ID NOs: 1-5, 7, 9, 20, 22, 24 and 31 of 964 publication), WO 2010/127097 (see, e.g., SEQ ID NOs: 5-38 of '097 publication), and WO 2015/191508 (see, e.g., SEQ ID NOs: 80-294 of '508 publication), and U.S. Appl. Publ. No. 20150023924 (see, e.g., SEQ ID NOs: 1, 5-10 of '924 publication).
In additional embodiments, rAAV particles comprise a pseudotyped AAV capsid. In some embodiments, the pseudotyped AAV capsids are rAAV2/8 or rAAV2/9 pseudotyped AAV capsids. Methods for producing and using pseudotyped rAAV particles are known in the art (see, e.g., Duan et al., J. Virol., 75:7662-7671 (2001); Halbert et al., J. Virol., 74:1524-1532 (2000); Zolotukhin et al., Methods 28:158-167 (2002); and Auricchio et al., Hum. Molec. Genet. 10:3075-3081, (2001).
AAV8-based, AAV9-based, and AAVrh10-based viral vectors are used in certain of the methods described herein. Nucleotide sequences of AAV based viral vectors and methods of making recombinant AAV and AAV capsids are taught, for example, in U.S. Pat. No. 7,282,199 B2, U.S. Pat. No. 7,790,449 B2, U.S. Pat. No. 8,318,480 B2, U.S. Pat. No. 8,962,332 B2 and International Patent Application No. PCT/EP2014/076466, each of which is incorporated herein by reference in its entirety. In one aspect, provided herein are AAV (e.g., AAV8, AAV9 or AAVrh10)-based viral vectors encoding a transgene (e.g., an HuPTM Fab). The amino acid sequences of AAV capsids, including AAV8, AAV9 and AAVrh10 are provided in
In certain embodiments, a single-stranded AAV (ssAAV) may be used supra. In certain embodiments, a self-complementary vector, e.g., scAAV, may be used (see, e.g., Wu, 2007, Human Gene Therapy, 18(2):171-82, McCarty et al, 2001, Gene Therapy, Vol 8, Number 16, Pages 1248-1254; and U.S. Pat. Nos. 6,596,535; 7,125,717; and 7,456,683, each of which is incorporated herein by reference in its entirety).
In certain embodiments, the viral vectors used in the methods described herein are adenovirus based viral vectors. A recombinant adenovirus vector may be used to transfer in the transgene encoding the HuPTMmAb or HuGlyFab or antigen-binding fragment. The recombinant adenovirus can be a first-generation vector, with an E1 deletion, with or without an E3 deletion, and with the expression cassette inserted into either deleted region. The recombinant adenovirus can be a second-generation vector, which contains full or partial deletions of the E2 and E4 regions. A helper-dependent adenovirus retains only the adenovirus inverted terminal repeats and the packaging signal (phi). The transgene is inserted between the packaging signal and the 3′ITR, with or without stuffer sequences to keep the genome close to wild-type size of approximately 36 kb. An exemplary protocol for production of adenoviral vectors may be found in Alba et al., 2005, “Gutless adenovirus: last generation adenovirus for gene therapy,” Gene Therapy 12:S18-S27, which is incorporated by reference herein in its entirety.
In certain embodiments, the viral vectors used in the methods described herein are lentivirus based viral vectors. A recombinant lentivirus vector may be used to transfer in the transgene encoding the HuPTM mAb antigen binding fragment. Four plasmids are used to make the construct: Gag/pol sequence containing plasmid, Rev sequence containing plasmids, Envelope protein containing plasmid (e.g., VSV-G), and Cis plasmid with the packaging elements and the anti-CGRP or anti-CGRPR antigen-binding fragment gene.
For lentiviral vector production, the four plasmids are co-transfected into cells (e.g., HEK293 based cells), whereby polyethylenimine or calcium phosphate can be used as transfection agents, among others. The lentivirus is then harvested in the supernatant (lentiviruses need to bud from the cells to be active, so no cell harvest needs/should be done). The supernatant is filtered (0.45 μm) and then magnesium chloride and benzonase added. Further downstream processes can vary widely, with using TFF and column chromatography being the most GMP compatible ones. Others use ultracentrifugation with/without column chromatography. Exemplary protocols for production of lentiviral vectors may be found in Lesch et al., 2011, “Production and purification of lentiviral vector generated in 293T suspension cells with baculoviral vectors,” Gene Therapy 18:531-538, and Ausubel et al., 2012, “Production of CGMP-Grade Lentiviral Vectors,” Bioprocess Int. 10(2):32-43, both of which are incorporated by reference herein in their entireties.
In a specific embodiment, a vector for use in the methods described herein is one that encodes an HuPTM mAb, such that, upon introduction of the vector into a relevant cell, a glycosylated and/or tyrosine sulfated variant of the HuPTM mAb is expressed by the cell.
5.1.3 Promoters and Modifiers of Gene Expression
In certain embodiments, the vectors provided herein comprise components that modulate gene delivery or gene expression (e.g., “expression control elements”). In certain embodiments, the vectors provided herein comprise components that modulate gene expression. In certain embodiments, the vectors provided herein comprise components that influence binding or targeting to cells. In certain embodiments, the vectors provided herein comprise components that influence the localization of the polynucleotide (e.g., the transgene) within the cell after uptake. In certain embodiments, the vectors provided herein comprise components that can be used as detectable or selectable markers, e.g., to detect or select for cells that have taken up the polynucleotide.
In certain embodiments, the viral vectors provided herein comprise one or more promoters that control expression of the transgene. These promoters (and other regulatory elements that control transcription, such as enhancers) may be constitutive (promote ubiquitous expression) or may specifically or selectively express in the liver (including promoting expression in the liver only or expressing in the liver at least at 1 to 100 fold greater levels than in a non-liver tissue). In certain embodiments, the promoter is a constitutive promoter.
In certain embodiments, the promoter is a CB7 (also referred to as a CAG promoter) (see Dinculescu et al., 2005, Hum Gene Ther 16: 649-663, incorporated by reference herein in its entirety). In some embodiments, the CAG (SEQ ID NO: 25) includes other expression control elements that enhance expression of the transgene driven by the vector. In certain embodiments, the other expression control elements include chicken β-actin intron and/or rabbit β-globin polyA signal. In certain embodiments, the promoter comprises a TATA box. In certain embodiments, the promoter comprises one or more elements. In certain embodiments, the one or more promoter elements may be inverted or moved relative to one another. In certain embodiments, the elements of the promoter are positioned to function cooperatively. In certain embodiments, the elements of the promoter are positioned to function independently. In certain embodiments, the viral vectors provided herein comprise one or more promoters selected from the group consisting of the human CMV immediate early gene promoter, the SV40 early promoter, the Rous sarcoma virus (RS) long terminal repeat, and rat insulin promoter. In certain embodiments, the vectors provided herein comprise one or more long terminal repeat (LTR) promoters selected from the group consisting of AAV, MLV, MMTV, SV40, RSV, HIV-1, and HIV-2 LTRs.
In certain embodiments, the promoter is the smooth muscle cell-specific promoter, particularly the sm22a promoter (SEQ ID NOS:184, 185-190) (see Li, L., et al, J Cell Biol 132 (5), 849-859 (1996) and Li, L., et al, J Cell Biol 132 (5), 849-859 (1996); incorporated by reference herein in its entirety). In other embodiments, the promoter is a CNS-specific promoter (see Table 1; SEQ ID NOs:191-195).
In certain embodiments, the vectors provided herein comprise one or more tissue specific promoters (e.g., a liver-specific promoter or a dual liver-muscle specific promoter). In particular embodiments, the viral vectors provided herein comprises a liver cell specific promoter, such as, a TBG (Thyroxine-binding Globulin) promoter (SEQ ID NO:183), an APOA2 promoter, a SERPINA1 (hAAT) promoter, or an ApoE.hAAT promoter (SEQ ID NO:166). In certain embodiments, the viral vector provided herein comprises a muscle specific promoter, such as a human desmin promoter (Jonuschies et al., 2014, Curr. Gene Ther. 14:276-288), a CK8 promoter (SEQ ID NO:182; Himeda et al., 2011 Muscle Gene Therapy: Methods and Protocols, Methods in Molecular Biology, Dongsheng Duan (ed.), 709:3-19), or a Pitx3 promoter (Coulon et al., 2007, JBC 282:33192). In other embodiments, the viral vector comprises a VMD2 promoter.
Provided are nucleic acid regulatory elements that are chimeric with respect to arrangements of elements in tandem in the expression cassette. Regulatory elements, in general, have multiple functions as recognition sites for transcription initiation or regulation, coordination with cell-specific machinery to drive expression upon signaling, and to enhance expression of the downstream gene.
Also provided are arrangements of combinations of nucleic acid regulatory elements that promote transgene expression in liver tissue, or liver and muscle (skeletal and/or cardiac) tissue. In particular, certain elements are arranged with two or more copies of the individual enhancer and promoter elements arranged in tandem and operably linked to a transgene to promote expression, particularly tissue specific expression. Exemplary nucleotide sequences of the individual promoter and enhancer elements are provided in Table 1. Also provided in Table 1 are exemplary composite nucleic acid regulatory elements comprising the individual tandem promoter and enhancer elements. In certain embodiments the downstream promoter is an hAAT promoter (in certain embodiments the hAAT promoter is an hAAT(ΔATG) promoter) and the other promoter is another hAAT promoter or is a TBG promoter).
These combinations of promoter and enhancer sequences provided herein improve transgene expression while maintaining tissue specificity. Transgene expression from tandem promoters (i.e. two promoter sequences driving expression of the same transgene) is improved by depleting the 3′ promoter sequence of potential ‘ATG’ initiation sites. This approach was employed to improve transgene expression from tandem tissue-specific promoter cassettes (such as those targeting the liver) as well as promoter cassettes to achieve dual expression in two separate tissue populations (such as liver and skeletal muscle, and in certain embodiments cardiac muscle, and liver and bone). Ultimately, these designs aim to improve the therapeutic efficacy of gene transfer by providing more robust levels of transgene expression, improved stability/persistence, and induction of immune tolerance to the transgene product. In certain aspects the hAAT promoter with the start codon deleted (ΔATG) is used in an expression cassette provided herein.
Accordingly, with respect to liver and muscle specific expression, provided are nucleic acid regulatory elements that comprise or consist of promoters and/or other nucleic acid elements, such as enhancers, that promote liver expression, such as ApoE enhancers, Mic/BiKE elements or hAAT promoters. These may be present as single copies or with two or more copies in tandem. The nucleic acid regulatory element may also comprise, in addition to the one or more elements that promote liver specific expression, one or more elements that promote muscle specific expression (including skeletal and/or cardiac muscle), for example, one or more copies, for example two copies, of the MckE element, which may be arranged as two or more copies in tandem or an MckE and MhcE elements arranged in tandem. In certain embodiments, a promoter element is deleted for the initiation codon to prevent translation initiation at that site, and preferably, the element with the modified start codon is the promoter that is the element at the 3′ end or the downstream end of the nucleic acid regulatory element, for example, closest within the nucleic acid sequence of the expression cassette to the transgene. In certain embodiments, the composite nucleic acid regulatory element comprises an hAAT promoter, in embodiments an hAAT which is start-codon modified (ΔATG) as the downstream promoter, and a second promoter in tandem with the hAAT promoter, which is an hAAT promoter, a CK8 promoter, an Spc5.12 promoter or an minSpc5.12 promoter. Nucleotide sequences are provided in Table 1.
In other embodiments, the composite promoter comprises a transcriptionally active portion of a muscle enhancer, such as a cis regulatory element or transcription factor binding site. As such, the muscle enhancer is active in muscle cells. In some embodiments, the muscle enhancer is active in skeletal muscle cells, and not active in cardiac cells. In other embodiment the muscle enhancer is upstream of a composite nucleic acid regulatory element which comprises a muscle promoter and an hAAT promoter which is start-codon modified (hAATΔATG) and downstream of the muscle promoter. In some embodiment the muscle enhancer is Mus022. In still other embodiments, an ApoE enhancer or a portion thereof may be placed upstream of the muscle enhancer or downstream of the muscle enhancer. In some embodiments, the composite nucleic acid regulatory element comprises LMTP24 of Table 1.
In certain embodiments, the nucleotide sequence encoding the CGRP or anti-CGRPR antibody heavy and light chains is operably linked to a composite nucleic acid regulatory element comprising a) two copies of Mic/BiKE arranged in tandem or two copies of ApoE arranged in tandem or two copies of Mic/BiKE arranged in tandem with one copy of ApoE, b) one promoter or, in tandem promoter embodiments, two promoters arranged in tandem comprising at least one copy of hAAT which is start-codon modified (ΔATG) (where in certain embodiments the hAAT promoter is the downstream or 3′ promoter). In some embodiments, the composite nucleic acid regulatory element comprises LSPX1, LSPX2, LTP1, LTP2, or LTP3 of Table 1.
In embodiments, the promoter is a LMTP24 (SEQ ID NO: 263), which is a tandem liver/muscle specific enhancer promoter which, in embodiments, has lower expression in cardiac muscle cells. The LMTP24 promoter is comprised of (i) synthetic ApoE enhancer region (SEQ ID NO: 264). (ii) a muscle enhancer region (for example, Mus022, SEQ ID NO: 265)), (iii) a CK promoter (SEQ ID NO: 266), and (IV) a hAAT promoter (ΔATG) (SEQ ID NO: 172).
In certain embodiments, the anti-CGRP or CGRPR therapeutic antibody coding sequence is operably linked to composite nucleic acid regulatory elements for enhancing gene expression in the liver LSPX1 (SEQ ID NO:154, LSPX2 (SEQ ID NO:155), LTP1 (SEQ ID NO:156), LTP2 (SEQ ID NO:157), or LTP3 (SEQ ID NO:158), liver and muscle expression, LMTP6 (SEQ ID NO:159), LMTP13 (SEQ ID NO:160), LMTP14 (SEQ ID NO:161), LMTP15 (SEQ ID NO:162), LMTP18 (SEQ ID NO:163), LMTP19 (SEQ ID NO:164), LMTP20 (SEQ ID NO:165), or LMTP24 (SEQ ID NO: 263) the sequences of which are provided in Table 1 below. Also included are composite regulatory elements that enhance gene expression in the liver, and in certain embodiments, also muscle or bone, which have 99%, 95%, 90%, 85% or 80% sequence identity with one of nucleic acid sequences LSPX1 (SEQ ID NO:154), LSPX2(SEQ ID NO:155), LTP1 (SEQ ID NO:156), LTP2(SEQ ID NO:157), or LTP3 (SEQ ID NO:15869), LMTP6 (SEQ ID NO:159), LMTP13 (SEQ ID NO:160), LMTP14 (SEQ ID NO:161), LMTP15 (SEQ ID NO:162), LMTP18 (SEQ ID NO:163), LMTP19 (SEQ ID NO:164), LMTP20 (SEQ ID NO:165), or LMTP24 (SEQ ID NO: 263).
The tandem and composite promoters described herein result in preferred transcription start sites within the promoter region. Thus, in certain embodiments, the constructs described herein have a tandem or composite nucleic acid regulatory sequence that comprises an hAAT promoter (particularly a modified start codon hAAT promoter) and has a transcription start site of TCTCC (corresponding to nt 1541-1545 of LMTP6 (SEQ ID NO:159), which overlaps with the active TTS found in hAAT (nt 355-359 of SEQ ID NO:171) or GGTACAATGACTCCTTTCG (SEQ ID NO:181), which corresponds to nucleotides 139-157 of SEQ ID NO:171, or GGTACAGTGACTCCTTTCG (SEQ ID NO:180), which corresponds to nucleotides 139-157 of SEQ ID NO:172. In other embodiments, the constructs described herein have a tandem or composite regulatory sequence that comprises a CK8 promoter and has a transcription start site at TCATTCTACC (SEQ ID NO:249), which corresponds to nucleotides 377-386 of SEQ ID NO:182, particularly starting at the nucleotide corresponding to nucleotide 377 of SEQ ID NO:182 or corresponding to nucleotide 1133 of SEQ ID NO:159.
In certain embodiments, the promoter is an inducible promoter. In certain embodiments the promoter is a hypoxia-inducible promoter. In certain embodiments, the promoter comprises a hypoxia-inducible factor (HIF) binding site. In certain embodiments, the promoter comprises a HIF-1α binding site. In certain embodiments, the promoter comprises a HIF-2a binding site. In certain embodiments, the HIF binding site comprises an RCGTG (SEQ ID NO:153) motif. For details regarding the location and sequence of HIF binding sites, see, e.g., Schödel, et al., Blood, 2011, 117(23):e207-e217, which is incorporated by reference herein in its entirety. In certain embodiments, the promoter comprises a binding site for a hypoxia induced transcription factor other than a HIF transcription factor. In certain embodiments, the viral vectors provided herein comprise one or more IRES sites that is preferentially translated in hypoxia. For teachings regarding hypoxia-inducible gene expression and the factors involved therein, see, e.g., Kenneth and Rocha, Biochem J., 2008, 414:19-29, which is incorporated by reference herein in its entirety. In specific embodiments, the hypoxia-inducible promoter is the human N-WASP promoter, see, e.g., Salvi, 2017, Biochemistry and Biophysics Reports 9:13-21 (incorporated by reference for the teaching of the N-WASP promoter) or is the hypoxia-induced promoter of human Epo, see, e.g., Tsuchiya et al., 1993, J. Biochem. 113:395-400 (incorporated by reference for the disclosure of the Epo hypoxia-inducible promoter). In other embodiments, the promoter is a drug inducible promoter, for example, a promoter that is induced by administration of rapamycin or analogs thereof. See, e.g., the disclosure of rapamycin inducible promoters in PCT publications WO94/18317, WO 96/20951, WO 96/41865, WO 99/10508, WO 99/10510, WO 99/36553, and WO 99/41258, and U.S. Pat. No. 7,067,526, which are hereby incorporated by reference in their entireties for the disclosure of drug inducible promoters.
Provided herein are constructs containing certain ubiquitous and tissue-specific promoters. Such promoters include synthetic and tandem promoters. Examples and nucleotide sequences of promoters are provided in Table 1 below. Table 1 also includes the nucleotide sequences of other regulatory elements useful for the expression cassettes provided herein
In certain embodiments, the viral vectors provided herein comprise one or more regulatory elements other than a promoter. In certain embodiments, the viral vectors provided herein comprise an enhancer. In certain embodiments, the viral vectors provided herein comprise a repressor. In certain embodiments, the viral vectors provided herein comprise an intron (e.g. VH4 intron (SEQ ID NO: 54) SV40 Intron (SEQ ID NO: 55) or a chimeric intron (β-globin/Ig Intron) (SEQ ID NO: 53).
In certain embodiments, the viral vectors provided herein comprise a polyadenylation sequence downstream of the coding region of the transgene. Any polyA site that signals termination of transcription and directs the synthesis of a polyA tail is suitable for use in AAV vectors of the present disclosure. Exemplary polyA signals are derived from, but not limited to, the following: the SV40 late gene, the rabbit β-globin gene (SEQ ID NO: 57), the bovine growth hormone (BPH) gene, the human growth hormone (hGH) gene, the synthetic polyA (SPA) site, and the bovine growth hormone (bGH) gene. See, e.g., Powell and Rivera-Soto, 2015, Discov. Med., 19(102):49-57.
5.1.4 Signal Peptides
In certain embodiments, the vectors provided herein comprise components that modulate protein delivery. In certain embodiments, the viral vectors provided herein comprise one or more signal peptides. Signal peptides (also referred to as “signal sequences”) may also be referred to herein as “leader sequences” or “leader peptides”. In certain embodiments, the signal peptides allow for the transgene product to achieve the proper packaging (e.g., glycosylation) in the cell. In certain embodiments, the signal peptides allow for the transgene product to achieve the proper localization in the cell. In certain embodiments, the signal peptides allow for the transgene product to achieve secretion from the cell.
There are two general approaches to select a signal sequence for protein production in a gene therapy context or in cell culture. One approach is to use a signal peptide from proteins homologous to the protein being expressed. For example, a human antibody signal peptide may be used to express IgGs in CHO or other cells. Another approach is to identify signal peptides optimized for the particular host cells used for expression. Signal peptides may be interchanged between different proteins or even between proteins of different organisms, but usually the signal sequences of the most abundant secreted proteins of that cell type are used for protein expression. For example, the signal peptide of human albumin, the most abundant protein in plasma, was found to substantially increase protein production yield in CHO cells. However, certain signal peptides may retain function and exert activity after being cleaved from the expressed protein as “post-targeting functions”. Thus, in specific embodiments, the signal peptide is selected from signal peptides of the most abundant proteins secreted by the cells used for expression to avoid the post-targeting functions. In a certain embodiment, the signal sequence is fused to both the heavy and light chain sequences. An exemplary sequence is MYRMQLLLLIALSLALVTNS (SEQ ID NO: 28) which can be encoded by a nucleotide sequence of SEQ ID NO:29 (see Table 2,
5.1.5 Polycistronic Messages—IRES and 2A Linkers and scFv Constructs
Internal ribosome entry sites. A single construct can be engineered to encode both the heavy and light chains separated by a cleavable linker or IRES so that separate heavy and light chain polypeptides are expressed by the transduced cells. In certain embodiments, the viral vectors provided herein provide polycistronic (e.g., bicistronic) messages. For example, the viral construct can encode the heavy and light chains separated by an internal ribosome entry site (IRES) elements (for examples of the use of IRES elements to create bicistronic vectors see, e.g., Gurtu et al., 1996, Biochem. Biophys. Res. Comm. 229(1):295-8, which is herein incorporated by reference in its entirety). IRES elements bypass the ribosome scanning model and begin translation at internal sites. The use of IRES in AAV is described, for example, in Furling et al., 2001, Gene Ther 8(11): 854-73, which is herein incorporated by reference in its entirety. In certain embodiments, the bicistronic message is contained within a viral vector with a restraint on the size of the polynucleotide(s) therein. In certain embodiments, the bicistronic message is contained within an AAV virus-based vector (e.g., an AAV8-based, AAV9-based or AAVrh10-based vector).
Furin-2A linkers. In other embodiments, the viral vectors provided herein encode the heavy and light chains separated by a cleavable linker such as the self-cleaving 2A and 2A-like peptides, with or without upstream furin cleavage sites, e.g. Furin/2A linkers, such as furin/F2A (F/F2A) or furin/T2A (F/T2A) linkers (Fang et al., 2005, Nature Biotechnology 23: 584-590, Fang, 2007, Mol Ther 15: 1153-9, and Chang, J. et al, MAbs 2015, 7(2):403-412, each of which is incorporated by reference herein in its entirety). For example, a furin/2A linker may be incorporated into an expression cassette to separate the heavy and light chain coding sequences, resulting in a construct with the structure:
Signal sequence-Heavy chain-Furin site-2A site-Signal Sequence-Light chain-PolyA. A 2A site or 2A-like site, such as an F2A site comprising the amino acid sequence RKRR(GSG)APVKQTLNFDLLKLAGDVESNPGP (SEQ ID NOS: 87 or 88) or a T2A site comprising the amino acid sequence RKRR(GSG)EGRGSLLTCGDVEENPGP (SEQ ID NOS:85 or 86), is self-processing, resulting in “cleavage” between the final G and P amino acid residues. Several linkers, with or without an upstream flexible Gly-Ser-Gly (GSG) linker sequence (SEQ ID NO:72), that could be used include but are not limited to:
(see also, e.g., Szymczak, et al., 2004, Nature Biotechnol 22(5):589-594, and Donnelly, et al., 2001, J Gen Virol, 82:1013-1025, each of which is incorporated herein by reference). Exemplary amino acid and nucleotide sequences encoding different parts of the flexible linker are described in Table 5.
In certain embodiments an additional proteolytic cleavage site, e.g. a furin cleavage site, is incorporated into the expression construct adjacent to the self-processing cleavage site (e.g. 2A or 2A like sequence), thereby providing a means to remove additional amino acids that remain following cleavage by the self processing cleavage sequence. Without being bound to any one theory, a peptide bond is skipped when the ribosome encounters the 2A sequence in the open reading frame, resulting in the termination of translation, or continued translation of the downstream sequence (the light chain). This self-processing sequence results in a string of additional amino acids at the end of the C-terminus of the heavy chain. However, such additional amino acids can then be cleaved by host cell Furin at the furin cleavage site(s), e.g. located immediately prior to the 2A site and after the heavy chain sequence, and further cleaved by carboxypeptidases. The resultant heavy chain may have one, two, three, or more additional amino acids included at the C-terminus, or it may not have such additional amino acids, depending on the sequence of the Furin linker used and the carboxypeptidase that cleaves the linker in vivo (See, e.g., Fang et al., 17 Apr. 2005, Nature Biotechnol. Advance Online Publication; Fang et al., 2007, Molecular Therapy 15(6):1153-1159; Luke, 2012, Innovations in Biotechnology, Ch. 8, 161-186). Furin linkers that may be used comprise a series of four basic amino acids, for example, RKRR (SEQ ID NO:73), RRRR (SEQ ID NO:74), RRKR (SEQ ID NO:75), or RKKR (SEQ ID NO:76). Once this linker is cleaved by a carboxypeptidase, additional amino acids may remain, such that an additional zero, one, two, three or four amino acids may remain on the C-terminus of the heavy chain, for example, R, RR, RK, RKR, RRR, RRK, RKK, RKRR (SEQ ID NO:73), RRRR (SEQ ID NO:74), RRKR (SEQ ID NO:75), or RKKR (SEQ ID NO:76). In certain embodiments, once the linker is cleaved by a carboxypeptidase, no additional amino acids remain. In certain embodiments, 0.5% to 1%, 1% to 2%, 5%, 10%, 15%, or 20% of the antibody, e.g., antigen-binding fragment, population produced by the constructs for use in the methods described herein has one, two, three, or four amino acids remaining on the C-terminus of the heavy chain after cleavage. In certain embodiments, the furin linker has the sequence R-X-K/R-R (SEQ ID NO:177/178), such that the additional amino acids on the C-terminus of the heavy chain are R, RX, RXK, RXR, RXKR (SEQ ID NO:177), or RXRR (SEQ ID NO:178), where X is any amino acid, for example, alanine (A). In certain embodiments, no additional amino acids may remain on the C-terminus of the heavy chain.
Flexible peptide linker. In some embodiments, a single construct can be engineered to encode both the heavy and light chains (e.g. the heavy and light chain variable domains) separated by a flexible peptide linker such as those encoding a scFv. A flexible peptide linker can be composed of flexible residues like glycine and serine so that the adjacent heavy chain and light chain domains are free to move relative to one another. The construct may be arranged such that the heavy chain variable domain is at the N-terminus of the scFv, followed by the linker and then the light chain variable domain. Alternatively, the construct may be arranged such that the light chain variable domain is at the N-terminus of the scFv, followed by the linker and then the heavy chain variable domain. That is, the components may be arranged as NH2-VL-linker-VH—COOH or NH2-VH-linker-VL-COOH.
In certain embodiments, an expression cassette described herein is contained within a viral vector with a restraint on the size of the polynucleotide(s) therein. In certain embodiments, the expression cassette is contained within an AAV virus-based vector. Due to the size restraints of certain vectors, the vector may or may not accommodate the coding sequences for the full heavy and light chains of the therapeutic antibody but may accommodate the coding sequences of the heavy and light chains of antigen binding fragments, such as the heavy and light chains of a Fab or F(ab′)2 fragment or an scFv. In particular, the AAV vectors described herein may accommodate a transgene of approximately 4.7 kilobases. Substitution of smaller expression elements would permit the expression of larger protein products, such as full-length therapeutic antibodies.
5.1.6 Untranslated Regions
In certain embodiments, the viral vectors provided herein comprise one or more untranslated regions (UTRs), e.g., 3′ and/or 5′ UTRs. In certain embodiments, the UTRs are optimized for the desired level of protein expression. In certain embodiments, the UTRs are optimized for the mRNA half-life of the transgene. In certain embodiments, the UTRs are optimized for the stability of the mRNA of the transgene. In certain embodiments, the UTRs are optimized for the secondary structure of the mRNA of the transgene.
5.1.7 Inverted Terminal Repeats
In certain embodiments, the viral vectors provided herein comprise one or more inverted terminal repeat (ITR) sequences. ITR sequences may be used for packaging the recombinant gene expression cassette into the virion of the viral vector. In certain embodiments, the ITR is from an AAV, e.g., AAV8 or AAV2 (see, e.g., Yan et al., 2005, J. Virol., 79(1):364-379; U.S. Pat. No. 7,282,199 B2, U.S. Pat. No. 7,790,449 B2, U.S. Pat. No. 8,318,480 B2, U.S. Pat. No. 8,962,332 B2 and International Patent Application No. PCT/EP2014/076466, each of which is incorporated herein by reference in its entirety). In preferred embodiments, nucleotide sequences encoding the ITRs may, for example, comprise the nucleotide sequences of SEQ ID NOS: 245 (5′-ITR) or 247 (3′-ITR). In certain embodiments, the modified ITRs used to produce self-complementary vector, e.g., scAAV, may be used (see, e.g., Wu, 2007, Human Gene Therapy, 18(2):171-82, McCarty et al, 2001, Gene Therapy, Vol 8, Number 16, Pages 1248-1254; and U.S. Pat. Nos. 6,596,535; 7,125,717; and 7,456,683, each of which is incorporated herein by reference in its entirety). In preferred embodiments, nucleotide sequences encoding the modified ITRs may, for example, comprise the nucleotide sequences of SEQ ID NOS:246 (5′-ITR) or 248 (3′-ITR).
5.1.8 Transgenes
The transgenes encode a HuPTM mAb, either as a full-length antibody or an antigen binding fragment thereof, e.g. a Fab fragment (an HuGlyFab) or a F(ab′)2, nanobody, or an scFv based upon a therapeutic antibody disclosed herein. In specific embodiments, the HuPTM mAb or antigen binding fragment, particularly the HuGlyFab, are engineered to contain additional glycosylation sites on the Fab domain (e.g., see Courtois et al., 2016, mAbs 8: 99-112 which is incorporated by reference herein in its entirety for it description of sites of hyperglycosylation on a Fab domain). In addition, for the HuPTM mAb comprising an Fc domain, the Fc domain may be engineered to alter the glycosylation site at N297 to prevent glycosylation at that site (for example, a substitution at N297 for another amino acid and/or a substitution at T297 for a residue that is not a T or S to knock out the glycosylation site). Such Fc domains are “aglycosylated”.
5.1.8.1 Constructs for Expression of Full Length HuPTM mAb
In certain embodiments, the transgenes encode a full length heavy chain (including the heavy chain variable domain, the heavy chain constant domain 1 (CH1), the hinge and Fc domain) and a full length light chain (light chain variable domain and light chain constant domain) that upon expression associate to form antigen-binding antibodies with Fc domains. The recombinant AAV constructs express the intact (i.e., full length) or substantially intact HuPTM mAb in a cell, cell culture, or in a subject. (“Substantially intact” refers to mAb having a sequence that is at least 95% identical to the full-length mAb sequence.) The nucleotide sequences encoding the heavy and light chains may be codon optimized for expression in human cells and have reduced incidence of CpG dimers in the sequence to promote expression in human cells. The transgenes may encode any full-length antibody. In preferred embodiments, the transgenes encode a full-length form of any of the therapeutic antibodies disclosed herein, for example, the Fab fragment of which depicted in
The full length mAb encoded by the transgene described herein preferably have the Fc domain of the full-length therapeutic antibody or is an Fc domain of the same type of immunoglobulin as the therapeutic antibody to be expressed. In certain embodiments, the Fc region is an IgG Fc region, but in other embodiments, the Fc region may be an IgA, IgD, IgE, or IgM. The Fc domain is preferably of the same isotype as the therapeutic antibody to be expressed, for example, if the therapeutic antibody is an IgG1 isotype, then the antibody expressed by the transgene comprises an IgG1 Fc domain. The antibody expressed from the transgene may have an IgG1, IgG2, IgG3 or IgG4 Fc domain.
The Fc region of the intact mAb has one or more effector functions that vary with the antibody isotype. The effector functions can be the same as that of the wild-type or the therapeutic antibody or can be modified therefrom to add, enhance, modify, or inhibit one or more effector functions using the Fc modifications disclosed in Section 5.1.9, infra. In certain embodiments, the HuPTM mAb transgene encodes a mAb comprising an Fc polypeptide comprising an amino acid sequence that is at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to the sequence set forth in the Fc domain polypeptides of the therapeutic antibodies described herein as set forth in Table 7 for erenumab, eptinezumab, fremanezumab, and galcanezumab or an exemplary Fc domain of an IgG1, IgG2 or IgG4 isotype as set forth in Table 7. In some embodiments, the HuPTM mAb comprises a Fc polypeptide of a sequence that is a variant of the Fc polypeptide sequence in Table 7 in that the sequence has been modified with one or more of the techniques described in Section 5.1.9, infra, to alter the Fc polypeptide's effector function.
In specific embodiments, provided are recombinant AAV constructs such as the constructs shown in
In specific embodiments for expressing an intact or substantially intact mAb in CNS, PNS, arterial smooth muscle, and/or liver cells, the constructs described herein comprise the following components: (1) AAV2 inverted terminal repeats that flank the expression cassette; (2) Control elements, which include a) an inducible promoter, preferably a hypoxia-inducible promoter, b) a chicken β-actin intron and c) a rabbit β-globin poly A signal; and (3) nucleic acid sequences coding for the heavy chain Fab of an anti-CGRP or anti-CGRPR mAb (e.g., erenumab, eptinezumab, fremanezumab, or galcanezumab); an Fc polypeptide associated with the therapeutic antibody (Table 7) or of the same isotype as the native form of the therapeutic antibody, such as an IgG isotype amino acid sequence from Table 7; and the light chain of an anti-CGRP or anti-CGRPR mAb (e.g. erenumab, eptinezumab, fremanezumab, or galcanezumab), wherein the heavy chain (Fab and Fc region) and the light chain are separated by a self-cleaving furin (F)/F2A or T2A or flexible linker, ensuring expression of equal amounts of the heavy and the light chain polypeptides. Exemplary constructs are provided in
In specific embodiments, provided are AAV vectors comprising a viral capsid that is at least 95% identical to the amino acid sequence of an AAV9 capsid (SEQ ID NO:139); and an artificial genome comprising an expression cassette flanked by AAV inverted terminal repeats (ITRs), wherein the expression cassette comprises a transgene encoding an intact or substantially intact anti-CGRP or anti-CGRPR mAb; operably linked to one or more regulatory sequences that control expression of the transgene in human liver or muscle cells.
The rAAV vectors that encode and express the full-length therapeutic antibodies may be administered to treat or prevent or ameliorate symptoms of a disease or condition amenable to treatment, prevention or amelioration of symptoms with the therapeutic antibodies. Also provided are methods of expressing HuPTM mAbs in human cells using the rAAV vectors and constructs encoding them.
5.1.8.2 Constructs for Expression of Antigen Binding Fragments
In some embodiments, the transgenes express antigen binding fragments, e.g. a Fab fragment (an HuGlyFab) or a F(ab′)2, nanobody, or an scFv based upon a therapeutic antibody disclosed herein.
Certain of these nucleotide sequences are codon optimized for expression in human cells. The transgene may encode a Fab fragment using nucleotide sequences encoding the amino acid sequences provided in Table 8, but not including the portion of the hinge region on the heavy chain that forms interchain di-sulfide bonds (e.g., the portion containing the sequence CPPCPA (SEQ ID NO:94)). Heavy chain Fab domain sequences that do not contain a CPPCP (SEQ ID NO:95) sequence of the hinge region at the C-terminus will not form intrachain disulfide bonds and, thus, will form Fab fragments with the corresponding light chain Fab domain sequences, whereas those heavy chain Fab domain sequences with a portion of the hinge region at the C-terminus containing the sequence CPPCP (SEQ ID NO:95) will form intrachain disulfide bonds and, thus, will form Fab2 fragments. For example, in some embodiments, the transgene may encode a scFv comprising a light chain variable domain and a heavy chain variable domain connected by a flexible linker in between (where the heavy chain variable domain may be either at the N-terminal end or the C-terminal end of the scFv), and optionally, may further comprise a Fc polypeptide (e.g., IgG1, IgG2, IgG3, or IgG4) on the C-terminal end of the heavy chain. Alternatively, in other embodiments, the transgene may encode F(ab′)2 fragments comprising a nucleotide sequence that encodes the light chain and the heavy chain sequence that includes at least the sequence CPPCA (SEQ ID NO:96) of the hinge region, as depicted in
In certain embodiments, the viral vectors provided herein comprise the following elements in the following order: a) a constitutive or inducible (e.g., hypoxia-inducible or rifamycin-inducible) promoter sequence or a tissue specific promoter/regulatory region, for example, one of the regulatory regions provided in Table 1, and b) a sequence encoding the transgene (e.g., a HuGlyFab). In certain embodiments, the sequence encoding the transgene comprises multiple ORFs separated by IRES elements. In certain embodiments, the ORFs encode the heavy and light chain domains of the HuGlyFab. In certain embodiments, the sequence encoding the transgene comprises multiple subunits in one ORF separated by F/F2A sequences or F/T2A sequences. In certain embodiments, the sequence comprising the transgene encodes the heavy and light chain domains of the HuGlyFab separated by an F/F2A sequence or a F/T2A sequence. In certain embodiments, the sequence comprising the transgene encodes the heavy and light chain variable domains of the HuGlyFab separated by a flexible peptide linker (as an scFv). In certain embodiments, the viral vectors provided herein comprise the following elements in the following order: a) a constitutive or an inducible promoter sequence or a tissue specific promoter, such as one of the promoters or regulatory regions in Table 1, and b) a sequence encoding the transgene (e.g., a HuGlyFab), wherein the transgene comprises a nucleotide sequence encoding a signal peptide, a light chain and a heavy chain Fab portion separated by an IRES element. In certain embodiments, the viral vectors provided herein comprise the following elements in the following order: a) a constitutive or a hypoxia-inducible promoter sequence or regulatory element listed in Table 1, and b) a sequence encoding the transgene comprising a signal peptide, a light chain and a heavy chain sequence separated by a cleavable F/F2A sequence (SEQ ID NOS:85 or 86) or a F/T2A sequence (SEQ ID NOS:87 or 88) or a flexible peptide linker.
5.1.8.1 Dual Cistron Constructs for Expression of Antigen Binding Fragments
In certain embodiments, the viral vectors provided herein comprise the following elements in the following order: a) a constitutive or a tissue specific promoter/regulatory region, for example, one of the regulatory regions provided in Table 1, and b) a sequence encoding the first transgene (e.g., a HuGlyFab), c) a second constitutive or a tissue specific promoter/regulatory region, and d) a sequence encoding the second transgene. In certain embodiments, the sequences encoding the first and second transgene comprise each multiple subunits in one ORF separated by F/F2A sequences or F/T2A sequences. In certain embodiments, the sequences comprising the first and second transgene encode each the heavy and light chain domains of a HuGlyFab separated by an F/F2A sequence or a F/T2A sequence. In certain embodiments, the sequences comprising the first and second transgene encode each the heavy and light chain variable domains of a HuGlyFab separated by a flexible peptide linker (as an scFv).
In certain embodiments, the viral vectors provided herein comprise a first and a second transgene, wherein the first transgene encodes a heavy chain and a light chain of an antigen-binding fragment of an anti-CGRP operably linked to a first regulatory sequence, and the second transgene encodes a heavy and light chain of an antigen binding fragment of an anti-CGRPR antibody, operably linked to a second regulatory sequence, wherein said first and second regulatory sequences promote expression of the transgene in human CNS, PNS, arterial smooth muscle and/or liver cells, and the first and second regulatory sequences promote expression of the first and second transgenes in different human cell types.
In certain embodiments, the viral vectors comprise the following elements in the following order: a) a first constitutive or a tissue specific promoter, b) a first sequence encoding the first transgene, c) a second constitutive or a tissue specific promoter, d) a second sequence encoding the second transgene, wherein both the first and second transgene comprise a nucleotide sequence encoding a signal peptide, a light chain and a heavy chain Fab portion. In certain embodiments, the viral vectors provided herein comprise the following elements in the following order: a) a first tissue-specific promoter, b) a first sequence encoding a first transgene, c) a second tissue specific promoter, d) a second sequence encoding the second transgene, wherein each transgene comprises a signal peptide, a light chain and a heavy chain sequence separated by a cleavable F/F2A sequence or a F/T2A sequence (SEQ ID NOS: 198 or 199) or a flexible peptide linker; and wherein the first and second promoter promote expression of the first and second transgene in different cell types.
In specific embodiments for expressing two Fabs, the constructs described herein comprise the following components: (1) AAV2 inverted terminal repeats that flank the expression cassette; (2) first group control elements, which include a) an ubiquitous (e.g. CAG promoter) or tissue-specific promoter (e.g. sm22a promoter), b) a chicken β-actin intron and c) a rabbit β-globin poly A signal; (d) a nucleic acid sequence coding for the heavy and light chain Fab of an anti-CGRP mAb (e.g., eptinezumab, fremanezumab, or galcanezumab); (4) a second group control elements, which include a) an ubiquitous (e.g. CAG promoter) or tissue-specific promoter (e.g. sm22a promoter), b) a chicken β-actin intron and c) a rabbit β-globin poly A signal; and (d) nucleic acid sequences coding for the heavy and light chain Fab of an anti-CGRPR mAb (including erenumab).
5.1.9. Fc Region Modifications
In certain embodiments, the transgenes encode full length or substantially full length heavy and light chains that associate to form a full length or intact antibody. (“Substantially intact” or “substantially full length” refers to a mAb having a heavy chain sequence that is at least 95% identical to the full-length heavy chain mAb amino acid sequence and a light chain sequence that is at least 95% identical to the full-length light chain mAb amino acid sequence). Accordingly, the transgenes comprise nucleotide sequences that encode, for example, the light and heavy chains of the Fab fragments including the hinge region of the heavy chain and C-terminal of the heavy chain of the Fab fragment, an Fc domain peptide. Table 7 provides the amino acid sequence of the Fc polypeptides for erenumab, eptinezumab, fremanezumab, and galcanezumab. Alternatively, an IgG1, IgG2, or IgG4 Fc domain, the sequences of which are provided in Table 7 may be utilized.
The term “Fc region” refers to a dimer of two “Fc polypeptides” (or “Fc domains”), each “Fc polypeptide” comprising the heavy chain constant region of an antibody excluding the first constant region immunoglobulin domain. In some embodiments, an “Fc region” includes two Fc polypeptides linked by one or more disulfide bonds, chemical linkers, or peptide linkers. “Fc polypeptide” refers to at least the last two constant region immunoglobulin domains of IgA, IgD, and IgG, or the last three constant region immunoglobulin domains of IgE and IgM and may also include part or all of the flexible hinge N-terminal to these domains. For IgG, e.g., “Fc polypeptide” comprises immunoglobulin domains Cgamma2 (Cγ2, often referred to as CH2 domain) and Cgamma3 (Cγ3, also referred to as CH3 domain) and may include the lower part of the hinge domain between Cgamma1 (Cγ1, also referred to as CH1 domain) and CH2 domain. Although the boundaries of the Fc polypeptide may vary, the human IgG heavy chain Fc polypeptide is usually defined to comprise residues starting at T223 or C226 or P230, to its carboxyl-terminus, wherein the numbering is according to the EU index as in Kabat et al. (1991, NIH Publication 91-3242, National Technical Information Services, Springfield, Va.). For IgA, e.g., Fc polypeptide comprises immunoglobulin domains Calpha2 (Cα2) and Calpha3 (Cα3) and may include the lower part of the hinge between Calpha1 (Cα1) and Cα2.
In certain embodiments, the Fc polypeptide is that of the therapeutic antibody or is the Fc polypeptide corresponding to the isotype of the therapeutic antibody). In still other embodiments, the Fc polypeptide is an IgG Fc polypeptide. The Fc polypeptide may be from the IgG1, IgG2, or IgG4 isotype (see Table 7) or may be an IgG3 Fc domain, depending, for example, upon the desired effector activity of the therapeutic antibody. In some embodiments, the engineered heavy chain constant region (CH), which includes the Fc domain, is chimeric. As such, a chimeric CH region combines CH domains derived from more than one immunoglobulin isotype and/or subtype. For example, the chimeric (or hybrid) CH region comprises part or all of an Fc region from IgG, IgA and/or IgM. In other examples, the chimeric CH region comprises part or all a CH2 domain derived from a human IgG1, human IgG2, or human IgG4 molecule, combined with part or all of a CH3 domain derived from a human IgG1, human IgG2, or human IgG4 molecule. In other embodiments, the chimeric CH region contains a chimeric hinge region.
In some embodiments, the recombinant vectors encode therapeutic antibodies comprising an engineered (mutant) Fc regions, e.g. engineered Fc regions of an IgG constant region. Modifications to an antibody constant region, Fc region or Fc fragment of an IgG antibody may alter one or more effector functions such as Fc receptor binding or neonatal Fc receptor (FcRn) binding and thus half-life, CDC activity, ADCC activity, and/or ADPC activity, compared to a corresponding antibody having a wild-type IgG constant region, or an IgG heavy chain constant region without the recited modification(s). Accordingly, in some embodiments, the antibody may be engineered to provide an antibody constant region, Fc region or Fc fragment of an IgG antibody that exhibits altered binding (as compared to a reference or wild-type constant region without the recited modification(s)) to one or more Fc receptors (e.g., FcγRI, FcγRIIA, FcγRIIB, FcγRIIIA, FcγRIIIB, FcγRIV, or FcRn receptor). In some embodiments, the antibody an antibody constant region, Fc region or Fc fragment of an IgG antibody that exhibits a one or more altered effector functions such as CDC, ADCC, or ADCP activity, compared to a corresponding antibody having a wild-type IgG constant region, or an IgG constant without the recited modification(s).
“Effector function” refers to a biochemical event that results from the interaction of an antibody Fc region with an Fc receptor or ligand. Effector functions include FcγR-mediated effector functions such as ADCC and ADCP and complement-mediated effector functions such as CDC.
An “effector cell” refers to a cell of the immune system that expresses one or more Fc receptors and mediates one or more effector functions. Effector cells include but are not limited to monocytes, macrophages, neutrophils, dendritic cells, eosinophils, mast cells, platelets, B cells, large granular lymphocytes, Langerhans' cells, natural killer (NK) cells, and T cells, and may be from any organism including but not limited to humans, mice, rats, rabbits, and monkeys.
“ADCC” or “antibody dependent cell-mediated cytotoxicity” refers to the cell-mediated reaction wherein nonspecific cytotoxic effector (immune) cells that express FcγRs recognize bound antibody on a target cell and subsequently cause lysis of the target cell.
“ADCP” or “antibody dependent cell-mediated phagocytosis” refers to the cell-mediated reaction wherein nonspecific cytotoxic effector (immune) cells that express FcγRs recognize bound antibody on a target cell and subsequently cause phagocytosis of the target cell.
“CDC” or “complement-dependent cytotoxicity” refers to the reaction wherein one or more complement protein components recognize bound antibody on a target cell and subsequently cause lysis of the target cell.
In some embodiments, the modifications of the Fc domain include, but are not limited to, the following modifications and combinations thereof, with reference to EU numbering of an IgG constant region (see
In certain embodiments, the Fc region comprises an amino acid addition, deletion, or substitution of one or more of amino acid residues 251-256, 285-290, 308-314, 385-389, and 428-436 of the IgG. In some embodiments, 251-256, 285-290, 308-314, 385-389, and 428-436 (EU numbering of Kabat; see
Enhancement of FcRn binding by an antibody having an engineered Fc leads to preferential binding of the affinity-enhanced antibody to FcRn as compared to antibody having wild-type Fc, and thus leads to a net enhanced recycling of the FcRn-affinity-enhanced antibody, which results in further increased antibody half-life. An enhanced recycling approach allows highly effective targeting and clearance of antigens, including e.g. “high titer” circulating antigens, such as C5, cytokines, or bacterial or viral antigens.
Provided in certain embodiments are modified constant region, Fc region or Fc fragment of an IgG antibody with enhanced binding to FcRn in serum as compared to a wild-type Fc region (without engineered modifications). In some instances, antibodies, e.g. IgG antibodies, are engineered to bind to FcRn at a neutral pH, e.g., at or above pH 7.4, to enhance pH-dependence of binding to FcRn as compared to a wild-type Fc region (without engineered modifications). In some instances, antibodies, e.g. IgG antibodies, are engineered to exhibit enhanced binding (e.g. increased affinity or KD) to FcRn in endosomes (e.g., at an acidic pH, e.g., at or below pH 6.0) relative to a wild-type IgG and/or reference antibody binding to FcRn at an acidic pH, as well as in comparison to binding to FcRn in serum (e.g., at a neutral pH, e.g., at or above pH 7.4). Provided are antibodies with an engineered antibody constant region, Fc region or Fc fragment of an IgG antibody that exhibits an improved serum or resident tissue half-life, compared to a corresponding antibody having a wild-type IgG constant region, or an IgG constant without the recited modification(s);
Non-limiting examples of such Fc modifications include, e.g., a modification at position 250 (e.g., E or Q); 250 and 428 (e.g., L or F); 252 (e.g., LN/Y/W or T), 254 (e.g., S or T), and 256 (e.g., S/R/Q/E/D or T); or a modification at position 428 and/or 433 (e.g., H/L/R/S/P/Q or K) and/or 434 (e.g., H/F or Y); or a modification at position 250 and/or 428; or a modification at position 307 or 308 (e.g., 308F, V308F), and 434. In one embodiment, the modification comprises a 428L (e.g., M428L) and 434S (e.g., N434S) modification; a 428L, 2591 (e.g., V2591), and 308F (e.g., V308F) modification; a 433K (e.g., H433K) and a 434 (e.g., 434Y) modification; a 252, 254, and 256 (e.g., 252Y, 254T, and 256E) modification; a 250Q and 428L modification (e.g., T250Q and M428L); and a 307 and/or 308 modification (e.g., 308F or 308P) (EU numbering; see
In some embodiments, the Fc region can be a mutant form such as hIgG1 Fc including M252 mutations, e.g. M252Y and S254T and T256E (“YTE mutation”) exhibit enhanced affinity for human FcRn (Dall'Acqua, et al., 2002, J Immunol 169:5171-5180) and subsequent crystal structure of this mutant antibody bound to hFcRn resulting in the creation of two salt bridges (Oganesyan, et al. 2014, JBC 289(11): 7812-7824). Antibodies having the YTE mutation have been administered to monkeys and humans, and have significantly improved pharmacokinetic properties (Haraya, et al., 2019, Drug Metabolism and Pharmacokinetics, 34(1):25-41).
In some embodiments, modifications to one or more amino acid residues in the Fc region may reduce half-life in systemic circulation (serum), however result in improved retainment in tissues (e.g. in the eye) by disabling FcRn binding (e.g. H435A, EU numbering of Kabat) (Ding et al., 2017, MAbs 9:269-284; and Kim, 1999, Eur J Immunol 29:2819).
In some embodiments, the Fc domain may be engineered to activate all, some, or none of the normal Fc effector functions, without affecting the Fc polypeptide's (e.g. antibody's) desired pharmacokinetic properties. Fc polypeptides having altered effector function may be desirable as they may reduce unwanted side effects, such as activation of effector cells, by the therapeutic protein.
Methods to alter or even ablate effector function may include mutation(s) or modification(s) to the hinge region amino acid residues of an antibody. For example, IgG Fc domain mutants comprising 234A, 237A, and 238S substitutions, according to the EU numbering system, exhibit decreased complement dependent lysis and/or cell mediated destruction. Deletions and/or substitutions in the lower hinge, e.g. where positions 233-236 within a hinge domain (EU numbering) are deleted or modified to glycine, have been shown in the art to significantly reduce ADCC and CDC activity.
In specific embodiments, the Fc domain is an aglycosylated Fc domain that has a substitution at residue 297 or 299 to alter the glycosylation site at 297 such that the Fc domain is not glycosylated. Such aglycosylated Fc domains may have reduced ADCC or other effector activity.
Non-limiting examples of proteins comprising mutant and/or chimeric CH regions having altered effector functions, and methods of engineering and testing mutant antibodies, are described in the art, e.g. K. L. Amour, et al., Eur. J. Immunol. 1999, 29:2613-2624; Lazar et al., Proc. Natl. Acad. Sci. USA 2006, 103:4005; US Patent Application Publication No. 20070135620A1 published Jun. 14, 2007; US Patent Application Publication No. 20080154025 A1, published Jun. 26, 2008; US Patent Application Publication No. 20100234572 A1, published Sep. 16, 2010; US Patent Application Publication No. 20120225058 A1, published Sep. 6, 2012; US Patent Application Publication No. 20150337053 A1, published Nov. 26, 2015; International Publication No. WO20/16161010A2 published Oct. 6, 2016; U.S. Pat. No. 9,359,437, issued Jun. 7,2016; and U.S. Pat. No. 10,053,517, issued Aug. 21, 2018, all of which are herein incorporated by reference.
The C-terminal lysines (-K) conserved in the heavy chain genes of all human IgG subclasses are generally absent from antibodies circulating in serum—the C-terminal lysines are cleaved off in circulation, resulting in a heterogeneous population of circulating IgGs. (van den Bremer et al., 2015, mAbs 7:672-680). In the vectored constructs for full length mAbs, the DNA encoding the C-terminal lysine (-K) or glycine-lysine (-GK) of the Fc terminus can be deleted to produce a more homogeneous antibody product in situ. (See, Hu et al., 2017 Biotechnol. Prog. 33: 786-794 which is incorporated by reference herein in its entirety).
5.1.10 Manufacture and Testing of Vectors
The viral vectors provided herein may be manufactured using host cells. The viral vectors provided herein may be manufactured using mammalian host cells, for example, A549, WEHI, 10T1/2, BHK, MDCK, COS1, COS7, BSC 1, BSC 40, BMT 10, VERO, W138, HeLa, 293, Saos, C2C12, L, HT1080, HepG2, primary fibroblast, hepatocyte, and myoblast cells. The viral vectors provided herein may be manufactured using host cells from human, monkey, mouse, rat, rabbit, or hamster.
The host cells are stably transformed with the sequences encoding the transgene and associated elements (e.g., the vector genome), and the means of producing viruses in the host cells, for example, the replication and capsid genes (e.g., the rep and cap genes of AAV). For a method of producing recombinant AAV vectors with AAV8 capsids, see Section IV of the Detailed Description of U.S. Pat. No. 7,282,199 B2, which is incorporated herein by reference in its entirety. Genome copy titers of said vectors may be determined, for example, by TAQMAN® analysis. Virions may be recovered, for example, by CsCl2 sedimentation.
Alternatively, baculovirus expression systems in insect cells may be used to produce AAV vectors. For a review, see Aponte-Ubillus et al., 2018, Appl. Microbiol. Biotechnol. 102:1045-1054 which is incorporated by reference herein in its entirety for manufacturing techniques.
In vitro assays, e.g., cell culture assays, can be used to measure transgene expression from a vector described herein, thus indicating, e.g., potency of the vector. In addition, in vitro neutralization assays can be used to measure the activity of the transgene expressed from a vector described herein. For example, Vero-E6 cells, a cell line derived from the kidney of an African green monkey, or HeLa cells engineered to stably express the ACE2 receptor (HeLa-ACE2), can be used to assess neutralization activity of transgenes expressed from a vector described herein. In addition, other characteristics of the expressed product can be determined, for example determination of the glycosylation and tyrosine sulfation patterns associated with the HuGlyFab. Glycosylation patterns and methods of determining the same are discussed in Section 5.3, while tyrosine sulfation patterns and methods of determining the same are discussed in Section 5.3. In addition, benefits resulting from glycosylation/sulfation of the cell-expressed HuGlyFab can be determined using assays known in the art, e.g., the methods described in Section 5.3.
Vector genome concentration (GC) or vector genome copies can be evaluated using digital PCR (dPCR) or ddPCR™ (BioRad Technologies, Hercules, CA, USA). In one example, liver biopsies are obtained at several timepoints. In another example, several mice are sacrificed at various timepoints post injection. Liver tissue samples are subjected to total DNA extraction and dPCR assay for vector copy numbers. Copies of vector genome (transgene) per gram of tissue may be measured in a single biopsy sample, or measured in various tissue sections at sequential timepoints will reveal spread of AAV throughout the liver. Total DNA from collected liver tissue is extracted with the DNeasy Blood & Tissue Kit and the DNA concentration measured using a Nanodrop spectrophotometer. To determine the vector copy numbers in each tissue sample, digital PCR was performed with Naica Crystal Digital PCR system (Stilla technologies). Two color multiplexing system were applied here to simultaneously measure the transgene AAV and an endogenous control gene. In brief, the transgene probe can be labelled with FAM (6-carboxyfluorescein) dye while the endogenous control probe can be labelled with VIC fluorescent dye. The copy number of delivered vector in a specific tissue section per diploid cell is calculated as: (vector copy number)/(endogenous control)×2. Vector copy in specific cell types, such as liver cells, over time may indicate sustained expression of the transgene by the tissue.
5.1.11 Compositions
Pharmaceutical compositions suitable for administration to human subjects comprise a suspension of the recombinant vector in a formulation buffer comprising a physiologically compatible aqueous buffer, a surfactant and optional excipients. Such formulation buffer can comprise one or more of a polysaccharide, a surfactant, polymer, or oil. In some embodiments, the pharmaceutical composition comprises rAAV combined with a pharmaceutically acceptable carrier for administration (e.g. intranasal, intravenous, intramuscular) to a subject. In one embodiment, the term “pharmaceutically acceptable” means approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, and more particularly in humans. The term “carrier” refers to a diluent, adjuvant (e.g., Freund's complete and incomplete adjuvant), excipient, or vehicle with which the agent is administered. Such pharmaceutical carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable, or synthetic origin, including, e.g., peanut oil, soybean oil, mineral oil, sesame oil and the like. Water is a common carrier when the pharmaceutical composition is administered intravenously. Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid carriers, particularly for injectable solutions. Suitable pharmaceutical excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like. Additional examples of pharmaceutically acceptable carriers, excipients, and stabilizers include, but are not limited to, buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid; low molecular weight polypeptides; proteins, such as serum albumin and gelatin; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, arginine or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as mannitol or sorbitol; salt-forming counterions such as sodium; and/or nonionic surfactants such as TWEEN™, polyethylene glycol (PEG), and PLURONICS™ as known in the art. The pharmaceutical composition of the present invention can also include a lubricant, a wetting agent, a sweetener, a flavoring agent, an emulsifier, a suspending agent, and a preservative, in addition to the above ingredients. These compositions can take the form of solutions, suspensions, emulsion, tablets, pills, capsules, powders, sustained-release formulations and the like.
In another aspect, methods for treating migraine, cluster headaches or other indication that can be treated with an anti-CGRP or anti-CGRPR antibody in a subject in need thereof comprising the administration of recombinant AAV particles comprising an expression cassette encoding anti-CGRP or anti-CGRPR antibodies and antibody-binding fragments and variants thereof, or peptides, are provided. A subject in need thereof includes a subject suffering from migraine or cluster headaches, or a subject pre-disposed thereto, e.g., a subject at risk of developing or having a recurrence of the migraine or cluster headaches, or other indication that may be treated with an anti-CGRP or anti-CGRPR antibody. Subjects to whom such gene therapy is administered can be those responsive to erenumab, eptinezumab, fremanezumab, or galcanezumab therapy. In particular embodiments, the methods encompass treating patients who have been diagnosed with migraine or cluster headaches, and, in certain embodiments, identified as responsive to treatment with an anti-CGRP or anti-CGRPR antibody or considered a good candidate for therapy with an anti-CGRP or anti-CGRPR antibody. In specific embodiments, the patients have previously been treated with an anti-CGRP or anti-CGRPR antibody. To determine responsiveness, the anti-CGRP or anti-CGRPR antibody or antigen-binding fragment transgene product (e.g., produced in human cell culture, bioreactors, etc.) may be administered directly to the subject.
In certain embodiments, the method of treating migraine or cluster headaches in a human subject in need thereof comprises intranasally or systemically administering to the subject a therapeutically effective amount of a composition or a recombinant nucleotide expression vector comprising a recombinant AAV comprising a transgene encoding an anti-CGRP or anti-CGRPR mAb, or antigen-binding fragment thereof, operably linked to one or more regulatory sequences that control expression of the transgene in CNS, PNS, liver and/or arterial smooth muscle cells.
In another aspect of the invention, a method of treating migraine or cluster headaches in a human subject in need thereof comprises intranasally or systemically administering to the subject a therapeutically effective amount of a composition comprising, i) a first recombinant AAV comprising a transgene encoding an anti-CGRP mAb, or antigen-binding fragment thereof, operably linked to one or more regulatory sequences that control expression of the transgene in CNS, PNS, liver and/or arterial smooth muscle cells; and ii) a second recombinant AAV comprising a transgene encoding an anti-CGRPR mAb, or antigen-binding fragment thereof, operably linked to one or more regulatory sequences that control expression of the transgene in CNS, PNS, liver and/or arterial smooth muscle cells.
The amino acid sequence (primary sequence) of HuGlyFabs or HuPTM Fabs, HuPTMmAbs, and HuPTM scFvs disclosed herein each comprises at least one site at which N-glycosylation or tyrosine sulfation takes place (see exemplary
Alternatively, mutations may be introduced into the Fc domain to alter the glycosylation site at residue N297 (EU numbering, see Table 7), in particular substituting another amino acid for the asparagine at 297 or the threonine at 299 to remove the glycosylation site resulting in an aglycosylated Fc domain.
5.3.1. N-Glycosylation
Reverse Glycosyladon Sites
The canonical N-glycosylation sequence is known in the art to be Asn-X-Ser(or Thr), wherein X can be any amino acid except Pro. However, it recently has been demonstrated that asparagine (Asn) residues of human antibodies can be glycosylated in the context of a reverse consensus motif, Ser(or Thr)-X-Asn, wherein X can be any amino acid except Pro. See Valliere-Douglass et al., 2009, J. Biol. Chem. 284:32493-32506; and Valliere-Douglass et al., 2010, J. Biol. Chem. 285:16012-16022. As disclosed herein, certain HuGlyFabs and HuPTM scFvs disclosed herein comprise such reverse consensus sequences.
Non-Consensus Glycosylation Sites
In addition to reverse N-glycosylation sites, it recently has been demonstrated that glutamine (Gln) residues of human antibodies can be glycosylated in the context of a non-consensus motif, Gln-Gly-Thr. See Valliere-Douglass et al., 2010, J. Biol. Chem. 285:16012-16022. Surprisingly, certain of the HuGlyFab fragments disclosed herein comprise such non-consensus sequences. In addition, O-glycosylation comprises the addition of N-acetyl-galactosamine to serine or threonine residues by the enzyme. It has been demonstrated that amino acid residues present in the hinge region of antibodies can be 0-glycosylated. The possibility of O-glycosylation confers another advantage to the therapeutic antibodies provided herein, as compared to, e.g., antigen-binding fragments produced in E. coli, again because the E. coli naturally does not contain machinery equivalent to that used in human O-glycosylation. (Instead, O-glycosylation in E. coli has been demonstrated only when the bacteria is modified to contain specific O-glycosylation machinery. See, e.g., Farid-Moayer et al., 2007, J. Bacteriol. 189:8088-8098.)
Engineered N-Glycosylation Sites
In certain embodiments, a nucleic acid encoding a HuPTM mAb, HuGlyFab or HuPTM scFv is modified to include 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more N-glycosylation sites (including the canonical N-glycosylation consensus sequence, reverse N-glycosylation site, and non-consensus N-glycosylation sites) than would normally be associated with the HuPTM mAb, HuGlyFab or HuPTM scFv (e.g., relative to the number of N-glycosylation sites associated with the HuPTM mAb, HuGlyFab or HuPTM scFv in its unmodified state). In specific embodiments, introduction of glycosylation sites is accomplished by insertion of N-glycosylation sites (including the canonical N-glycosylation consensus sequence, reverse N-glycosylation site, and non-consensus N-glycosylation sites) anywhere in the primary structure of the antigen-binding fragment, so long as said introduction does not impact binding of the antibody or antigen-binding fragment to its antigen. Introduction of glycosylation sites can be accomplished by, e.g., adding new amino acids to the primary structure of the antigen-binding fragment, or the antibody from which the antigen-binding fragment is derived (e.g., the glycosylation sites are added, in full or in part), or by mutating existing amino acids in the antigen-binding fragment, or the antibody from which the antigen-binding fragment is derived, in order to generate the N-glycosylation sites (e.g., amino acids are not added to the antigen-binding fragment/antibody, but selected amino acids of the antigen-binding fragment/antibody are mutated so as to form N-glycosylation sites). Those of skill in the art will recognize that the amino acid sequence of a protein can be readily modified using approaches known in the art, e.g., recombinant approaches that include modification of the nucleic acid sequence encoding the protein.
In a specific embodiment, a HuGlyMab or antigen-binding fragment is modified such that, when expressed in mammalian cells, such as retina, CNS, liver or muscle cells, it can be hyperglycosylated. See Courtois et al., 2016, mAbs 8:99-112 which is incorporated by reference herein in its entirety.
N-Glycosylation of HuPTM mAbs and HuPTM Antigen-Binding Fragments
Unlike small molecule drugs, biologics usually comprise a mixture of many variants with different modifications or forms that could have a different potency, pharmacokinetics, and/or safety profile. It is not essential that every molecule produced either in the gene therapy or protein therapy approach be fully glycosylated and sulfated. Rather, the population of glycoproteins produced should have sufficient glycosylation (including 2,6-sialylation) and sulfation to demonstrate efficacy. The goal of gene therapy treatment provided herein can be, for example, to slow or arrest the progression of a disease or abnormal condition or to reduce the severity of one or more symptoms associated with the disease or abnormal condition.
When a HuPTM mAb, HuGlyFab or HuPTM scFv is expressed in a human cell, the N-glycosylation sites of the antigen-binding fragment can be glycosylated with various different glycans. N-glycans of antigen-binding fragments and the Fc domain have been characterized in the art. For example, Bondt et al., 2014, Mol. & Cell. Proteomics 13.11:3029-3039 (incorporated by reference herein in its entirety for its disclosure of Fab-associated N-glycans; see also,
Glycosylation of the Fc domain has been characterized and is a single N-linked glycan at asparagine 297 (EU numbering; see Table 7). The glycan plays an integral structural and functional role, impacting antibody effector function, such as binding to Fc receptor (see, for example, Jennewein and Alter, 2017, Trends In Immunology 38:358 for a discussion of the role of Fc glycosylation in antibody function). Removal of the Fc region glycan almost completely ablates effector function (Jennewien and Alter at 362). The composition of the Fc glycan has been shown to impact effector function, for example hypergalactosylation and reduction in fucosylation have been shown to increase ADCC activity while sialylation correlates with anti-inflammatory effects (Id at 364). Disease states, genetics and even diet can impact the composition of the Fc glycan in vivo. For recombinantly expressed antibodies, the glycan composition can differ significantly by the type of host cell used for recombinant expression and strategies are available to control and modify the composition of the glycan in therapeutic antibodies recombinantly expressed in cell culture, such as CHO to alter effector function (see, for example, US 2014/0193404 by Hansen et al.). Accordingly, the HuPTM mAbs provided herein may advantageously have a glycan at N297 that is more like the native, human glycan composition than antibodies expressed in non-human host cells.
Importantly, when the HuPTM mAb, HuGlyFab or HuPTM scFv are expressed in human cells, the need for in vitro production in prokaryotic host cells (e.g., E. coli) or eukaryotic host cells (e.g., CHO cells or NS0 cells) is circumvented. Instead, as a result of the methods described herein, N-glycosylation sites of the HuPTM mAb, HuGlyFab or HuPTM scFv are advantageously decorated with glycans relevant to and beneficial to treatment of humans. Such an advantage is unattainable when CHO cells, NS0 cells, or E. coli are utilized in antibody/antigen-binding fragment production, because e.g., CHO cells (1) do not express 2,6 sialyltransferase and thus cannot add 2,6 sialic acid during N-glycosylation; (2) can add Neu5Gc as sialic acid instead of Neu5Ac; and (3) can also produce an immunogenic glycan, the α-Gal antigen, which reacts with anti-α-Gal antibodies present in most individuals, which at high concentrations can trigger anaphylaxis; and because (4) E. coli does not naturally contain components needed for N-glycosylation.
Assays for determining the glycosylation pattern of antibodies, including antigen-binding fragments are known in the art. For example, hydrazinolysis can be used to analyze glycans. First, polysaccharides are released from their associated protein by incubation with hydrazine (the Ludger Liberate Hydrazinolysis Glycan Release Kit, Oxfordshire, UK can be used). The nucleophile hydrazine attacks the glycosidic bond between the polysaccharide and the carrier protein and allows release of the attached glycans. N-acetyl groups are lost during this treatment and have to be reconstituted by re-N-acetylation. Glycans may also be released using enzymes such as glycosidases or endoglycosidases, such as PNGase F and Endo H, which cleave cleanly and with fewer side reactions than hydrazines. The free glycans can be purified on carbon columns and subsequently labeled at the reducing end with the fluorophor 2-amino benzamide. The labeled polysaccharides can be separated on a GlycoSep-N column (GL Sciences) according to the HPLC protocol of Royle et al, Anal Biochem 2002, 304(1):70-90. The resulting fluorescence chromatogram indicates the polysaccharide length and number of repeating units. Structural information can be gathered by collecting individual peaks and subsequently performing MS/MS analysis. Thereby the monosaccharide composition and sequence of the repeating unit can be confirmed and additionally in homogeneity of the polysaccharide composition can be identified. Specific peaks of low or high molecular weight can be analyzed by MALDI-MS/MS and the result used to confirm the glycan sequence. Each peak in the chromatogram corresponds to a polymer, e.g., glycan, consisting of a certain number of repeat units and fragments, e.g., sugar residues, thereof. The chromatogram thus allows measurement of the polymer, e.g., glycan, length distribution. The elution time is an indication for polymer length, while fluorescence intensity correlates with molar abundance for the respective polymer, e.g., glycan. Other methods for assessing glycans associated with antigen-binding fragments include those described by Bondt et al., 2014, Mol. & Cell. Proteomics 13.11:3029-3039, Huang et al., 2006, Anal. Biochem. 349:197-207, and/or Song et al., 2014, Anal. Chem. 86:5661-5666.
Homogeneity or heterogeneity of the glycan patterns associated with antibodies (including antigen-binding fragments), as it relates to both glycan length or size and numbers glycans present across glycosylation sites, can be assessed using methods known in the art, e.g., methods that measure glycan length or size and hydrodynamic radius. HPLC, such as size exclusion, normal phase, reversed phase, and anion exchange HPLC, as well as capillary electrophoresis, allows the measurement of the hydrodynamic radius. Higher numbers of glycosylation sites in a protein lead to higher variation in hydrodynamic radius compared to a carrier with less glycosylation sites. However, when single glycan chains are analyzed, they may be more homogenous due to the more controlled length. Glycan length can be measured by hydrazinolysis, SDS PAGE, and capillary gel electrophoresis. In addition, homogeneity can also mean that certain glycosylation site usage patterns change to a broader/narrower range. These factors can be measured by Glycopeptide LC-MS/MS.
In certain embodiments, the HuPTM mAbs, or antigen binding fragments thereof, also do not contain detectable NeuGc and/or α-Gal. By “detectable NeuGc” or “detectable α-Gal” or “does not contain or does not have NeuGc or α-Gal” means herein that the HuPTM mAb or antigen-binding fragment, does not contain NeuGc or α-Gal moieties detectable by standard assay methods known in the art. For example, NeuGc may be detected by HPLC according to Hara et al., 1989, “Highly Sensitive Determination of N-Acetyl- and N-Glycolylneuraminic Acids in Human Serum and Urine and Rat Serum by Reversed-Phase Liquid Chromatography with Fluorescence Detection.” J. Chromatogr., B: Biomed. 377, 111-119, which is hereby incorporated by reference for the method of detecting NeuGc. Alternatively, NeuGc may be detected by mass spectrometry. The α-Gal may be detected using an ELISA, see, for example, Galili et al., 1998, “A sensitive assay for measuring α-Gal epitope expression on cells by a monoclonal anti-Gal antibody.” Transplantation. 65(8):1129-32, or by mass spectrometry, see, for example, Ayoub et al., 2013, “Correct primary structure assessment and extensive glyco-profiling of cetuximab by a combination of intact, middle-up, middle-down and bottom-up ESI and MALDI mass spectrometry techniques.” Landes Bioscience. 5(5):699-710. See also the references cited in Platts-Mills et al., 2015, “Anaphylaxis to the Carbohydrate Side-Chain Alpha-gal” Immunol Allergy Clin North Am. 35(2): 247-260.
Benefits of N-Glycosylation
N-glycosylation confers numerous benefits on the HuPTM mAb, HuGlyFab or HuPTM scFv described herein. Such benefits are unattainable by production of antigen-binding fragments in E. coli, because E. coli does not naturally possess components needed for N-glycosylation. Further, some benefits are unattainable through antibody production in, e.g., CHO cells (or murine cells such as NS0 cells), because CHO cells lack components needed for addition of certain glycans (e.g., 2,6 sialic acid and bisecting GlcNAc) and because either CHO or murine cell lines add N—N-Glycolylneuraminic acid (“Neu5Gc” or “NeuGc”) which is not natural to humans (and potentially immunogenic), instead of N-Acetylneuraminic acid (“Neu5Ac”) the predominant human sialic acid. See, e.g., Dumont et al., 2015, Crit. Rev. Biotechnol. 36(6):1110-1122; Huang et al., 2006, Anal. Biochem. 349:197-207 (NeuGc is the predominant sialic acid in murine cell lines such as SP2/0 and NS0); and Song et al., 2014, Anal. Chem. 86:5661-5666, each of which is incorporated by reference herein in its entirety). Moreover, CHO cells can also produce an immunogenic glycan, the α-Gal antigen, which reacts with anti-α-Gal antibodies present in most individuals, which at high concentrations can trigger anaphylaxis. See, e.g., Bosques, 2010, Nat. Biotech. 28:1153-1156. The human glycosylation pattern of the HuGlyFab of HuPTM scFv described herein should reduce immunogenicity of the transgene product and improve efficacy.
While non-canonical glycosylation sites usually result in low level glycosylation (e.g., 1-5%) of the antibody population, the functional benefits may be significant (See, e.g., van de Bovenkamp et al., 2016, J. Immunol. 196:1435-1441). For example, Fab glycosylation may affect the stability, half-life, and binding characteristics of an antibody. To determine the effects of Fab glycosylation on the affinity of the antibody for its target, any technique known to one of skill in the art may be used, for example, enzyme linked immunosorbent assay (ELISA), or surface plasmon resonance (SPR). To determine the effects of Fab glycosylation on the half-life of the antibody, any technique known to one of skill in the art may be used, for example, by measurement of the levels of radioactivity in the blood or organs in a subject to whom a radiolabelled antibody has been administered. To determine the effects of Fab glycosylation on the stability, for example, levels of aggregation or protein unfolding, of the antibody, any technique known to one of skill in the art may be used, for example, differential scanning calorimetry (DSC), high performance liquid chromatography (HPLC), e.g., size exclusion high performance liquid chromatography (SEC-HPLC), capillary electrophoresis, mass spectrometry, or turbidity measurement.
The presence of sialic acid on HuPTM mAb, HuGlyFab or HuPTM scFv used in the methods described herein can impact clearance rate of the HuPTM mAb, HuGlyFab or HuPTM scFv. Accordingly, sialic acid patterns of a HuPTM mAb, HuGlyFab or HuPTM scFv can be used to generate a therapeutic having an optimized clearance rate. Methods of assessing antigen-binding fragment clearance rate are known in the art. See, e.g., Huang et al., 2006, Anal. Biochem. 349:197-207.
In another specific embodiment, a benefit conferred by N-glycosylation is reduced aggregation. Occupied N-glycosylation sites can mask aggregation prone amino acid residues, resulting in decreased aggregation. Such N-glycosylation sites can be native to an antigen-binding fragment used herein or engineered into an antigen-binding fragment used herein, resulting in HuGlyFab or HuPTM scFv that is less prone to aggregation when expressed, e.g., expressed in human cells. Methods of assessing aggregation of antibodies are known in the art. See, e.g., Courtois et al., 2016, mAbs 8:99-112 which is incorporated by reference herein in its entirety.
In another specific embodiment, a benefit conferred by N-glycosylation is reduced immunogenicity. Such N-glycosylation sites can be native to an antigen-binding fragment used herein or engineered into an antigen-binding fragment used herein, resulting in HuPTM mAb, HuGlyFab or HuPTM scFv that is less prone to immunogenicity when expressed, e.g., expressed in human retinal cells, human CNS cells, human liver cells or human muscle cells.
In another specific embodiment, a benefit conferred by N-glycosylation is protein stability. N-glycosylation of proteins is well-known to confer stability on them, and methods of assessing protein stability resulting from N-glycosylation are known in the art. See, e.g., Sola and Griebenow, 2009, J Pharm Sci., 98(4): 1223-1245.
In another specific embodiment, a benefit conferred by N-glycosylation is altered binding affinity. It is known in the art that the presence of N-glycosylation sites in the variable domains of an antibody can increase the affinity of the antibody for its antigen. See, e.g., Bovenkamp et al., 2016, J. Immunol. 196:1435-1441. Assays for measuring antibody binding affinity are known in the art. See, e.g., Wright et al., 1991, EMBO J. 10:2717-2723; and Leibiger et al., 1999, Biochem. J. 338:529-538.
5.3.2 Tyrosine Sulfation
Tyrosine sulfation occurs at tyrosine (Y) residues with glutamate (E) or aspartate (D) within +5 to −5 position of Y, and where position −1 of Y is a neutral or acidic charged amino acid, but not a basic amino acid, e.g., arginine (R), lysine (K), or histidine (H) that abolishes sulfation. The HuGlyFabs and HuPTM scFvs described herein comprise tyrosine sulfation sites (see exemplary
Importantly, tyrosine-sulfated antigen-binding fragments cannot be produced in E. coli, which naturally does not possess the enzymes required for tyrosine-sulfation. Further, CHO cells are deficient for tyrosine sulfation-they are not secretory cells and have a limited capacity for post-translational tyrosine-sulfation. See, e.g., Mikkelsen & Ezban, 1991, Biochemistry 30: 1533-1537. Advantageously, the methods provided herein call for expression of HuPTM Fab in human cells that are secretory and have capacity for tyrosine sulfation.
Tyrosine sulfation is advantageous for several reasons. For example, tyrosine-sulfation of the antigen-binding fragment of therapeutic antibodies against targets has been shown to dramatically increase avidity for antigen and activity. See, e.g., Loos et al., 2015, PNAS 112: 12675-12680, and Choe et al., 2003, Cell 114: 161-170. Assays for detection tyrosine sulfation are known in the art. See, e.g., Yang et al., 2015, Molecules 20:2138-2164.
5.3.3 O-Glycosylation
O-glycosylation comprises the addition of N-acetyl-galactosamine to serine or threonine residues by the enzyme. It has been demonstrated that amino acid residues present in the hinge region of antibodies can be 0-glycosylated. In certain embodiments, the HuGlyFab comprise all or a portion of their hinge region, and thus are capable of being O-glycosylated when expressed in human cells. The possibility of O-glycosylation confers another advantage to the HuGlyFab provided herein, as compared to, e.g., antigen-binding fragments produced in E. coli, again because the E. coli naturally does not contain machinery equivalent to that used in human O-glycosylation. (Instead, O-glycosylation in E. coli has been demonstrated only when the bacteria is modified to contain specific O-glycosylation machinery. See, e.g., Farid-Moayer et al., 2007, J. Bacteriol. 189:8088-8098.) O-glycosylated HuGlyFab, by virtue of possessing glycans, shares advantageous characteristics with N-glycosylated HuGlyFab (as discussed above).
5.4.1 Anti-CGRP Receptor HuPTM Constructs and Formulations for Migraines and Cluster Headaches.
Compositions and methods are described for the delivery of HuPTM mAbs and antigen-binding fragments thereof, such as HuPTM Fabs, that bind to calcitonin gene-related peptide receptor (CGRPR) that may have benefit in treating migraines or cluster headaches. In particular embodiments, the HuPTM mAb is erenumab or an antigen binding fragment of one of the foregoing. An amino acid sequence for Fab fragments of erenumab is provided in
Transgenes
Provided are recombinant vectors containing a transgene encoding a HuPTM mAb or HuPTM Fab (or other antigen binding fragment of the HuPTM mAb) that binds to CGRPR that can be administered to deliver the HuPTM mAb or antigen binding fragment in a patient. The transgene is a nucleic acid comprising the nucleotide sequences encoding an antigen binding fragment of an antibody that binds to CGRPR, such as erenumab, or variants thereof as detailed herein or in accordance with the details herein. The transgene may also encode anti-CGRPR antigen binding fragment that contains additional glycosylation sites (e.g., see Courtois et al., 2016, mAbs 8: 99-112 which is incorporated by reference herein in its entirety).
In certain embodiments, the anti-CGRPR antigen-binding fragment transgene comprises the nucleotide sequences encoding the heavy and light chains of the Fab portion of erenumab (having amino acid sequences of SEQ ID NOs. 1 and 2, respectively, see Table 8 and FIG. 2A). The nucleotide sequences may be codon optimized for expression in human cells and may, for example, comprise the nucleotide sequences of SEQ ID NO: 9 (encoding the erenumab heavy chain Fab portion) and SEQ ID NO: 10 (encoding the erenumab light chain Fab portion) or the nucleotide sequence of 267 encoding the vectorized erenumab (signal sequences underlined) as set forth in Table 9. The heavy and light chain sequences both have a signal or leader sequence at the N-terminus appropriate for expression and secretion in human cells, in particular, human CNS cells. The signal sequence may have the amino acid sequence of MYRMQLLLLIALSLALVTNS (SEQ ID NO: 28) or the one of the sequences found in Tables 2-4, supra.
In addition to the heavy and light chain variable domain sequences, the transgenes may comprise, at the C-terminus of the heavy chain variable domain sequence, all or a portion of the hinge region. In specific embodiments, the anti-CGRPR-antigen binding domain has a heavy chain variable domain of SEQ ID NO: 1 with additional hinge region sequence starting after the C-terminal aspartate (D), contains all or a portion of the amino acid sequence all or a portion of the amino acid sequence ERKCCVECPPCPAPPVAG (SEQ ID NO:115) or ERKCCVECPPCPA (SEQ ID NO:116) as set forth in
In certain embodiments, the anti-CGRPR antigen-binding fragment transgene encodes a CGRPR antigen-binding fragment comprising a light chain comprising an amino acid sequence that is at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to the sequence set forth in SEQ ID NO: 2. In certain embodiments, the anti-CGRPR antigen-binding fragment transgene encodes a CGRPR antigen-binding fragment comprising a heavy chain comprising an amino acid sequence that is at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to the sequence set forth in SEQ ID NO: 1. In certain embodiments, the anti-CGRPR antigen-binding fragment transgene encodes an antigen-binding fragment comprising a light chain comprising an amino acid sequence that is at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to the sequence set forth in SEQ ID NO: 2 and a heavy chain comprising an amino acid sequence that is at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to the sequence set forth in SEQ ID NO: 1. In specific embodiments, the CGRPR antigen-binding fragment comprises a heavy chain comprising an amino acid sequence of SEQ ID NO: 1 with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more amino acid substitutions, insertions or deletions, and the substitutions, insertions or deletions preferably are made in the framework regions (i.e., those regions outside of the CDRs, which CDRs are underlined in
In certain embodiments, the anti-CGRPR antigen-binding fragment transgene encodes a hyperglycosylated erenumab Fab, comprising a heavy chain and a light chain of SEQ ID NOs: 1 and 2, respectively, with one or more of the following mutations: T125N (heavy chain) and/or Q198N (light chain).
In certain embodiments, the anti-CGRPR antigen-binding fragment transgene encodes an antigen-binding fragment and comprises the nucleotide sequences encoding the six erenumab CDRs which are underlined in the heavy and light chain variable domain sequences of
DYFPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT
VPSSNFGTQT YTCNVDHKPS NTKVDKTVER KCCVE +/−CPPCPA +/−
LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADGSPVK
AGVETTKPSK QSNNKYAASS YLSLTPEQWK SHRSYSCQVT
HEGSTVEKTV APTECS
PLAPSSKSTS GGTAALGCLV KDYFPEPVTV SWNSGALTSG
VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP
SNTKVDARVE PKSCD +/− KTHT (or KTHL) +/−
VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSNFGT
QTYTCNVDHK PSNTKVDKTV ERKCCVE +/− CPPCPA +/−
STKGPSVFPL APCSRSTSES TAALGCLVKD YFPEPVTVSW
NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTKTY
TCNVDHKPSN TKVDKRVESK Y+/−GPPCPPCPA (or GPPCPSCPA)
ATGTACAGAATGCAGCTGCTGCTGCTCATTGCCCTGTCTCTGGCCCTGGTCA
CCAATTCTCAGGTGCAGCTGGTTGAATCTGGTGGTGGTGTTGTGCAGCCTGG
ATGTACAGAATGCAGCTGCTGCTGCTCATTGCCCTGTCTCTGGCCCTGGTCA
CCAATTCTGAAGTGCAGCTGGTGGAATCTGGTGGTGGACTGGTTCAGCCTGG
ATGTACAGAATGCAGCTGCTGCTGCTCATTGCCCTGTCTCTGGCCCTGGTCA
CCAATTCTCAGGTGCAGCTGGTTCAGTCTGGGGCTGAAGTGAAGAAACCTGG
ATGTACAGAATGCAGCTGCTGCTGCTCATTGCCCTGTCTCTGGCCCTGGTCA
CCAATTCTGAAGTGCAGCTGGTGGAATCTGGTGGTGGACTGGTTCAGCCTGG
Gene Therapy Methods
Provided are methods of treating human subjects for migraines and cluster headaches by administration of a viral vector containing a transgene encoding an anti-CGRPR antibody, or antigen binding fragment thereof. The antibody may be erenumab and is preferably a Fab fragment thereof, or other antigen-binding fragment thereof. In certain embodiments, the patient has been diagnosed with and/or has symptoms associated with episodic migraines or chronic migraines. In certain embodiments, the patient has been diagnosed with and/or has symptoms associated with episodic cluster headaches or chronic cluster headaches. A recombinant vector used for delivering the transgene is described in Section 5.4.1 and shown in
Subjects to whom such gene therapy is administered can be those responsive to anti-CGRPR therapy. In particular embodiments, the methods encompass treating patients who have been diagnosed with migraines or cluster headaches or have one or more symptoms associated therewith, and identified as responsive to treatment with an anti-CGRPR antibody or considered a good candidate for therapy with an anti-CGRPR antibody. In specific embodiments, the patients have previously been treated with erenumab, eptinezumab, fremanezumab, or galcanezumab, and have been found to be responsive to one or more of erenumab, eptinezumab, fremanezumab, and galcanezumab. To determine responsiveness, the anti-CGRPR antibody or antigen-binding fragment transgene product (e.g., produced in human cell culture, bioreactors, etc.) may be administered directly to the subject.
Human Post Translationally Modified Antibodies
The production of the anti-CGRPR HuPTM mAb or HuPTM Fab, should result in a “biobetter” molecule for the treatment of migraines or cluster headaches accomplished via gene therapy—e.g., by administering a viral vector or other DNA expression construct encoding the anti-CGRPR HuPTM Fab intranasal, intravenous, or intramuscular administration to human subjects (patients) diagnosed with or having one or more symptoms of migraines or cluster headaches, to create a permanent depot in CNS, PNS, arterial smooth muscle, and/or liver cells that continuously supplies the fully-human post-translationally modified, e.g., human-glycosylated, sulfated transgene product produced by transduced c
The cDNA construct for the anti-CGRPR HuPTM mAb or anti-CGRPR HuPTM Fab should include a signal peptide that ensures proper co- and post-translational processing (glycosylation and protein sulfation) by the transduced CNS cells. For example, the signal sequence may be MYRMQLLLLIALSLALVTNS (SEQ ID NO: 28).
As an alternative, or an additional treatment to gene therapy, the anti-CGRPR HuPTM mAb or HuPTM Fab can be produced in human cell lines by recombinant DNA technology, and administered to patients diagnosed with migraines or cluster headaches, or for whom therapy for migraines or cluster headaches is considered appropriate.
In specific embodiments, the anti-CGRPR HuPTM mAb or antigen-binding fragment thereof has heavy and light chains with the amino acid sequences of the heavy and light chain Fab portions of erenumab as set forth in
In certain embodiments, the HuPTM mAb or Fab is therapeutically effective and is at least 0.5%, 1% or 2% 2,6 sialylated and/or sulfated and may be at least 5%, 10% or even 50% or 100% glycosylated 2,6 sialylation and/or sulfated. The goal of gene therapy treatment provided herein is to prevent or reduce the intensity or frequency of migraines, cluster headaches, or one or more of the symptoms associated therewith, including nausea, light sensitivity, sound sensitivity, red eye, eyelid edema, forehead and facial sweating, tearing (lacrimation), abnormal small size of the pupil (miosis), nasal congestion, runny nose (rhinorrhea), and drooping eyelid (ptosis). Efficacy may be monitored by measuring a reduction in the intensity or frequency of migraines or cluster headaches, or a reduction in the amount of acute migraine-specific medication used over a defined period of time (e.g. number of days of use of any acute headache medication per month). For example, a therapeutically effective HuPTM mAb or Fab reduces the average number of headache and/or migraine days per month compared to placebo by at least 2, at least, 3, at least 4, or at least 5 days.
Combinations of delivery of the anti-CGRPR HuPTM mAb or antigen-binding fragment thereof, to the CNS accompanied by delivery of other available treatments are encompassed by the methods provided herein. The additional treatments may be administered before, concurrently or subsequent to the gene therapy treatment. Available treatments for cluster headaches or migraines that could be combined with the gene therapy provided herein include but are not limited to triptans, ergotamine derivatives and NSAIDs, to name a few, and administration with anti-CGRPR or anti-CGRP agents, including but not limited to erenumab, eptinezumab, fremanezumab, and galcanezumab.
5.4.2 Anti-CGRP HuPTM Constructs and Formulations for Migraine
Compositions and methods are described for the delivery of HuPTM mAbs and antigen-binding fragments thereof, such as HuPTM Fabs, that bind to calcitonin gene-related peptide (CGRP) that may have benefit in treating migraines and cluster headaches (referred to collectively as headache disorders). In certain embodiments, the HuPTM mAb is eptinezumab, fremanezumab, galcanezumab or an antigen binding fragment of one of the foregoing. The amino acid sequences of Fab fragments of these antibodies are provided in
Transgenes
Provided are recombinant vectors containing a transgene encoding a HuPTM mAb or HuPTM Fab (or other antigen binding fragment of the HuPTM mAb) that binds to CGRP that can be administered to deliver the HuPTM mAb or antigen binding fragment in a patient. The transgene is a nucleic acid comprising the nucleotide sequences encoding an antigen binding fragment of an antibody that binds to CGRP, such as eptinezumab, fremanezumab, galcanezumab or variants thereof as detailed herein or in accordance with the details herein. The transgene may also encode anti-CGRP antigen binding fragment that contains additional glycosylation sites (e.g., see Courtois et al., 2016, mAbs 8: 99-112 which is incorporated by reference herein in its entirety).
In certain embodiments, the anti-CGRP antigen-binding fragment transgene comprises the nucleotide sequences encoding the heavy and light chains of the Fab portion of eptinezumab (having amino acid sequences of SEQ ID NOs. 3 and 4, respectively, see Table 8 and
In addition to the heavy and light chain variable domain and CH1 and CL domain sequences, the transgenes may comprise, at the C-terminus of the heavy chain CH1 domain sequence, all or a portion of the hinge region. In specific embodiments, the anti-CGRP-antigen binding domain has a heavy chain Fab fragment of SEQ ID NO: 3 with additional hinge region sequence starting after the C-terminal valine (V), contains all or a portion of the amino acid sequence EPKSCDKTHTCPPCPAPELLGG (SEQ ID NO:97), and specifically, EPKSCDKTHL (SEQ ID NO:99), EPKSCDKTHT (SEQ ID NO:100), EPKSCDKTHTCPPCPA (SEQ ID NO:101), EPKSCDKTHLCPPCPA (SEQ ID NO:102), EPKSCDKTHTCPPCPAPELLGGPSVFL (SEQ ID NO:103) or EPKSCDKTHLCPPCPAPELLGGPSVFL (SEQ ID NO:104) as set forth in
In certain embodiments, the anti-CGRP antigen-binding fragment transgene encodes a CGRP antigen-binding fragment comprising a light chain comprising an amino acid sequence that is at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to the sequence set forth in SEQ ID NO: 4. In certain embodiments, the anti-CGRP antigen-binding fragment transgene encodes a CGRP antigen-binding fragment comprising a heavy chain comprising an amino acid sequence that is at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to the sequence set forth in SEQ ID NO: 3. In certain embodiments, the anti-CGRP antigen-binding fragment transgene encodes an antigen-binding fragment comprising a light chain comprising an amino acid sequence that is at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to the sequence set forth in SEQ ID NO: 4 and a heavy chain comprising an amino acid sequence that is at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to the sequence set forth in SEQ ID NO: 3. In specific embodiments, the CGRP antigen-binding fragment comprises a heavy chain comprising an amino acid sequence of SEQ ID NO: 3 with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more amino acid substitutions, insertions or deletions, and the substitutions, insertions or deletions are made, e.g., in the framework regions (e.g., those regions outside of the CDRs, which CDRs are underlined in
In certain embodiments, the anti-CGRP antigen-binding fragment transgene encodes a hyperglycosylated eptinezumab Fab, comprising a heavy chain and a light chain of SEQ ID NOs: 3 and 4, respectively, with one or more of the following mutations: L106N (heavy chain), Q165N or Q165S (light chain), and/or E200N (light chain).
In certain embodiments, the anti-CGRP antigen-binding fragment transgene encodes an antigen-binding fragment and comprises the nucleotide sequences encoding the six eptinezumab CDRs which are underlined in the heavy and light chain variable domain sequences of
In certain embodiments, the anti-CGRP antigen-binding fragment transgene comprises the nucleotide sequences encoding the heavy and light chains of the Fab portion of fremanezumab (having amino acid sequences of SEQ ID NOs. 5 and 6, respectively, see Table 8 and
In addition to the heavy and light chain variable domain and CH1 and CL sequences, the transgenes may comprise, at the C-terminus of the heavy chain CH1 domain sequence, all or a portion of the hinge region. In specific embodiments, the anti-CGRPR-antigen binding domain has a heavy chain Fab fragment of SEQ ID NO: 5 with additional hinge region sequence starting after the C-terminal valine (V), contains all or a portion of the amino acid sequence ERKCCVECPPCPAPPVAG (SEQ ID NO:115) or ERKCCVECPPCPA (SEQ ID NO:116) as set forth in
In certain embodiments, the anti-CGRP antigen-binding fragment transgene encodes a CGRP antigen-binding fragment comprising a light chain comprising an amino acid sequence that is at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to the sequence set forth in SEQ ID NO: 6. In certain embodiments, the anti-CGRPR antigen-binding fragment transgene encodes a CGRP antigen-binding fragment comprising a heavy chain comprising an amino acid sequence that is at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to the sequence set forth in SEQ ID NO: 5. In certain embodiments, the anti-CGRP antigen-binding fragment transgene encodes an antigen-binding fragment comprising a light chain comprising an amino acid sequence that is at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to the sequence set forth in SEQ ID NO: 6 and a heavy chain comprising an amino acid sequence that is at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to the sequence set forth in SEQ ID NO: 5. In specific embodiments, the CGRP antigen-binding fragment comprises a heavy chain comprising an amino acid sequence of SEQ ID NO: 5 with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more amino acid substitutions, insertions or deletions, and the substitutions, insertions or deletions are made, e.g., in the framework regions (e.g., those regions outside of the CDRs, which CDRs are underlined in
In certain embodiments, the anti-CGRP antigen-binding fragment transgene encodes a hyperglycosylated fremanezumab Fab, comprising a heavy chain and a light chain of SEQ ID NOs: 5 and 6, respectively, with one or more of the following mutations: L117N (heavy chain), Q160N or Q160S (light chain), and/or E195N (light chain).
In certain embodiments, the anti-CGRP antigen-binding fragment transgene encodes an antigen-binding fragment and comprises the nucleotide sequences encoding the six fremanezumab CDRs which are underlined in the heavy and light chain variable domain sequences of
In certain embodiments, the anti-CGRP antigen-binding fragment transgene comprises the nucleotide sequences encoding the heavy and light chains of the Fab portion of galcanezumab (having amino acid sequences of SEQ ID NOs. 7 and 8, respectively, see Table 8 and
In addition to the heavy and light chain variable domain and CH1 and CL domain sequences, the transgenes may comprise, at the C-terminus of the heavy chain CH1 domain sequence, all or a portion of the hinge region. In specific embodiments, the anti-CGRP-antigen binding domain has a heavy chain Fab domain of SEQ ID NO: 7 with additional hinge region sequence starting after the C-terminal valine (V), contains all or a portion of the amino acid sequence contains all or a portion of the amino acid sequence ESKYGPPCPPCPAPEAAGG (SEQ ID NO:250) or ESKYGPPCPSCPAPEAAGG (SEQ ID NO:251) as set forth in
In certain embodiments, the anti-CGRP antigen-binding fragment transgene encodes a CGRP antigen-binding fragment comprising a light chain comprising an amino acid sequence that is at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to the sequence set forth in SEQ ID NO: 8. In certain embodiments, the anti-CGRP antigen-binding fragment transgene encodes a CGRP antigen-binding fragment comprising a heavy chain comprising an amino acid sequence that is at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to the sequence set forth in SEQ ID NO: 7. In certain embodiments, the anti-CGRP antigen-binding fragment transgene encodes an antigen-binding fragment comprising a light chain comprising an amino acid sequence that is at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to the sequence set forth in SEQ ID NO: 8 and a heavy chain comprising an amino acid sequence that is at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to the sequence set forth in SEQ ID NO: 7. In specific embodiments, the CGRP antigen-binding fragment comprises a heavy chain comprising an amino acid sequence of SEQ ID NO: 7 with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more amino acid substitutions, insertions or deletions, and the substitutions, insertions or deletions are made, e.g., in the framework regions (e.g., those regions outside of the CDRs, which CDRs are underlined in
In certain embodiments, the anti-CGRPR antigen-binding fragment transgene encodes a hyperglycosylated galcanezumab Fab, comprising a heavy chain and a light chain of SEQ ID NOs: 7 and 8, respectively, with one or more of the following mutations: T114N (heavy chain), Q16ON or Q160S, and/or E195N (light chain).
In certain embodiments, the anti-CGRPR antigen-binding fragment transgene encodes an antigen-binding fragment and comprises the nucleotide sequences encoding the six galcanezumab CDRs which are underlined in the heavy and light chain variable domain sequences of
Gene Therapy Methods
Provided are methods of treating human subjects for migraines and cluster headaches by administration of a viral vector containing a transgene encoding an anti-CGRP antibody, or antigen binding fragment thereof. The antibody may be eptinezumab, fremanezumab, or galcanezumab and is, e.g., a Fab fragment thereof, or other antigen-binding fragment thereof or is a full length anti-CGRP antibody with an Fc region. In certain embodiments, the patient has been diagnosed with and/or has symptoms associated with episodic migraines or chronic migraines. In certain embodiments, the patient has been diagnosed with and/or has symptoms associated with episodic cluster headaches or chronic cluster headaches. Recombinant vectors used for delivering the transgenes are described in Section 5.4.1 and shown in
Subjects to whom such gene therapy is administered can be those responsive to anti-CGRP therapy. In certain embodiments, the methods encompass treating patients who have been diagnosed with migraines or cluster headaches or have one or more symptoms associated therewith, and identified as responsive to treatment with an anti-CGRP antibody or considered a good candidate for therapy with an anti-CGRP antibody. In specific embodiments, the patients have previously been treated with eptinezumab, fremanezumab, or galcanezumab, and have been found to be responsive to one or more of eptinezumab, fremanezumab, and galcanezumab. To determine responsiveness, the anti-CGRP antibody or antigen-binding fragment transgene product (e.g., produced in human cell culture, bioreactors, etc.) may be administered directly to the subject.
Human Post Translationally Modified Antibodies
The production of the anti-CGRP HuPTM mAb or HuPTM Fab, should result in a “biobetter” molecule for the treatment of migraines or cluster headaches accomplished via gene therapy—e.g., by administering a viral vector or other DNA expression construct encoding the anti-CGRP HuPTM Fab, intranasal, intravenous, or intramuscular administration to human subjects (patients) diagnosed with or having one or more symptoms of migraines or cluster headaches, to create a permanent depot in the CNS, PNS, arterial smooth muscle, and/or liver cells that continuously supplies the fully-human post-translationally modified, e.g., human-glycosylated, sulfated transgene product produced by transduced CNS, PNS, arterial smooth muscle, and/or liver cells.
The cDNA construct for the anti-CGRP HuPTM mAb or anti-CGRP HuPTM Fab should include a signal peptide that ensures proper co- and post-translational processing (glycosylation and protein sulfation) by the transduced CNS, PNS, arterial smooth muscle, and/or liver cells. For example, the signal sequence may be MYRMQLLLLIALSLALVTNS (SEQ ID NO: 28).
As an alternative, or an additional treatment to gene therapy, the anti-CGRP HuPTM mAb or HuPTM Fab can be produced in human cell lines by recombinant DNA technology, and administered to patients diagnosed with migraines or cluster headaches, or for whom therapy for migraines or cluster headaches is considered appropriate.
In specific embodiments, the anti-CGRP HuPTM mAb or antigen-binding fragment thereof has heavy and light chains with the amino acid sequences of the heavy and light chain Fab portions of eptinezumab as set forth in
In specific embodiments, the anti-CGRP HuPTM mAb or antigen-binding fragment thereof has heavy and light chains with the amino acid sequences of the heavy and light chain Fab portions of fremanezumab as set forth in
In specific embodiments, the anti-CGRP HuPTM mAb or antigen-binding fragment thereof has heavy and light chains with the amino acid sequences of the heavy and light chain Fab portions of galcanezumab as set forth in
In certain embodiments, the HuPTM mAb or Fab is therapeutically effective and is at least 0.5%, 1% or 2% 2,6 sialylated and/or sulfated and may be at least 5%, 10% or even 50% or 100% glycosylated 2,6 sialylation and/or sulfated. The goal of gene therapy treatment provided herein is to prevent or reduce the intensity or frequency of migraines, cluster headaches, or one or more of the symptoms associated therewith, including nausea, light sensitivity, sound sensitivity, red eye, eyelid edema, forehead and facial sweating, tearing (lacrimation), abnormal small size of the pupil (miosis), nasal congestion, runny nose (rhinorrhea), and drooping eyelid (ptosis). Efficacy may be monitored by measuring a reduction in the intensity or frequency of migraines or cluster headaches, or a reduction in the amount of acute migraine-specific medication used over a defined period of time.
Combinations of delivery of the anti-CGRP HuPTM mAb or antigen-binding fragment thereof, to the CNS, PNS, arterial smooth muscle, and/or liver cells accompanied by delivery of other available treatments are encompassed by the methods provided herein. The additional treatments may be administered before, concurrently or subsequent to the gene therapy treatment. Available treatments for cluster headaches or migraines that could be combined with the gene therapy provided herein include but are not limited to triptans, ergotamine derivatives and NSAIDs, to name a few, and administration with anti-CGRPR agents, including but not limited to eptinezumab, fremanezumab, and galcanezumab.
5.4.3 Dual Constructs and Vector Combinations
Dual delivery of an anti-CGRP HuPTM mAb, or antigen-binding fragment thereof, particularly eptinezumab, fremanezumab, or galcanezumab, and an anti-CGRPR HuPTM mAb, or antigen-binding fragment thereof, particularly erenumab, may be achieved by administration of a single dual cistron vector expressing an anti-CGRP HuPTM Fab and an anti-CGRPR HuPTM Fab wherein the anti-CGRP HuPTM Fab and the anti-CGRPR HuPTM Fab are each under the control of different promoters to promote expression in different tissue types. Thus, in certain embodiments, the anti-CGRP HuPTM Fab will be expressed in a different or substantially different set of cells than the anti-CGRPR HuPTM Fab due to the controlling regulatory sequences. Alternatively, delivery of both anti-CGRP HuPTM mAb and anti-CGRPR HuPTM mAb (or antigen binding fragments thereof) may be accomplished by administration of a first and second viral vector, wherein the first vector expresses an anti-CGRP HuPTM mAb, or antigen-binding fragment thereof, and the second viral vector expresses an anti-CGRPR HuPTM mAb, or antigen-binding fragment thereof. The HuPTM Fabs may be under the control of the same of different regulatory sequences and the AAV serotype of the rAAV vector used may be the same of different.
Provided are combinations of construct, regulatory elements, AAV serotype and whether the first and second transgenes are in the same vector, as a dual cistronic vector, or in separate vectors for effective delivery of the combination of anti-CGRP antibodies and anti-CGRPR antibodies (and antigen binding fragments thereof). Structural component parts of a dual cistron vector expression cassette (AGT1 and AGT2) and, alternatively, a first and a second vector administered as dual therapy, are outlined in Table 10. For example, in certain embodiments, the dual cistron vector comprises a first transgene (ATG1, upstream of AGT2) encoding erenumab, operably linked to a CNS-specific promoter or a neuron-specific promoter (e.g. hSyn or CamKII), and a second transgene (ATG2) encoding eptinezumab, operably linked to an arterial smooth muscle cell-specific promoter (e.g., SM22a), wherein the capsid protein is an AAV9. In other embodiments, the first vector comprises a first transgene (ATG1) encoding erenumab, operably linked to a CNS-specific promoter or a neuron-specific promoter (e.g. hSyn or CamKII), and the second vector comprises a second transgene (ATG2) encoding eptinezumab, operably linked to an arterial smooth muscle cell-specific promoter (e.g SM22a), wherein the capsid protein of the first and second viral vector may be the same (e.g. AAV9) or different (e.g. AGT1: AAV9 and AGT2:AAV8). Promoters or active fragments thereof can include, but are not limited to, liver- (“LIV”, e.g. TBG or ApoE.hAAT), CNS- or neuron- (“CNS”, e.g. hSYN or CAMKII), arterial smooth muscle cell (“SM22a”), or ubiquitous promoters (“CAG” or other suitable universal promoter). Exemplary combinations are indicated below in Table 9. Other tissue specific promoters and capsid serotypes may be substituted in the exemplary embodiments.
5.4.4. Dose Administration of Anti-CGRP and Anti-CGRPR Antibodies and Efficacy Monitoring
Section 5.2. and 5.4.1 describe recombinant vectors that contain a transgene encoding a HuPTM mAb or HuPTM Fab (or other antigen binding fragment of the HuPTM mAb) that binds to CGRP or CGRPR. Therapeutically effective doses of any such recombinant vector should be administered in any manner such that the recombinant vector enters the CNS, PNS, liver, and/or arteries (e.g., arterial smooth muscle cells), e.g. by introducing the recombinant vector into the bloodstream. Alternatively, the vector may be administered directly to the liver through hepatic blood flow, e.g., via the suprahepatic veins or via the hepatic artery, or directly to the CNS via introduction into the cerebral spinal fluid (CSF). In specific, embodiments, the vector is administered intranasally, intravenously, or intramuscularly. Intranasal, intravenous, intramuscular, intrathecal, or hepatic administration should result in expression of the soluble transgene product in cells of the liver, CNS, PNS, and/or arterial smooth muscle cells. The expression of the transgene encoding an anti-CGRP or anti-CGRPR antibody creates a permanent depot in CNS, PNS, arterial smooth muscle, and/or liver cells of the patient that continuously supplies the anti-CGRP or anti-CGRPR HuPTM mAb, or antigen binding fragment of the anti-CGRP or anti-CGRPR mAb to targeted tissue structures of the subject, e.g. dural vessels or TG.
In certain embodiments, intravenous administration of an AAV gene therapy vector encoding an anti-CGRPR antibody (erenumab) results in at least 1.5 μg/mL, 2 μg/mL, 5 μg/mL, 10 μg/mL, 15 μg/mL or at least 20 μg/mL transgene product expression in human serum at least 20, 30, 40, 50 or 60 days after administration. In certain embodiments, the target human serum concentration (Cmin) of the transgene product is about 1.5 μg/mL to about 20 μg/mL mAb.
In certain embodiments, doses that maintain a serum concentration of the anti-CGRPR antibody transgene product at a Cmin of at least 1.5 μg/mL or at least 15 μg/mL (e.g., Cmin of 1.5 to 5 μg/ml, 5 to 10 μg/ml or 10 to 20 μg/mL) at least 30, 40, 50 or 69 days after administration are provided.
However, in all cases because the transgene product is continuously produced, maintenance of lower concentrations can be effective. Notwithstanding, because the transgene product is continuously produced, maintenance of lower concentrations can be effective. The concentration of the transgene product can be measured in patient blood serum samples.
Pharmaceutical compositions suitable for intravenous, intrathecal, intranasal, intramuscular, or hepatic administration comprise a suspension of the recombinant vector comprising the transgene encoding the anti-CGRP or anti-CGRPR antibody, or antigen-binding fragment thereof, in a formulation buffer comprising a physiologically compatible aqueous buffer. The formulation buffer can comprise one or more of a polysaccharide, a surfactant, polymer, or oil.
The efficacy of the methods and compositions may be assessed in either animal models, such as those disclosed herein, or in human subjects using methods known in the art. The efficacy may be assessed as determined to reduce nausea, light sensitivity, sound sensitivity, red eye, eyelid edema, forehead and facial sweating, tearing (lacrimation), abnormal small size of the pupil (miosis), nasal congestion, runny nose (rhinorrhea), and/or drooping eyelid (ptosis) in mouse models or in human subjects. In addition, efficacy may be determined by the ability of the composition when administered to a subject to reduce the intensity or frequency of migraines, such as change from baseline in the number of headache and/or migraine days per month (for example, reduction in greater than 1, 2, 3, 4, 5, 6, or 7 headache days per month), number of cluster headaches per month from baseline (for example, a reduction in 1, 2, 3, 4, 5, 6, or 6 cluster headaches per month from baseline) or a reduction in the amount of acute migraine-specific medication used over a defined period of time.
An erenumab Fab cDNA-based vector is constructed comprising a transgene comprising nucleotide sequences encoding the Fab portion of the heavy and light chain sequences of erenumab (amino acid sequences being SEQ ID NOs. 1 and 2, respectively). The nucleotide sequence coding for the Fab portion of the heavy and light chain may be the nucleotide sequence of SEQ ID NOs. 9 and 10, respectively. The transgene also comprises nucleotide sequences that encodes a signal peptide, e.g., MYRMQLLLLIALSLALVTNS (SEQ ID NO: 28). The nucleotide sequences encoding the light chain and heavy chain are separated by IRES elements or 2A cleavage sites (See Table 5, particularly, Furin/T2A SEQ ID NO: 85 or 86) to create a bicistronic vector. The vector additionally includes a constitutive promoter, such as CAG (SEQ ID NO: 25), a tissue-specific promoter, such as an arterial smooth muscle cell-specific promoter, particularly sm22a promoter (SEQ ID NO: 52, 206-211), or an LMTP6 promoter (SEQ ID NO: 159) or LMTP24 promoter (SEQ ID NO: 263) or an inducible promoter, such as a hypoxia-inducible promoter. The vector may further have an intron sequence between the coding region and the regulatory region, such as the VH4 intron (SEQ ID NO: 241). Exemplary constructs include pAAV.CAG.erenumab (SEQ ID NO: 268 (promoter to polyadenylation signal sequence) or 269 (including flanking ITR sequences); pAAV.LMTP6.VH4i.erenumab.T2A (SEQ ID NO: 270 (promoter to polyadenylation signal sequence) or 271 (including flanking ITR sequences)) or pAAV.LMTP24.VH4i.erenumab.T2A (SEQ ID NO: 272 (promoter to polyadenylation signal sequence) or 273 (including flanking ITR sequences)).
An eptinezumab Fab cDNA-based vector is constructed comprising a transgene comprising nucleotide sequences encoding the Fab portion of the heavy and light chain sequences of eptinezumab (amino acid sequences being SEQ ID NOs. 3 and 4, respectively). The nucleotide sequence coding for the Fab portion of the heavy and light chain may be the nucleotide sequence of SEQ ID NOs. 11 and 12, respectively. The transgene also comprises nucleotide sequences that encodes a signal peptide, e.g., MYRMQLLLLIALSLALVTNS (SEQ ID NO: 28). The nucleotide sequences encoding the light chain and heavy chain are separated by IRES elements or 2A cleavage sites (See Table 5, particularly, Furin/T2A SEQ ID NO: 85 or 86) to create a bicistronic vector. The vector additionally includes a constitutive promoter, such as CAG (SEQ ID NO: 25), a tissue-specific promoter, such as an arterial smooth muscle cell-specific promoter, particularly sm22a promoter (SEQ ID NO: 52, 206-211), or an LMTP6 promoter (SEQ ID NO: 159) or LMTP24 promoter (SEQ ID NO: 263) or an inducible promoter, such as a hypoxia-inducible promoter. The vector may further have an intron sequence between the coding region and the regulatory region, such as the VH4 intron (SEQ ID NO: 241). Exemplary constructs include pAAV.CAG. Eptinezumab (SEQ ID NO: 289 (promoter to polyadenylation signal sequence) or 290 (including flanking ITR sequences); pAAV.LMTP6.VH4i. eptinezumab.T2A (SEQ ID NO: 291 (promoter to polyadenylation signal sequence) or 292 (including flanking ITR sequences)) or pAAV.LMTP24.VH4i. eptinezumab.T2A (SEQ ID NO: 293 (promoter to polyadenylation signal sequence) or 273 (including flanking ITR sequences)).
A fremanezumab Fab cDNA-based vector is constructed comprising a transgene comprising nucleotide sequences encoding the Fab portion of the heavy and light chain sequences of fremanezumab (amino acid sequences being SEQ ID NOs. 5 and 6, respectively). The nucleotide sequence coding for the Fab portion of the heavy and light chain may be the nucleotide sequence of SEQ ID NOs. 13 and 14, respectively. The transgene also comprises nucleotide sequences that encodes a signal peptide, e.g., MYRMQLLLLIALSLALVTNS (SEQ ID NO: 28). The nucleotide sequences encoding the light chain and heavy chain are separated by IRES elements or 2A cleavage sites (See Table 5, particularly, Furin/T2A SEQ ID NO: 85 or 86) to create a bicistronic vector. The vector additionally includes a constitutive promoter, such as CAG (SEQ ID NO: 25), a tissue-specific promoter, such as an arterial smooth muscle cell-specific promoter, particularly sm22a promoter (SEQ ID NO: 52, 206-211), or an LMTP6 promoter (SEQ ID NO: 159) or LMTP24 promoter (SEQ ID NO: 263) or an inducible promoter, such as a hypoxia-inducible promoter. The vector may further have an intron sequence between the coding region and the regulatory region, such as the VH4 intron (SEQ ID NO: 241). Exemplary constructs include pAAV.CAG.fremanezumab (SEQ ID NO: 275 (promoter to polyadenylation signal sequence) or 276 (including flanking ITR sequences); pAAV.LMTP6.VH4i. fremanezumab.T2A (SEQ ID NO: 277 (promoter to polyadenylation signal sequence) or 278 (including flanking ITR sequences)) or pAAV.LMTP24.VH4i.fremanezumab.T2A (SEQ ID NO: 279 (promoter to polyadenylation signal sequence) or 280 (including flanking ITR sequences)).
A galcanezumab Fab cDNA-based vector is constructed comprising a transgene comprising nucleotide sequences encoding the Fab portion of the heavy and light chain sequences of galcanezumab (amino acid sequences being SEQ ID NOs. 7 and 8, respectively). The nucleotide sequence coding for the Fab portion of the heavy and light chain may be the nucleotide sequence of SEQ ID NOs. 15 and 16, respectively. The transgene also comprises nucleotide sequences that encodes a signal peptide, e.g., MYRMQLLLLIALSLALVTNS (SEQ ID NO: 28). The nucleotide sequences encoding the light chain and heavy chain are separated by IRES elements or 2A cleavage sites (See Table 5, particularly, Furin/T2A SEQ ID NO: 85 or 86) to create a bicistronic vector. The vector additionally includes a constitutive promoter, such as CAG (SEQ ID NO: 25), a tissue-specific promoter, such as an arterial smooth muscle cell-specific promoter, particularly sm22a promoter (SEQ ID NO: 52, 206-211), or an LMTP6 promoter (SEQ ID NO: 159) or LMTP24 promoter (SEQ ID NO: 263) or an inducible promoter, such as a hypoxia-inducible promoter. The vector may further have an intron sequence between the coding region and the regulatory region, such as the VH4 intron (SEQ ID NO: 241). Exemplary constructs include pAAV.CAG.galcanezumab (SEQ ID NO: 282 (promoter to polyadenylation signal sequence) or 283 (including flanking ITR sequences); pAAV.LMTP6.VH4i. galcanezumab.T2A (SEQ ID NO: 284 (promoter to polyadenylation signal sequence) or 285 (including flanking ITR sequences)) or pAAV.LMTP24.VH4i. galcanezumab.T2A (SEQ ID NO: 286 (promoter to polyadenylation signal sequence) or 286 (including flanking ITR sequences)).
A dual cistron cDNA-based AAV vector is constructed comprising two transgenes comprising nucleotide sequences encoding the Fab portion of the heavy and light chain sequences of erenumab (amino acid sequences being SEQ ID NOs. 1 and 2) and the Fab portion of the heavy and light chain sequences of an anti-CGRP mAb, in particular eptinezumab (SEQ ID NO: 3 and 4), fremanezumab (SEQ ID NOs: 5 and 6), or galcanezumab (SEQ ID NOs: 7 and 8). Each transgene also comprises nucleotide sequences that encodes a signal peptide, e.g., MYRMQLLLLIALSLALVTNS (SEQ ID NO: 28). Nucleotide sequences encoding the light chain and heavy chain of each transgene are separated by IRES elements or 2A cleavage sites (See Table 5, particularly, SEQ ID NO:86 or 87) to create a dual bicistronic vector. The vector additionally includes two promoters (see Table 1 for promoter elements), e.g. a constitutive promoter, such as mU1a (SEQ ID NO:26) or EFIα (SEQ ID NO:27), a tissue-specific promoter, such as an arterial smooth muscle cell-specific promoter, particularly sm22a promoter (SEQ ID NO:184, 185-190), or an CNS promoter, such as hSyn promoter (SEQ ID NO:191-195). Components of the dual cistronic construct expression cassette may be arranged as following: 5′-ITR-(Promoter 1-NH2-VH1-Furin 2A-VL1-COOH-PolyA)-(Promoter 2-NH2-VH2-Furin 2A-VL2-COOH-polyA)-3′-ITR).
Rat experiments will be performed with AAV9 containing an AAV construct (as depicted in
NOs:86 or 87). Expression of the heavy and light chain is driven by a CAG promoter (SEQ ID NO: 25), mU1a promoter (SEQ ID NO:26) or sm22a promoter (SEQ ID NO:184, 185-190). Dual cistronic constructs that contain both anti-CGRP Fab and anti-CGRPR Fabs each separately under the control of a mU1a promoter or sm22a promoter are also tested. In addition, a combination of an rAAV that has a transgene encoding an anti-CGRP mAb or Fab and an rAAV that has a transgene encoding an anti-CGRPR mAb or Fab. Other combinations are set forth in Table 10.
AAV9 vectors (n=3-5 mice per group) will be administered to Wister rats via either intravenous (IV) or intranasal (IN) routes. IV administrations will be into the tail vein. Rats injected with vehicle will be included as controls. Seven weeks post administration rats will be sacrificed and serum human antibody levels will be determined by enzyme-linked immunosorbent assay (ELISA). An exemplary study layout is shown in Table 12. Alternatively, NSG mice can be used as model system. Animals will be tested for transgene expression, vector biodistribution or in a migraine pain model, for example as described in example 7A, 7B or 8.
A. Electrical stimulation of trigeminal neurons: Direct electrical stimulation of trigeminal neurons can be achieved by electrical stimulation of the trigeminal ganglion or electrical stimulation of the meningeal nerve. The trigeminal ganglion of anesthetized animals will be electrically stimulated using inserted stereotactic bipolar electrodes. Trigeminal ganglion neurons are then activated using low frequency (˜5 Hz) stimulation. Electrical stimulation of meningeal nerve terminals innervating the superior sagittal sinus, transverse sinus, or middle meningeal arteries will be used to elicit trigeminal afferent activation. Direct stimulation of nerve terminals innervating the intracranial vasculature and their meningeal afferents as well as direct stimulation of the trigeminal ganglion have proven robust models to test differential responses to drug administration.
B. Administration of Inflammatory Substances to the Meninges: Dural application of algogenic substances will be used to model meningeal neurogenic inflammation which is thought to initiate the migraine-related pain via trigeminovascular afferent and central neuronal sensitization. Inflammatory substances (histamine, serotonin, bradykinin, or PGE2) will be applied to the dura singly or in combination as an inflammatory soup in order to activate and sensitize trigemino-vascular meningeal afferents as, for example, measured by enhanced trigeminal ganglion responses to mechanical stimulation of the meninges. Alternatively, the inflammatory soup will be administrated repetitively to induce chronic periorbital hypersensitivity to tactile stimuli that may last for up to 3 weeks (model of chronic migraine).
C. Exogenous Administration of Algogenic Substances: Sustained mechanical allodynia is a common response associated with the local administration of various proalgesic substances in experimental animals. Exogenous administration of algogenic substances, including but not limited to, CGRP, nitric oxid donors (e.g. nitroglycerine), cilostazol, and PACAP, will be used to trigger migraine pain and other migraine-related features. The selection of the specific algogenic agent will dependent on the individual study requirements.
Exogenous administration of CGRP: Administration of CGRP will be used to study therapeutic effects of anti-CGRP and/or anti-CGRPR gene therapy on neurogenic dural vasodilation, photophobia, periorbital hypersensitivity, and spontaneous pain behaviors in rats and/or mice. AAV9 vectors comprising the heavy and light chain sequences of an anti-CGRP or anti-CGRPR mAb will be administered to Wister rats (or alternatively mice) via either intravenous (IV) or intranasal (IN) routes. 7, 14, 21, 28, or 35 days later, CGRP will be administered by subcutaneous injection in the periorbital area of rats at a dose of 1 μg/kg (in a volume of 10 μl) in order to trigger photophobia, periorbital hypersensitivity and spontaneous pain behaviors.
Experimental readouts may include elecrophysiology and immunohistrochemistry (e.g. expression of neuronal activation markers such as c-Fos), or behavioral assays (e.g. measuring pain-like behaviors in awake, freely-behaving animals such as by measuring mechanical, or tactile, sensitivity by using calibrated von Frey filaments or thermal sensitivity). Spontaneous pain behaviors may also be assessed as alternate read out, for example, increase of grooming reflexes (see Harriot A. M. (2019), Journal of Headache and Pain, 20:91 for more details).
A mouse model is utilized to detect whether intravenous injection of AAV vector-encoding antibodies can diminish behavioral changes and dural vasodilation that reflect headaches in the mouse (Gao and Drew, J. Neurosci., Feb. 24, 2016, 36(8):2503-2516; Shi, A Y, et al. Journal of Cerebral Blood Flow & Metabolism (2012), 1-33). Briefly, after a baseline period of establishing mice with PoRTS window and 2-photon microscopy imaging (Gao and Drew, supra), each mouse is retro-orbitally injected or tail-vein injected with CGRP, imaging and behavioral changes measure the mouse response to CGRP within 5, 10, 15, 20, 25 and/or 30 minutes following CGRP injection. Administration of AAV vectors (packaging anti-CGRP and/or anti-CGRP receptor antibody transgene) will occur in individual mice following CGRP treatment. Dural vessel dilation will be monitored subsequent to AAV injection (up to and including 3 weeks following AAV injection, e.g. 1 week, 2 weeks and 3 weeks following administration of AAV). Dural vessel imaging is done as described by Gao and Drew, supra. Subsequent CGRP administration (or control, e.g. saline) will be provided (e.g. 1, 2 or 3 weeks post-AAV treatment) and behavioral changes (locomotion) and dural dilation changes will again be measured. Parallel mice receiving the same treatment can be sacrificed for determination of antibody transgene DNA and protein expression in various tissues at similar time intervals in which dural vessel images are obtained. It is expected that antibody-encoding AAV treatment can block intravenous CGRP-induced dural vasodilation.
Vascular changes at the level of the dura mater after CGRP-induced or electrical stimulation of the dural vasculature will be used to determine the extent of trigeminovascular activation with or without prior administration of anti-CGRP/CGRPR gene therapy. AAV9 vectors (n=3-5 mice per group) will be administered to Wister rats via either intravenous (IV) or intranasal (IN) routes. Rats injected with vehicle will be included as controls. The effect of administration of vectorized CGRP or CGRPR antibodies on dural vasodilation evoked by a) electrical stimulation of the cranial window and/or b) CGRP administration will be assessed. Dural vasodilation will be induced 7, 14, 21, or 28 days after administration of the vectorized antibody. Laser-Doppler flowmetry or intravital microscopy will be used to measure changes to the diameter of the blood vessels in response to the stimulus (Holland P. R. et al, 2005, The Journal of Pharmacology and Experimental Therapeutics; Vol. 315, No. 3; Akerman S. et al, (2013), Cephalalgia, 33(8) 577-592)
A. CGRP-induced dural vasodilation: CGRP will be administered by subcutaneous injection in the periorbital area of rats at a dose of 1 mg/kg (in a volume of 10 ml).
B. Electrical Stimulation: Electrical stimulation will be used to evoke dilation of the dural blood vessels with a bipolar stimulating electrode placed on the surface of the cranial window. The surface of the cranial window will be stimulated with increasing voltage until maximal dilation is observed. Subsequent electrically induced responses in the same animal will then be evoked with the same voltage. The mean maximum percentage increase in dural vessel diameter relative to pre-stimulation baseline (%) will be calculated.
Analysis: Two control responses to dural electrical stimulation or CGRP-induced dilation will be performed (baseline). Effects of electrical stimulation and CGRP administration on dural vessel diameter in animal treated with or without anti-CGRP or anti-CGRPR gene therapy will be calculated as a percentage increase (%) of post-stimulation diameters from the pre-stimulation baseline diameters and compared to saline control animals. Statistical analysis will be performed using analysis of variance for repeated measures with Boneferri post hoc correction for multiple comparisons followed by Student's paired t-test.
Anti-CGRP and/or anti-CGRPR antibody serum levels will be measured as described above.
Cell culture studies were performed to assess the expression of full length mAb sequences (containing Fc region) from AAV constructs in human cells.
A therapeutic antibody cDNA-based vector was constructed comprising a transgene comprising a nucleotide sequence encoding the heavy and light chain sequences of the therapeutic antibody (amino acid sequences being SEQ ID NOs: 263 and 264, respectively). The nucleotide sequence coding for the heavy and light chain of the therapeutic antibody was codon optimized to generate coding sequences, L01, L02, and L03. L02 and L03 also have reduced incidence of CpG dimers in the sequence. The transgene also comprised a nucleotide sequence that encodes the signal peptide MYRMQLLLLIALSLALVTNS (SEQ ID NO:28). The nucleotide sequences encoding the light chain and heavy chain were separated by a Furin-F2A linker (SEQ ID NOS:87 or 88) or a Furin T2A linker (SEQ ID NOS:85 or 86) to create a bicistronic vector. The vector additionally included a constitutive CAG promoter (SEQ ID NO:47).
Regulatory sequences may be incorporated into expression cassettes and be operably linked to the transgene to promote liver-specific expression (LSPX1, LSPX2, LTP1, LTP2, or LTP3, SEQ ID NOS:66-70, respectively) and liver and muscle expression (LMTP6, LMTP13, LMTP15, LMTP18, LMTP19, LMTP20 or LMTP24) (See Table 1). Other promoter sequences provided, include the ApoE.hAAT (SEQ ID NO:166) promoter, wherein four copies of the liver-specific apolipoprotein E (ApoE) enhancer were placed upstream of the human alpha 1-antitrypsin (hAAT) promoter).
HEK293 cells were plated at a density of 7.5×105 cells/well in each well of a standard 6-well dish containing Dulbecco's modified eagle medium (DMEM) supplied with 10% fetal bovine serum (FBS). The next day, cells were transfected with CAG.L01, CAG.L02, and CAG.L03 AAV constructs using Lifpofectamine 2000 (Invitrogen) according the manufacturer's protocol). Non-transfected cells were used as negative control. Cell culture medium was changed 24 hours post-transfection to opti-mem I reduced serum media (2 mL/well). Cell culture supernatant was harvested at 48 hours post-transfection, and cell lysates were harvested with RIPA buffer (Pierce) supplemented with EDTA-free protease inhibitor tablets (Pierce). Supernatant and lysates samples were stored at −80 C.
Proteins from supernatant or cell lysate samples were separated via the NUPAGE electrophoresis system (Thermo Fisher Scientific). For samples derived from cell lysates, 40 μg of protein was loaded unless indicated otherwise. Purified human IgG or a therapeutic antibody IgG (produced by Genscript) were used as loading controls (50-100 ng). Samples were heated with LDS sample buffer and NUPAGE reducing agent at 70 C for 10 minutes and then loaded into NUPAGE 4-12% Bis-Tris protein gels. Separated proteins were transferred to PVDF membranes using the iBlot2 dry blotting system according to manufacturer's instructions (P3 default setting was used for the protein transfer). Membranes were immediately washed in phosphate buffer saline with 0.1% v/v Tween-20 (PBST). Membranes were then incubated in blocking solution containing PBST and 1% Clear Milk Blocking Buffer (Thermo Scientific) for 1 hour at room temperature. Membranes were then incubated in fresh blocking solution supplemented with goat anti-human kappa light chain-HRP antibody (Bethyl Laboratories; 1:2000 dilution) and goat anti-human IgG Fc-HRP antibody (1:2000 dilution). Following antibody incubation, membranes were washed three times in PBST for 5 minutes per wash. Finally, membranes were incubated in SuperSignal West Pico PLUS chemiluminescent substrate for 5 minutes and imaged on the BioRad Universal Hood II gel doc system for detection of horseradish peroxidase (HRP) signal.
Expression analysis of reporter transgene (eGFP) following transfection of different plasmid quantities (4 μg-nontransfected) showed a dose dependent increase in eGFP levels. Protein expression analysis of the therapeutic antibody in the cell lysate and in the cell supernatant showed dose-dependent levels of the therapeutic antibody in cell lysates and supernatant. Transfection with the construct containing the L02 transgene, CAG.L02, a codon-optimized and depleted of CpG dinucleotide sequences construction, resulted in higher expression levels compared to L01 transgene. Transfection of CAG.L02 and CAG.L03 resulted in similar expression levels.
A. Mouse experiments were performed with either AAV8 or AAV9 containing an AAV construct comprising the L01 sequence, which contains the Furin and F2A sequence. AAV8 and AAV9 vectors (n=5 mice per group; 2e11 genome copies (gc)) were administered to immunocompromised NSG mice via either intravenous (IV) or intramuscular (IM) routes. IV administrations were into the tail vein and IM administrations were bilateral into the gastrocnemius muscles. Mice injected with vehicle were included as controls. Seven weeks post administration mice were sacrificed and serum human antibody levels were determined by enzyme-linked immunosorbent assay (ELISA).
Therapeutic antibody levels in NSG mouse serum was assessed by ELISA. Briefly, mouse serum was obtained before treatment and at 1, 3, 5 and 7 weeks post in vivo gene transfection and stored at −80° C. 96-well plate was coated with 1 μg/ml human IgG-Fc fragment antibody (Bethyl, Montgomery, TX) in carbonate bicarbonate buffer (0.05M, pH 9.6, Sigma-Aldrich, St. Louis, MO) and incubated overnight at 4° C. After washing with Tween 20 washing buffer (PBST, 0.05%, Alfa Aesar, Haverhill, MA), plate was incubated with blocking buffer (3% BSA in PBS, ThermoFisher Scientific, Waltham, MA) for 1 h at 37° C. followed by washing. Mouse serum samples diluted in sample dilution buffer (0.1% Tween 20 and 3% BSA in PBS) was added to the plate (50 μl/well) and incubated for 2 h at 37° C. A standard curve of known therapeutic antibody concentrations ranging from 360 to 0.001 ng/mL was included in each plate. Plate was washed with PBST for five times after incubation. The levels of therapeutic antibody was detected by incubation with horseradish peroxidase-conjugated goat anti-human IgG (H+L) (200 ng/mL; Bethyl, Montgomery, TX) for 1 h at 37° C. The optical density was assessed using KPL TMB Microwell Peroxidase Substrate System (Seracare, Milford, MA) following the manufacturer's specifications. Data analysis was performed with SoftMax Pro version 7.0.2 software (Molecular Devices, Sunnyvale, CA).
A. Results from a representative experiment are shown in
B. In an analogous experiment, a time course of therapeutic antibody serum levels in NSG mice post-AAV9 administration (n=5 per group) was performed. AAV9 vectors (2E11 gc) were injected either IV or IM (as above, in experiment A), and serum antibody levels were determined by ELISA at day 7 (D7), day 21 (D21), day 35 (D35), and day 49 (D49).
Serum therapeutic antibody expression is detectable as early as 1 week (D7) after AAV9 administration in NSG mice. The expression levels increased at 3 weeks (D2), peaked at 5 weeks (D35) and then sustained up to 7 week post-injection (D49). It was observed that serum therapeutic antibody concentration is higher in IV vs. IM injected mice over the entire time course. See
C. In an analogous experiment, a time course of therapeutic antibody serum levels in C/57BL6 mice post AAV8 administration was performed. The optimized expression cassette containing a liver-specific promoter and a codon optimized and CpG depleted transgene with a modified furin-2A processing signal resulted in robust serum antibody concentration when delivered intravenously using an AAV8 vector. Very high (>1 mg/ml) and sustained levels of functional anti-kallikrein antibody were achieved in the serum of C57BL/6 mice following IV vector administration at a dose of 1E13gc/kg.
Cis plasmids expressing vectorized therapeutic antibody were packaged in AAV, then rAAV particles evaluated for potency of the transduction by AAV. Each cis plasmid contained therapeutic antibody (Mab1) antibody light chain and heavy chain which are multicistrons driven by the CAG, ApoE.hAAT (SEQ ID NO:166) or LMTP6 (SEQ ID NO:159) promoter. Full-length therapeutic antibody light chain and antibody heavy chain genes were separated by a furin 2A linker to ensure separate expression of each antibody chain. The entire cassette is flanked by AAV2 ITRs, and the genome is encapsidated in an AAV8 capsid for delivery to C2C12 cells (1E10 vg per well). For detection of antibody protein, following transduction, the cells are treated with FITC conjugated anti-Fc (IgG) antibody. The AAV8.CAG.Mab1 and AAV8.LMTP6.Mab1 infected cells show high expression in muscle cells, whereas the AAV8.hAAT.Mab1 infection does not result in expression of the antibody in muscle cells. Cells appeared to be equally confluent and viable in all test wells, as seen by DAPI (DNA) staining.
Thyroxine binding globulin (TBG) and alpha-1 antitrypsin (hAAT) promoters have been widely used as liver-specific promoters in previous pre-clinical and clinical gene therapy studies. A panel of designed promoter cassettes derived from multiple promoters and enhancers were generated and tested them in vitro by transfecting Huh7 cells, a human liver cell line. Promoter candidates were selected, which include ApoE.hAAT (SEQ ID NO:166), LSPX1, LSPX2, LTP1 and LMTP6 (SEQ ID NO:159). AAV8 vectors encoding vectorized therapeutic antibody regulated by these promoter candidates were then generated. CAG (SEQ ID NO:47) and TBG (SEQ ID NO:183) promoters served as controls for ubiquitous and liver-specific promoters, respectfully. Strength of these promoters and vector biodistribution were tested in vivo by measuring therapeutic antibody protein expression compared to vector genome copy in each wild type mouse.
Vectors were administered intravenously to C57Bl/6 mice at equivalent doses (2.5×1012 vg/kg). Mouse serum was collected biweekly, and therapeutic antibody protein expression levels were determined by ELISA. Liver samples were harvested at 49 days post vector administration. The presence of viral genomes in each sample was quantified using a therapeutic antibody probe and primer by Droplet Digital PCR (ddPCR)(the NAICA™ system from Stilla). The genome copy number of glucagon was also measured simultaneously in each sample, the viral genomes were then normalized and demonstrated as vector genome copy number per cell (assuming 2 glucagon/cell). Statistical analysis was performed using one-way ANOVA in GraphPad Prism 8.
Among the AAV8 vectors with liver-specific promoters, the vectors driven by the ApoE.hAAT (SEQ ID NO:166) and LMTP6 (SEQ ID NO:155) promoters provided the highest amount of protein expression at all time points (
vectors driven by different promoters (
All liver-specific promoters outperform the TBG promoter (SEQ ID NO:183), and the dual-specific LMTP6 promoter (SEQ ID NO:159) consistently shows the highest expression in the serum (μg/ml) (
A high level of therapeutic antibody expression was detected in the serum of mice treated with AAV-therapeutic antibody via IV administration. In parts of the study, the therapeutic antibody expression levels in different rat strains treated with different doses of AAV-therapeutic antibody vectors and controls were examined.
To evaluate the route and the dose of vector administration in rats, a control vector AAV.CAG-LANv2.T2A (CAG.L02) was tested in Wistar rat. Eight to ten weeks old male Wistar rats were assigned into three groups (n=3 per group) to receive vector administration via IM or IV injection at a dose of 1×1013 vg/kg or 1×1014 vg/kg. Blood was collected at 7 days before treatment and 7, 10, 14, 17, 21, 28, 35, 42 and 49 days post vector administration and processed into serum.
Levels of human IgG antibody in collected rat serum were detected by ELISA. Statistical analysis was done by one-way ANOVA with multiple comparisons at each time point using Prism
The levels of antibody in rat serum were detectable at 7 days post treatment. It increased over time and reached the peak level at 17 (lower dose) and 21 (higher dose) days post treatment in IV groups and 28 days in IM group. The antibody levels gradually decreased and sustains up to 48 days post treatment in all groups. For animals treated with lower dose (1×1013 vg/kg) vector, the antibody expression levels in IV groups are significantly higher than that in IM group at 7, 14 and 21 days post vector administration. For animals received IV administration, the antibody expression levels were dose-dependent at all time points. The highest level of therapeutic antibody expression was 252.6±149.4 μg/ml, which was detected in animals treated with higher dose (1×1014 vg/kg) at 21 days post IV administration. See
The aim of this experiment was to investigate the rat strain and the vector dose that will be used for a rat efficacy study. Eight to ten weeks old male Wistar and Sprague-Dawley (SD) rats were assigned into four groups (n=3 per group) to receive treatment of AAV8 vector carrying genome encoding therapeutic antibody driven by a universal promoter, CAG.L02, or a liver-specific promoter, ApoE.hAAT.L02. Vectors were administered via IV injection at a dose of 5×1013 vg/kg. Blood was collected at 7 days before treatment and 7, 10, 14, 17, 21, 28, 35, 42 and 49 days post vector administration and processed into the serum (Table 15). Levels of human IgG antibody in collected rat serum were detected by ELISA. Statistical analysis was done by one-way ANOVA with multiple comparisons at each time point using Prism.
In this experiment, a control vector (CAG.L02) and vector ApoE.hAAT.L02 were tested in Wistar and SD rats, respectively. Therapeutic antibody expression levels were higher in Wistar rat than SD rat in both vector groups at all time points. At the early time points, animals treated with control vector showed significant higher serum antibody levels than those treated with the liver-specific promoter containing vector. This was observed in Wistar rat at 7 days post treatment, and in SD rat at 7, 14 and 17 days post treatment. In Wistar rats, the concentrations of antibody gradually increased over time in both vectors group. The highest antibody levels were 173.1±78.8 μg/ml and 109.57±18.9 μg/ml at 35 and 49 days respectively in control CAG-Therapeutic antibody and hAAT-Therapeutic antibody vector-treated animals. In SD rats, however, the levels of antibody reached peaks at 14 and 21 days in control and lead vector-treated animals, respectively, and decreased gradually afterward in both groups. The highest antibody concentrations were 48.23±3.1 μg/ml and 22.33 f 8.98 μg/ml in CAG.L02 and ApoE.hAAT.L02 vector groups, respectively. See Table 16 and
In a previous study, high liver-driven expression of vectorized therapeutic antibody with AAV8 regulated by the ApoE.hAAT or LMTP6 promoters was identified. The goal of this study was to characterize muscle-driven expression of the LMTP6 promoter following direct injection of therapeutic antibody vectors into the gastrocnemius (GA) muscle. Animals received bilateral injections of 5×1010 vg into the GA muscle. Serum was collected biweekly to measure systemic therapeutic antibody concentration (
Vectors regulated by the hAAT and LMTP6 promoters demonstrated significantly increased antibody concentrations in serum compared to CAG at all time points (
Different AAV production protocols were developed to identify methods that can increase AAV titer and scalability, as well as assess the quality of vector product. Cis and trans plasmids to generate AAV8.therapeutic antibody rAAV vectors (all having the same transgene driven by a CAG promoter) were constructed by well-known methods suitable for HEK293-transfected cell and also baculovirus (BV)/Sf9 insect cell production methods. Three different BV/Sf9 vector systems, BV1, BV2 and BV3, were provided as well as rAAV vector produced by an HEK293 method as a control. Purified rAAV product was injected into wild-type mice for this protein expression study (Table 17).
Young adult C57BL/6 mice (aged 8-10 weeks) were administered with above-mentioned vectors at 2.5E12 vg/kg via tail vein injection (n=5 per group). Serum was collected from each animal at 7, 21, 35, and 49 days post vector administration. Serum collected two days before injection (Day 0) served as baseline control. Levels of antibody (therapeutic antibody) expression were detected via ELISA. Data analysis was done by one-way ANOVA with multiple comparisons at each time point using Prism.
All production methods tested are viable based on this study, with greater yields from the HEK cell production method at the time points tested. Antibody expression in serum is detectable as early as 7 days post administration in all groups. The average of antibody concentration at Day 7 in the HEK production group is 386 μg/ml, which is significantly higher than other groups (61-102 μg/ml). The levels of antibody expression increase at day 21 by 1-, 6-, 7-, and 4-fold in BV1, BV2 and BV3 groups, respectively. Antibody expression levels sustained at 35 and 49 days post administration. There is no significant difference in between HEK produced vector and BV3 produced vectors at day 21, 35 and 49 time points.
In order to measure pKal function of therapeutic antibody derived from mouse serum following AAV-therapeutic antibody administration, a fluorescence-based kinetic enzymatic functional assay was performed. First, activated human plasma kallikrein (Enzyme Research Laboratories) was diluted in sample dilution buffer (SDB; 1×PBS, 3% BSA, 0.1% Tween-20) to top concentration of 100 nM. This pKal was two-fold serially diluted for a total of 12 concentrations in the dilution series (100 nM-0.05 nM). From each dilution, and in duplicate, 25 μL was placed in one well of a 96-well, opaque flat-bottomed plate along with 25 μL of SDB. Then, 50 μL of the fluorogenic substrate Pro-Phe-Arg-7-Amino-4-Methylcoumarin (PFR-AMC) (Bachem) prepared at 100 μM in assay buffer (50 mM Tris, 250 mM NaCl, pH 7.5) was added to each well. The samples were immediately run in kinetic mode for AMC fluorescence at excitation/emission wavelengths of 380/460 nm, respectively, for 3 hours using a SpectraMax 3 fluorescent plate reader.
The signal-to-noise ratio for each pKal concentration RFU (last RFU fluorescent value chosen) was calculated by dividing its RFU by background PFR-AMC substrate fluorescence. The two lowest pKal concentrations with a signal-to-noise ratio≥2 (6.25 nM and 12.5 nM) were then chosen to evaluate the suppressive effect and range of therapeutic antibody of pKal function in a therapeutic antibody dose response. Therapeutic antibody (GenScript) or human IgG control antibody was diluted in SDB to top concentration of 200 nM and two-fold serially diluted to 0.39 nM. Next, 25 μL pKal (each of two chosen concentrations) was incubated with 25 μL therapeutic antibody or human IgG at 30° C. for 1 hour. Antibody-pKal mixture was then given PFR-AMC and immediately run in kinetic mode for AMC fluorescence at excitation/emission wavelengths of 380/460 nm, respectively, for 3 hours using a SpectraMax fluorescent plate reader.
In vitro pKal functional assay. When used, mouse serum was diluted in sample dilution buffer and incubated 1:1 with 6.25 nM (1.56 nM in-well) pKal for 30° C./1 hour. For total IgG purification from mouse serum, antibody was purified using the Protein A Spin Antibody Purification Kit (BioVision) according to manufacturer's protocol. Total antibody concentration was measured using a Nanodrop spectrophotometer, with OD absorbance=280 nM. AMC standard curve was generated by a two-fold downward dilution series of AMC (500 nM, eleven dilutions and blank subtracted) diluted in assay buffer. AMC was read as end point fluorescence at excitation/emission wavelengths of 380/460 nm, respectively. Specific plasma kallikrein activity was calculated as: (adjusted experimental sample Vmax, RFU/sec)×(Conversion factor, AMC standard curve μM/RFU)/(pKal concentration, nM). Percent reduction in pKal activity was derived from calculating day 49 by day −7 pKal activity.
To determine whether AAV-derived therapeutic antibody can suppress plasma kallikrein function, we developed the in vitro AMC substrate-based functional assay to address this in a proof-of-concept study. In this assay, antibody-containing medium is incubated with activated human pKal, as described above. Antibody-bound pKal is then given the synthetic peptide substrate Pro-Phe-Arg conjugated to AMC (PFR-AMC) and amount of released AMC is measured over time at excitation/emission wavelengths of 380/460 nm, respectively, for 3 hours. The assay showed noticeable therapeutic antibody-mediated suppression of pKal activity down to 0.1 nM (in-well concentration) at a defined enzyme concentration. We first sought to determine whether serum from mice administered therapeutic antibody-encoded AAV could suppress pKal activity. Serum from mice 49 days post-administration was diluted 1:25 (in range predicted to be suppressive), incubated with pKal in vitro, and pKal activity was assayed. Serum from mice post-vector administration, as opposed to 7 days pre-administration, suppressed pKal activity, as reflected in a significant reduction of enzyme activity and a ˜50% percent reduction in pKal activity between the two time points.
Further experiments show that suppression was due to the therapeutic antibody within the serum. Reasoning that the human IgG, namely therapeutic antibody, would only be found in the day 49 post-administration IgG fraction, but not the day −7 pre-administration samples, purified and total IgG antibody was used from the aforementioned day −7 and day 49 mouse serum samples to test pKal suppression. Indeed, only therapeutic antibody-containing purified IgG from day 49 post-administration serum, but not IgG from the pre-administration time point, suppressed human pKal function.
The goal of this study is to understand transgene immunogenicity and/or tolerance induction in the context of ubiquitous, tissue-specific, or tandem promoters. Hypothesis: Vectors driven by liver-specific and liver-muscle tandem promoters will demonstrate reduced immunogenicity compared to vectors driven by a ubiquitous promoter. To test this hypothesis, four AAV vectors that drive expression of a highly immunogenic membrane-bound ovalbumin (mOVA) were constructed. These vectors differ in their promoter sequences which includes: a) a ubiquitous CAG promoter (SEQ ID NO:25) b) the liver-specific hAAT promoter with upstream ApoE enhancer), the muscle-specific CK8 promoter cassette composed of the CK core promoter and three copies of a modified MCK enhancer (SEQ ID NO:90), and d) liver-muscle tandem promoter 6 (LMTP6, SEQ ID NO:71) that contains sequence elements derived from hAAT and CK8. Initial experiments will measure the immune response following intravenous (IV) vector administration within mice. Study endpoints will include characterization of humoral and cell-mediated immune responses against the mOVA transgene product. In addition, tissues will be harvested for vector biodistribution and transgene expression analysis.
Plasma kinetics of therapeutic antibody expression in non-human primates administered AAV vectors encoding therapeutic antibody antibodies were assessed. The goal of this study was to assess and select the dose of AAV8.ApoE.hAAT.Lan vector that results in sustained therapeutic antibody expression of at least 200 μg/ml therapeutic antibody by three months or more. The cynomolgus monkey were chosen as the test system because of its established usefulness and acceptance as a model for AAV biodistribution studies in a large animal species and for further translation to human. All animals on this study were naïve with respect to prior treatment.
Nine cynomolgus animals were used. Animals judged suitable for experimentation based on clinical sign data and prescreening antibody titers were placed in three study groups, each receiving a different dosage of AAV vector, by body weight using computer-generated random numbers. Each set of three animals were administered a single i.v. dose of the vector AAV8.ApoE.hAAT.Lan vector (described above) at the dose of 1E12 gc/kg (Group 1), 1E13 gc/kg (Group 2), and 1E14 gc/kg (Group 3).
Clinical signs were recorded at least once daily beginning approximately two weeks prior to initiation of dosing and continuing throughout the study period. The animals were observed for signs of clinical effects, illness, and/or death. Additional observations were recorded based upon the condition of the animal at the discretion of the Study Director and/or technicians.
Blood samples were collected from a peripheral vein for bioanalytical analysis prior to dose administration and then at weekly intervals for 10 weeks. The samples were collected in clot tubes and the times were recorded. The tubes were maintained at room temperature until fully clotted, then centrifuged at approximately 2400 rpm at room temperature for 15 minutes. The serum was harvested, placed in labeled vials, frozen in liquid nitrogen, and stored at −60° C. or below.
All animals were sedated with 8 mg/kg of ketamine HCl IM, maintained on an isoflurane/oxygen mixture and provided with an intravenous bolus of heparin sodium, 200 IU/kg. The animals were perfused via the left cardiac ventricle with 0.001% sodium nitrite in saline.
As primary endpoint analysis, plasma samples were assayed for therapeutic antibody concentration by ELISA and/or western blot, to be reported at least as μg therapeutic antibody per ml plasma; and therapeutic antibody activity, for example, kallikrein inhibition, by fluorogenic assay.
The presence of antibodies against therapeutic antibody (ADAs) in the serum were evaluated by ELISA and therapeutic antibody binding assays. Biodistribution of the vector and therapeutic antibody coding transcripts were assessed in necroscopy samples by quantitative PCR and NGS methods. Tissues to be assayed included liver, muscle, and heart. Toxicity assessment was done by full pathology, including assaying liver enzymes, urinalysis, cardiovascular health, and more.
The optimized expression cassette containing a liver-specific promoter and a codon optimized and CpG depleted transgene with a modified furin-T2A processing signal resulted in dose-dependent serum antibody concentrations when delivered intravenously using an AAV8 vector. Sustained levels of functional anti-kallikrein antibody were achieved in the serum of 7 out of 9 cynomolgus monkeys following IV vector administration at all three doses (1E12 gc/kg, 1E13 gc/kg, and 1E14 gc/kg)). Functional anti-kallikrein antibody was detected in the serum of all animals regardless of the administered dose. A plateau was reached at 29 days after dose administration with mean maximum levels of 0.144 μg/mL, 0.635 μg/mL, and 35.16 μg/mL being detected in animals 29 days after receiving 1E12 gc/kg, 1E13 gc/kg, and 1E14 gc/kg, respectively.
The optimized expression cassette containing either a ubiquitous CAG promoter or liver/muscle dual-specific promoters LMTP6 or LMPT24, and a codon optimized and CpG-depleted transgene with a modified furin-T2A processing sequence (SEQ ID NO: 86) encoding for CGRP or CGRP-R antibody (See Table 9 for nucleotide sequences) will be screened in animals (rats and NHPs) for serum antibody concentrations. Vector is delivered intravenously or intramuscularly using an AAV9 vector. The dose can be adjusted and will be in the range of 1e10 to 1e14. The volume injected is approximately 1 μl but may be a range of 0.1 μl to 3 μl depending upon the dose and concentration. Sustained levels of functional anti-CGRP or CGRP-R antibody via different routes of administration will be measured by ELISA to elucidate levels achieved in the serum and compared to functional outcomes in the brain. To that end, each anti-CGRP and anti-CGRP-R antibody will be analyzed in the brain by capsaicin-induced dermal blood flow measured by laser doppler imaging. The ‘capsaicin model’ is considered a target engagement biomarker, which is also used as a human model for the development of CGRP blocking therapeutics. By applying capsaicin onto the skin, Transient Receptor Potential Vanilloid subtype 1 (TRPV1) channels are activated and a CGRP-mediated increase in dermal blood flow can be quantified with laser Doppler perfusion imaging. Effective CGRP blocking therapeutics in turn, display blockade of this response (Buntinx, et al. 2015, Br J Clin Pharmacol. 80(5): 992-1000. Published online 2015 Oct. 6. doi: 10.1111/bcp.12704). Sufficient serum levels of antibody to cross the blood brain barrier will achieve therapeutic levels upon observation of a blockade of the TRPV1 response.
Although the invention is described in detail with reference to specific embodiments thereof, it will be understood that variations which are functionally equivalent are within the scope of this invention. Indeed, various modifications of the invention in addition to those shown and described herein will become apparent to those skilled in the art from the foregoing description and accompanying drawings. Such modifications are intended to fall within the scope of the appended claims. 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. Such equivalents are intended to be encompassed by the following claims.
All publications, patents and patent applications mentioned in this specification are herein incorporated by reference into the specification to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated herein by reference in their entireties.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US21/57155 | 10/28/2021 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 63106854 | Oct 2020 | US |
