WO2023133574A1 - Compositions and methods useful for treatment of c9orf72-mediated disorders - Google Patents

Compositions and methods useful for treatment of c9orf72-mediated disorders Download PDF

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WO2023133574A1
WO2023133574A1 PCT/US2023/060354 US2023060354W WO2023133574A1 WO 2023133574 A1 WO2023133574 A1 WO 2023133574A1 US 2023060354 W US2023060354 W US 2023060354W WO 2023133574 A1 WO2023133574 A1 WO 2023133574A1
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sequence
c9orf72
mirna
aav
certain embodiments
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Christian HINDERER
James M. Wilson
Eileen WORKMAN
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The Trustees Of The University Of Pennsylvania
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
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    • C—CHEMISTRY; METALLURGY
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    • C12N2506/00—Differentiation of animal cells from one lineage to another; Differentiation of pluripotent cells
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    • C12N2750/00011—Details
    • C12N2750/14011—Parvoviridae
    • C12N2750/14111—Dependovirus, e.g. adenoassociated viruses
    • C12N2750/14141—Use of virus, viral particle or viral elements as a vector
    • C12N2750/14143—Use of virus, viral particle or viral elements as a vector viral genome or elements thereof as genetic vector

Definitions

  • ALS Amyotrophic lateral sclerosis
  • FDD frontotemporal dementia
  • FTD is the second most common form of early-onset dementia, manifesting as frontal and/or temporal lobe atrophy, accompanied by personality and behavioral changes as well as language dysfunction. In fact, a proportion of patients with FTD also develop ALS.
  • TDP-43 ubiquitin-positive tau-negative inclusion bodies
  • ALS and FTD present significant clinical, genetic, and histopathological overlaps; therefore, they are considered as two extremes of the same disease continuum.
  • Viral and non-viral vectors and compositions useful for treating patients having symptoms associated with defects in human C9ORF72 expression and/or patients having ALS or FTD, are provided herein.
  • a recombinant adeno-associated virus comprising an AAV capsid and a vector genome.
  • the rAAV comprises: (a) an engineered nucleic acid sequence encoding human C9orf72; (b) a spacer sequence located between (a) and (c); (c) a nucleic acid sequence encoding at least one miRNA sequence specific for endogenous human C9orf72 in an ALS or FTD patient located 3’ to the sequence of (a) and (b); wherein the engineered nucleic acid sequence of (a) lacks the target site for the encoded at least one miRNA, thereby preventing the encoded miRNA from targeting the engineered human C9orf72 coding sequence; and (c) regulatory sequences operably linked to (a) and (c).
  • the AAV capsid is selected from AAV9, AAVhu68, AAV1 or AAVrh91.
  • the spacer is 75 nucleotides to about 250 nucleotides in length.
  • a vector is provided which comprises an engineered human C9orf72 coding sequence operably linked to regulatory sequences which direct expression thereof in a human target cell.
  • a vector is provided which comprises a nucleic acid sequence encoding at least one hairpin miRNA, wherein the encoded miRNA is specific for endogenous human C9orf72 in a human subject operably linked to regulatory sequences which direct expression thereof in the subject.
  • a vector or other composition comprises both the engineered human C9orf72 coding sequence and the at least one miRNA coding sequence.
  • the engineered C9orf72 coding sequence lacks the target site for the at least one miRNA, thereby preventing the miRNA from targeting the engineered human C9orf72 coding sequence.
  • the vector is a replication-defective viral vector which comprises a vector genome comprising the human C9orf72 coding sequences, the coding sequence for the at least one miRNA and the regulatory sequences.
  • the viral vector is a recombinant adeno-associated virus (rAAV) particle having an AAV capsid which has the packaged therein the vector genome.
  • the AAV capsid is AAVhu68, AAV1 or AAVrh91.
  • a vector which comprises a engineered C9orf72 coding sequence has the nucleic acid sequence of SEQ ID NO: 13 or a sequence at least 90% identical thereto, provided that the nucleic acid sequences targeted by the encoded miRNA are different from the endogenous human C9orf72 sequence.
  • the composition comprises a recombinant nucleic acid sequence encoding an engineered human C9orf72 coding sequence operably linked to regulatory sequences which direct expression thereof in a human target cell and a nucleic acid sequence encoding at least one miRNA specific for endogenous human C9orf72 in a patient operably linked to regulatory sequences which direct expression thereof in the subject, wherein the engineered C9orf72 coding sequence lacks a target site for the encoded at least one miRNA, thereby preventing the miRNA from targeting the engineered C9orf72 coding sequence.
  • a pharmaceutical composition comprising the vector, rAAV, or a composition, and a pharmaceutically acceptable aqueous suspending liquid, excipient, and/or diluent.
  • a method for treating a patient having a C9orf72-associated disorder comprising delivering an effective amount of the vector, a recombinant AAV, or a composition to a patient in need thereof.
  • a C9orf72-associated disorder e.g., ALS or FTD
  • a combination regimen for treating a patient having a C9orf72- associated disorder comprises co-administering (a) a recombinant nucleic acid sequence encoding an engineered human C9orf72 coding sequence operably linked to regulatory sequences which direct expression thereof in a human target cell, wherein the human c9orf72 coding sequence has the sequence of SEQ ID NO: 13 or a sequence at least 95% identical thereto and which differs from endogenous human c9 in the patient by having a mismatch in the miRNA target sequence of (b), (b) at least one miRNA specific for an endogenous human c9 sequence in a human subject, wherein the mRNA is operably linked to regulatory sequences which direct expression thereof in the subject.
  • FIGs 1A to ID provide qPCR results from spinal cord of 11-14 week old mice (09 LI 12 Het) injected (iv-tail vein) with a 3 x 10 11 GC/100 pl of rAAV-PHP.eb- CB7.CLC9miR.WPRE.rBG, the miR is NT or PBS, miR487, miR32, or miR32-101.
  • FIG1A provides the results in spinal cord for a C9 intron spliced primer.
  • FIG IB provides the results in spinal cord for C9 intron retained primers.
  • FIGs 1C and ID provide qPCR results from brain for C9 intron spliced primers (FIG 1C) or C9 intron retained primers (FIG ID).
  • FIGs 2A-2D provides the results of DPR protein pathology assessment in a poly(GP) Meso Scale Discovery (MSD)-Immunoassay, soluble fraction.
  • MSD Meso Scale Discovery
  • C57BL/6J- Tg(C9orf72_i3)l 12Lutzy/J (JR: 023099) mice show significant increases in poly(GP) soluble fraction in brain lysates: at 1, and 3 months of age and spinal cord lysate: at 12 months of age compared to NCAR, controls.
  • As mice age decrease of DPRs in the soluble fraction in mice in brain as observed in (GrC2)149 mice. Data represented as mean ⁇ SD.
  • FIG 2A shows (G4C2) 149 mice show significant increases in poly(GP) soluble fraction in brain lysates at 6, 9 & 12 months of age compared to (0462)149 controls.
  • FIGs 2B and 2C show that as mice age, decrease of DPRs in the soluble fraction in (6462)149 mice is expected (FIG 2B), as they accumulate in the insoluble fraction (FIG 26).
  • FIG 3 provides a survival curve with percent survival graphed over age in weeks to 14 weeks for various groups of wild-type control (WT/NGAR) female or male mice or Hemizygous/TG mice receiving PBS only (VEH) or receiving 3x10 11 one of two different rAAV:
  • AAV-1 is an AAV PHP.eB capsid with a vector genome of GB7.GI.69miR487.WPRE.rBG
  • AAV-2 is an AAV PHP.eB capsid with a vector genome of GB7.GI.G9miR487.WPRE.rBG, via tail vein injection at 4 weeks of age.
  • FIG 4 provides body weights by group (male and female together) from the animals study described in FIG 3, as studied from inception (4 weeks of age) through termination.
  • FIG 5 provides body weights for the females by group from the animals study described in FIG 3, as studied from inception (4 weeks of age) through termination.
  • FIG 6 provides body weights for the males by group from the animals study described in FIG 3, as studied from inception (4 weeks of age) through termination.
  • FIGs 7A and 7B provides the poly(GP) response in brain for a wild-type mouse (WT/N CAR vehicle) (Group 1), hemizygous/TG mice receiving PBS only (Vehicle) and two treatment groups receiving 3xl0 n one of two different rAAV: AAV-1 is an AAV PHP.eB capsid with a vector genome of CB7.CI.C9miR487.WPRE.rBG and AAV-2 is an AAV PHP.eB capsid with a vector genome of CB7.CI.C9miR487.WPRE.rBG, via tail vein injection at 4 weeks of age.
  • FIG 7A is corrected for background and FIG 7B is uncorrected for background.
  • Sequences, vectors and compositions are provided here for co-administering to a patient a nucleic acid sequence which expresses human c9orf72 protein and a nucleic acid sequence encoding at least one miRNA which specifically targets a site in the endogenous hexanucleotide repeat expansion in the first intron of the human C9orf72 gene which target site is not present on the engineered C9orf72 coding sequence.
  • the engineered c9orf72 coding sequence is engineered to remove the specific target site for the miRNA.
  • Novel engineered C9orf72 and novel miRNA target sequences are provided herein. These may be used alone or in combination with each other and/or other therapeutics for the treatment of C9orf72-associated ALS, FTD, and related disorders.
  • endogenous C9orf72 refers to the C9orf72 gene (chromosome 9 open reading frame 72) which encodes the C9 protein in humans.
  • the human C9orf72 gene is located on the short (p) arm of chromosome 9 open reading frame 72, from base pair 27,546,546 to base pair 27,573,866 (GRCh38). Its cytogenetic location is at 9p21. 2.
  • the protein has less than 100% identity to the amino acid sequence of SEQ ID NO: 14 may be delivered by the compositions provided herein (e.g., an ORF a protein having 97% to 100% identity to SEQ ID NO: 14).
  • an engineered C9orf72 coding sequence which has the nucleic acid sequence of SEQ ID NO: 13 or a sequence of about 90%, at least 95% identical, at least 97% identical, at least 98% identical, or 99% to 100% identical to SEQ ID NO: 13 and which expresses the human C9 protein found in non-C9orf72-associated ALS and FTD patients. See, e.g., SEQ ID NO: 14.
  • an engineered C9orf72 coding sequence which has the nucleic acid sequence of SEQ ID NO: 13 or a sequence at least 90% identical when the engineered coding sequence is co-administered with the miR487 sequence comprising at least a 5’ flanking region, at least SEQ ID NO: 15 (miR487) or a sequence at least 99% identical to SEQ ID NO: 15, and a 3’ flanking region, wherein the at least one miRNA does not bind to the engineered C9orf72 coding sequence of (a) or its encoded messenger RNA (mRNA).
  • the 5’ flank is selected from a sequence of SEQ ID NO: 5 or SEQ ID NO: 22.
  • the sequence having identity to SEQ ID NO: 13 expresses the same protein.
  • a “5’ UTR” is upstream of the initiation codon for a gene product coding sequence.
  • the 5’ UTR is generally shorter than the 3’ UTR.
  • the 5’ UTR is about 3 nucleotides to about 200 nucleotides in length, but may optionally be longer.
  • a “3 ’ UTR” is downstream of the coding sequence for a gene product and is generally longer than the 5’ UTR. In certain embodiments, the 3’ UTR is about 200 nucleotides to about 800 nucleotides in length, but may optionally be longer or shorter.
  • RNA refers to a microRNA which is a small non-coding RNA molecule which regulates mRNA and stops it from being translated to protein.
  • hairpin-forming RNAs have a self-complementary “stem-loop” structure that includes a single nucleic acid encoding a stem portion having a duplex comprising a sense strand (e.g., passenger strand) connected to an antisense strand (e.g., guide strand) by a loop sequence.
  • the passenger strand and the guide strand share complementarity. In some embodiments, the passenger strand and guide strand share 100% complementarity.
  • the passenger strand and guide strand share at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or at least 99% complementarity.
  • a passenger strand and a guide strand may lack complementarity due to a base-pair mismatch.
  • the passenger strand and guide strand of a hairpin-forming RNA have at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7 at least 8, at least 9, or at least 10 mismatches.
  • the first 2-8 nucleotides of the stem are referred to as “seed” residues and play an important role in target recognition and binding.
  • the miRNA contains a “seed sequence” which is a region of nucleotides which specifically binds to mRNA (e.g., in the endogenous C9orf72) by complementary base pairing, leading to destruction or silencing of the mRNA. Such silencing may result in downregulation rather than complete extinguishing of the endogenous hC9orf72.
  • the term “miRNA” encompasses artificial microRNA (amiRNA), which are artificially designed.
  • a “self-complementary nucleic acid” refers to a nucleic acid capable of hybridizing with itself (i.e., folding back upon itself) to form a single-stranded duplex structure, due to the complementarity (e.g., base-pairing) of the nucleotides within the nucleic acid strand.
  • Self- complementary nucleic acids can form a variety of secondary structures, such as hairpin loops, loops, bulges, junctions and internal bulges.
  • Certain self-complementary nucleic acids e.g., miRNA or AmiRNA perform regulatory functions, such as gene silencing.
  • the encoded miRNA provided herein have been designed to specifically target the endogenous human C9orf72 gene in patients having a C9ORF72-associated disorder such as ALS or FTD.
  • the miRNA coding sequence comprises an anti-sense sequence.
  • the seed sequence is 100% identical to the antisense sequence describe in the table.
  • the seed sequence is located on the mature miRNA (5’ to 3’) and is generally starts at position 2 to 7, 2 to 8, or about 6 nucleotides from the 5’ end of the miRNA sense strand (from the 5’ end of the sense (+) strand) of the miRNA, although it may be longer than in length.
  • the length of the seed sequence is no less than about 30% of the length of the miRNA sequence, which may be at least 7 nucleotides to about 28 nucleotides in length, at least 8 nucleotides to about 28 nucleotides in length, 7 nucleotides to 28 nucleotides, 8 nucleotides to 18 nucleotides, 12 nucleotides to 28 nucleotides in length, about 20 to about 26 nucleotides, about 21 nucleotides, about 24 nucleotides, or about 26 nucleotides.
  • the miRNA is delivered in the form of a stem-loop miRNA precursor sequences, e.g., about 50 to about 80 nucleotides in length, or about 55 nucleotides to about 70 nucleotides, or 60 to 65 nucleotides in length.
  • this miRNA precursor comprises about 5 nucleotides, about a 21 -nucleotide seed sequence, about a 19 nucleotide stem loop and about a 19 nucleotide sense sequence, wherein the sense sequence corresponds to the anti-sense sequence with one or two nucleotides being mismatched.
  • miRNA coding sequence is the miR487 sequence (see, e.g., in the vector genome of SEQ ID NO: 17: The 5’ flank (nt 3438)..(nt 3460) (1-23 of SEQ ID NO: 5), miR487 (nt 3461)..(nt 3524), antisense (nt 3466)..(nt 3486), loop (nt 3487)..(nt 3505), sense (nt 3506)..(nt 3524), and 3’ flank (nt 3525).. (nt 3568). See, also SEQ ID NO:9.
  • the nucleic acid molecules may contain at least one, or more than one miRNA coding sequence.
  • the nucleic acid molecules e.g., an expression cassette or vector genome
  • the nucleic acid molecules e.g., an expression cassette or vector genome
  • an “miRNA target sequence” is a sequence located on the DNA positive strand (5’ to 3’) (e.g., of C9orf72) and is at least partially complementary to a miRNA sequence, including the miRNA seed sequence.
  • the miRNA target sequence is exogenous to the untranslated region of the encoded transgene product and is designed to be specifically targeted by miRNA in cells in which repression of transgene expression is desired.
  • the miRNA preferentially target the endogenous hC9orf72 gene while avoiding targeting the engineered hC9orf72 gene which is delivered to the patient. More particularly, the sequences encoding the hC9orf72 which are delivered via a vector are designed to contain altered codon sequences at the target site.
  • the miRNA target sequence is at least 7 nucleotides to about 28 nucleotides in length, at least 8 nucleotides to about 28 nucleotides in length, 7 nucleotides to 28 nucleotides, 8 nucleotides to 18 nucleotides, 12 nucleotides to 28 nucleotides in length, about 20 to about 26 nucleotides, about 22 nucleotides, about 24 nucleotides, or about 26 nucleotides, and which contains at least one consecutive region (e.g., 7 or 8 nucleotides) which is complementary to the miRNA seed sequence.
  • at least one consecutive region e.g., 7 or 8 nucleotides
  • the target sequence comprises a sequence with exact complementarity (100%) or partial complementarity to the miRNA seed sequence with some mismatches. In certain embodiments, the target sequence comprises at least 7 to 8 nucleotides which are 100% complementary to the miRNA seed sequence. In certain embodiments, the target sequence consists of a sequence which is 100% complementary to the miRNA seed sequence. In certain embodiments, the target sequence contains multiple copies (e.g., two or three copies) of the sequence which is 100% complementary to the seed sequence. In certain embodiments, the region of 100% complementarity comprises at least 30% of the length of the target sequence. In certain embodiments, the remainder of the target sequence has at least about 80 % to about 99% complementarity to the miRNA. In certain embodiments, in an expression cassette containing a DNA positive strand, the miRNA target sequence is the reverse complement of the miRNA.
  • sequences provided herein which are 95% to 99.9% identical to the mutant C9 coding sequences of SEQ ID NO: 13, are designed to avoid reverting to a native human sequence to which a selected miRNA in the construct is targeted.
  • these sequence encode native functional human C9 protein which is not associated with any disorder.
  • the protein may have the sequence of SEQ ID NO: 14 or a sequence about 95 to about 100% identical, or at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 14.
  • the miRNA preferentially targets the endogenous hC9 gene while avoiding targeting the engineered hc9 gene, wherein the endogenous C9orf72 isoform 2 nucleic acid sequence is reproduced in SEQ ID NO: 44 and the encoded protein is reproduced in SEQ ID NO: 45.
  • the miRNA coding sequence comprises one or more of : (i) 15 or 16.
  • the engineered hC9 nucleic acid sequence is of SEQ ID NO: 13.
  • the engineered hC9 nucleic acid sequence is of SEQ ID NO: 13 wherein 1, 2, 3, or 4 nucleotide mismatches are present.
  • a single nucleic acid (e.g., an expression cassette or vector genome containing same) contains both the engineered hC9 coding sequence and at least one miRNA coding sequence, wherein the miRNA is specifically targeted to a region of the endogenous human C9 sequence not present in the engineered hC9 sequence.
  • the human C9 coding sequence is upstream (5’) of the at least one miRNA and these two elements are separated by a spacer or linker sequence.
  • the spacer is about 75 nucleotides to about 300 nucleotides, or about 75 nucleotides to about 250 nucleotides, or about 75 nucleotides to about 200 nucleotides, or about 75 nucleotides to about 150 nucleotides, or about 75 nucleotides to about 100 nucleotides, or about 80 nucleotides to about 300 nucleotides, or about 80 nucleotides to about 250 nucleotides, or about 80 nucleotides to about 200 nucleotides, or about 80 nucleotides to about 150 nucleotides, or about 80 nucleotides to about 100 nucleotides,.
  • the engineered hC9 coding sequence and the at least one miRNA coding sequence are separated by about 75 nucleotides.
  • the spacer sequence is a non-coding sequence which lacks any restriction enzyme sites.
  • the spacer may include one or more intron sequences.
  • one or more of the miRNA sequences may be located within the intron.
  • the engineered hC9 coding sequence and the miRNA coding sequence(s) are delivered via different nucleic acid sequences, e.g., two or more different vectors, a combination comprising a vector and an LNP, etc.
  • the two different vectors are AAV vectors.
  • these vectors have different expression cassettes.
  • these vectors have the same capsid.
  • the vectors have different embodiments.
  • the miRNA coding sequence(s) are delivered via an LNP or another non-viral delivery system.
  • the engineered hC9 sequence is delivered via an LNP or another non-viral delivery system.
  • combinations of two or more different delivery systems are used.
  • the two or more different vectors or other delivery systems may be administered substantially simultaneously, or one or more of these systems may be delivered before the other.
  • the engineered hC9 sequence is SEQ ID NO: 13, or a sequence 90% to 100% identical thereto which encodes an mRNA which is not bound by the miR with which it is co-administered and which encodes functional human C9orf72.
  • AAV ,C9orf72 or “rAAV.h9ORF72” are used to refer to a recombinant adeno-associated virus which has an AAV capsid having therewithin a vector genome comprising a human C9orf72 coding sequence (e.g., a cDNA) under the control of regulatory sequences.
  • a human C9orf72 coding sequence e.g., a cDNA
  • AAV.C9orf72.miRXXX or “rAAV.C9orf72.miRXXX” are used to refer to a recombinant adeno-associated virus which has an AAV capsid having therewithin a vector genome comprising an miR targeting an endogenous human C9ORF72 coding sequence.
  • capsid types may be specified, such as, e.g., AAV.C9orf72 or rAAVl.C9orf72, which refers to a recombinant AAV having an AAV1 capsid; AAVhu68.C9orf72 or AAVhu68.C9orf72, which refers to recombinant AAV having an AAVhu68 capsid. AAVrh91.C9orf72 or AAVrh91.C9orf72, which refers to recombinant AAV having an AAVrh91 capsid.
  • a “recombinant AAV” or “rAAV” is a DNAse-resistant viral particle containing two elements, an AAV capsid and a vector genome containing at least non-AAV coding sequences packaged within the AAV capsid. Unless otherwise specified, this term may be used interchangeably with the phrase “rAAV vector”.
  • the rAAV is a “replication-defective virus” or “viral vector”, as it lacks any functional AAV rep gene or functional AAV cap gene and cannot generate progeny.
  • the only AAV sequences are the AAV inverted terminal repeat sequences (ITRs), typically located at the extreme 5’ and 3’ ends of the vector genome in order to allow the gene and regulatory sequences located between the ITRs to be packaged within the AAV capsid.
  • ITRs AAV inverted terminal repeat sequences
  • an AAV capsid is composed of 60 capsid (cap) protein subunits, VP1, VP2, and VP3, that are arranged in an icosahedral symmetry in a ratio of approximately 1: 1: 10 to 1: 1:20, depending upon the selected AAV.
  • Various AAVs may be selected as sources for capsids of AAV viral vectors as identified above.
  • the AAV capsid is an AAV9 capsid or an engineered variant thereof.
  • the variant AAV9 capsid is an AAV9.PhP.eB capsid.
  • the PhP.eB capsid is selected for use in mouse studies and is a suitable model for a clade F vector (e.g., AAVhu68) in humans.
  • the capsid protein is designated by a number or a combination of numbers and letters following the term “AAV” in the name of the rAAV vector.
  • the AAV capsid, ITRs, and other selected AAV components described herein may be readily selected from among any AAV, including, without limitation, the AAVs identified as AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAVrhlO, AAVhu37, AAVrh32.33, AAV8bp, AAV7M8 and AAVAnc80, AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9.47, AAV9(hul4), AAV10, AAV11, AAV12, AAVrh8, AAVrh74, AAV-DJ8, AAV-DJ, AAVhu68, AAV9 variants (e.g., PCT/US21/61312, filed December 1, 2021 and US Provisional Application No.
  • AAV9 variants e.g., PCT/US21/61312, filed December 1, 2021 and US Provisional Application No.
  • the capsid has two encoded amino acid differences as compared to another Clade F capsid, AAV9, with differences at positions 67 and 157, based on the numbering of the VP1 protein, shown in SEQ ID NO: 34 (see, SEQ ID NO: 32 and 33 for nucleotide sequence).
  • the other Clade F AAV AAV9, hu31, hu31
  • an AAVhu68 capsid is further characterized by one or more of the following.
  • AAVhu68 capsid proteins comprise: AAVhu68 vpl proteins produced by expression from a nucleic acid sequence which encodes the amino acid sequence of 1 to 736 of SEQ ID NO: 34, vpl proteins produced from SEQ ID NO: 32 or 33, or vpl proteins produced from a nucleic acid sequence at least 70% identical to SEQ ID NO: 33 which encodes the predicted amino acid sequence of 1 to 736 of SEQ ID NO: 34;
  • an AAVhu68 capsid comprises: (i) heterogenous populations of AAVhu68 vpl proteins, AAVhu68 vp2 proteins, and AAVhu68 vp3 proteins produced from a nucleic acid sequence encoding SEQ ID NO: 34, wherein the AAVhu68vp 1 proteins comprise a glutamic acid at position 67 and a valine at position 157 and the AAVhu68vp2 proteins comprise a valine at position 157 based on the numbering of SEQ ID NO: 34; or (ii) heterogenous populations of AAVhu68 vpl, AAVhu68 vp2 and AAVhu68 vp3 proteins, wherein the AAVhu68 vpl proteins are amino acids 1 to 736 of SEQ ID NO: 34 (vpl) which comprise a glutamic acid at position 67 and a valine at position 157 and further comprise subpopulations of vpl proteins comprising modified amino acids
  • the AAVhu68 capsid comprises: (a) a subpopulation of vpl proteins in which 75% to 100% of the N at position 57 of the vpl proteins are deamidated, as determined using mass spectrometry; and/or (b) subpopulations of vpl proteins, vp2 proteins, and/or vp3 proteins in which 75% to 100% of the N at position 329, based on the numbering of SEQ ID NO:34, are deamidated as determined using mass spectrometry; and/or (c) subpopulations of vpl proteins, vp2 proteins, and/or vp3 proteins in which 75% to 100% of the N at position 452, based on the numbering of SEQ ID NO:34, are deamidated as determined using mass spectrometry; and/or (d) subpopulations of vpl proteins, vp2 proteins, and/or vp3 proteins in which 75% to 100% of the N at position 512, based on
  • suitable sequences may include, e.g., AAVhu95 [engineered VP1 nucleic acid sequence SEQ ID NO: 26; amino acid sequence SEQ ID NO: 1 and 35]; AAVhu96 [engineered AAVhu96 VP1 nucleic acid sequence, SEQ ID NO: 28; AAV hu96 VP1 amino acid sequence, SEQ ID NO: 29],
  • AAVrh90 [PCT/US20/30273, fded April 28, 2020]
  • AAVrh91 [see, SEQ ID NO: 37 and 38; PCT/US20/30266, filed April 28, 2020 and US Provisional Patent Applications No. 63/109,734, filed November 4, 2020 and US Provisional Patent Application No. 63/065,616, filed August 14, 2020]
  • AAVrh92, AAVrh93, AAVrh91.93 [PCT/US20/30281, filed April 28, 2020], which are incorporated by reference herein.
  • AAV3B variants which are described in PCT/US20/56511, filed October 20, 2020, describing AAV3B.AR2.01, AAV3B.AR2.02, AAV3B.AR2.03, AAV3B.AR2.04, AAV3B.AR2.05, AAV3B.AR2.06, AAV3B.AR2.07, AAV3B.AR2.08, AAV3B.AR2. 10, AAV3B.AR2. 11, AAV3B.AR2. 12, AAV3B.AR2. 13, AAV3B.AR2. 14, AAV3B.AR2. 15, AAV3B.AR2. 16, or AAV3B.AR2. 17, which are incorporated herein by reference.
  • AAV capsids which may be selected for generating rAAV and are incorporated by reference.
  • human AAV2 is the first AAV that was developed as a gene transfer vector; it has been widely used for efficient gene transfer experiments in different target tissues and animal models.
  • a “vector genome” refers to the nucleic acid sequence packaged inside a parvovirus (e.g., rAAV) capsid which forms a viral particle.
  • a nucleic acid sequence contains AAV inverted terminal repeat sequences (ITRs).
  • ITRs AAV inverted terminal repeat sequences
  • a vector genome contains, at a minimum, from 5’ to 3’, an AAV 5’ ITR, coding sequence(s) (i.e., transgene(s)), and an AAV 3’ ITR. ITRs from AAV2, a different source AAV than the capsid, or other than full-length ITRs may be selected.
  • the ITRs are from the same AAV source as the AAV which provides the rep function during production or a transcomplementing AAV.
  • ITRs e.g., self-complementary (scAAV) ITRs
  • scAAV self-complementary
  • Both single-stranded AAV and self-complementary (sc) AAV are encompassed with the rAAV.
  • the transgene is a nucleic acid coding sequence, heterologous to the vector sequences, which encodes a polypeptide, protein, functional RNA molecule (e.g., miRNA, miRNA inhibitor) or other gene product, of interest.
  • the nucleic acid coding sequence is operatively linked to regulatory components in a manner which permits transgene transcription, translation, and/or expression in a cell of a target tissue. Suitable components of a vector genome are discussed in more detail herein.
  • a “vector genome” contains, at a minimum, from 5’ to 3’, a vectorspecific sequence, a nucleic acid sequence comprising an engineered human C9orf72 coding sequence and optionally an miRNA sequences targeting the endogenous C9orf72 operably linked to regulatory control sequences (which direct their expression in a target cell), where the vector-specific sequence may be a terminal repeat sequence which specifically packages the vector genome into a viral vector capsid or envelope protein.
  • AAV inverted terminal repeats are utilized for packaging into AAV and certain other parvovirus capsids.
  • a composition which comprises an aqueous liquid suitable for intrathecal injection and a stock of vector (e.g., rAAV having a AAV capsid which preferentially targets cells in the central nervous system and/or the dorsal root ganglia (e.g., CNS, including, e.g., nerve cells (such as, pyramidal, purkinje, granule, spindle, and interneuron cells) and glia cells (such as astrocytes, oligodendrocytes, microglia, and ependymal cells), wherein the vector having an engineered hC9orf72 coding sequence and/or an at least one miRNA specific endogenous hC9orf72 for delivery to the central nervous system (CNS).
  • vector e.g., rAAV having a AAV capsid which preferentially targets cells in the central nervous system and/or the dorsal root ganglia (e.g., CNS, including, e.g
  • the composition comprising one or more vectors as described herein is formulated for sub-occipital injection into the cistema magna (intra- cistema magna).
  • the composition is administered via a computed tomography- (CT-) rAAV injection.
  • CT- computed tomography-
  • the composition is administered using Ommaya reservoir.
  • the patient is administered a single dose of the composition.
  • an “expression cassette” refers to a nucleic acid molecule which comprises a biologically useful nucleic acid sequence (e.g., a gene cDNA encoding a protein, enzyme or other useful gene product, mRNA, etc.) and regulatory sequences operably linked thereto which direct or modulate transcription, translation, and/or expression of the nucleic acid sequence and its gene product.
  • a biologically useful nucleic acid sequence e.g., a gene cDNA encoding a protein, enzyme or other useful gene product, mRNA, etc.
  • regulatory sequences operably linked thereto which direct or modulate transcription, translation, and/or expression of the nucleic acid sequence and its gene product.
  • “operably linked” sequences include both regulatory sequences that are contiguous or non-contiguous with the nucleic acid sequence and regulatory sequences that act in trans or cis nucleic acid sequence.
  • Such regulatory sequences typically include, e.g., one or more of a promoter, an enhancer, an intron, a Kozak sequence, a polyadenylation sequence, and a TATA signal.
  • the expression cassette may contain regulatory sequences upstream (5’ to) of the gene sequence, e.g., one or more of a promoter, an enhancer, an intron, etc., and one or more of an enhancer, or regulatory sequences downstream (3’ to) a gene sequence, e.g., 3’ untranslated region (3’ UTR) comprising a polyadenylation site, among other elements.
  • the regulatory sequences are operably linked to the nucleic acid sequence of a gene product, wherein the regulatory sequences are separated from nucleic acid sequence of a gene product by an intervening nucleic acid sequences, i.e., 5 ’-untranslated regions (5’UTR).
  • the expression cassette comprises nucleic acid sequence of one or more of gene products.
  • the expression cassette can be a monocistronic or a bicistronic expression cassette.
  • the term “transgene” refers to one or more DNA sequences from an exogenous source which are inserted into a target cell.
  • such an expression cassette can be used for generating a viral vector and contains the coding sequence for the gene product described herein flanked by packaging signals of the viral genome and other expression control sequences such as those described herein.
  • a vector genome may contain two or more expression cassettes.
  • expression cassette comprises the C9orf72 coding sequences and miRNA sequences targeting the endogenous C9orf72), promoter, and may include other regulatory sequences therefor, which cassette may be packaged into a vector (e.g., rAAV, lentivirus, retrovirus, etc.).
  • Recombinant parvoviruses are particularly well suited as vectors.
  • recombinant parvoviruses may contain an AAV capsid (or bocavirus capsid).
  • the capsid targets cells within the dorsal root ganglion and/or cells within the lower motor neurons and/or primary sensory neurons.
  • compositions provided herein may have a single rAAV stock which comprises an rAAV comprising an engineered hC9orf72 and an miRNA specifically targeting endogenous hC9orf72 in order to downregulate the endogenous hC9orf72 levels and to reduce any toxicity associated with overexpression of hC9orf72.
  • an rAAV may be comprise the hC9orf72 and may be co-administered with a different vector comprising an miRNA which downregulates endogenous hC9orf72.
  • an rAAV may be comprise the at least one miRNA which downregulates endogenous hC9orf72 and a second vector (or other composition) delivers the hC9orf72.
  • vectors generated using AAV capsids from Clade F can be used to produce vectors which target and express hC9orf72 in the CNS.
  • vectors generated using AAV capsids from Clade A e.g., AAV1, AAVrh91
  • other parvovirus or other AAV viruses may be suitable sources of AAV capsids.
  • An AAV 1 capsid refers to a capsid having AAV vp 1 proteins, AAV vp2 proteins and AAV vp3 proteins.
  • the AAV 1 capsid comprises a pre-determined ratio of AAV vpl proteins, AAV vp2 proteins and AAV vp3 proteins of about 1: 1: 10 assembled into a T1 icosahedron capsid of 60 total vp proteins.
  • An AAV1 capsid is capable of packaging genomic sequences to form an AAV particle (e.g., a recombinant AAV where the genome is a vector genome).
  • capsid nucleic acid sequences encoding the longest of the vp proteins, i.e., VP1 is expressed in trans during production of an rAAV having an AAV1 capsid are described in, e.g., US Patent 6,759,237, US Patent 7,105,345, US Patent 7,186,552, US Patent 8,637,255, and US Patent 9,567,607, which are incorporated herein by reference. See, also, WO 2018/168961, which is incorporated by reference.
  • AAV 1 is characterized by a capsid composition of a heterogenous population of VP isoforms which are deamidated as defined in WO 2018/160582, incorporated herein by reference in its entirety, based on the total amount of VP proteins in the capsid, as determined using mass spectrometry.
  • the AAV capsid is modified at one or more of the following positions, in the ranges provided below, as determined using mass spectrometry. Suitable modifications include those described in the paragraph above labelled modulation of deamidation, which is incorporated herein.
  • one or more of the following positions, or the glycine following the N is modified as described herein.
  • an AAV 1 mutant is constructed in which the glycine following the N at position 57, 383, 512 and/or 718 are preserved (i.e., remain unmodified).
  • the NG at the four positions identified in the preceding sentence are preserved with the native sequence.
  • an artificial NG is introduced into a different position than one of the positions as defined and identified in WO 2018/160582, incorporated herein by reference.
  • an AAVhu68 capsid refers to a capsid as defined in WO 2018/160582, incorporated herein by reference.
  • a rAAVhu68 has a rAAVhu68 capsid produced in a production system expressing capsids from an AAVhu68 nucleic acid.
  • the AAVhu68 nucleic acid sequence is SEQ ID NO: 32 or 33, encoding and for an amino acid sequence of SEQ ID NO 34.
  • the AAVhu68 nucleic acid sequence is SEQ ID NO: 32 or 33, encoding for an amino acid sequence of SEQ ID NO: 34.
  • the rAAVhu68 resulting from production using a single nucleic acid sequence vpl produces the heterogenous populations of vpl proteins, vp2 proteins and vp3 proteins. These subpopulations include, at a minimum, deamidated asparagine (N or Asn) residues. For example, asparagines in asparagine - glycine pairs are highly deamidated.
  • the vp2 and/or vp3 proteins may be expressed additionally or alternatively from different nucleic acid sequences than the vpl, e.g., to alter the ratio of the vp proteins in a selected expression system.
  • Genomic sequences which are packaged into an AAV capsid and delivered to a host cell are typically composed of, at a minimum, a transgene and its regulatory sequences, and AAV inverted terminal repeats (ITRs). Both single-stranded AAV and self-complementary (sc) AAV are encompassed with the rAAV.
  • the transgene is a nucleic acid coding sequence, heterologous to the vector sequences, which encodes a polypeptide, protein, functional RNA molecule (e.g., miRNA, miRNA inhibitor) or other gene product, of interest.
  • the nucleic acid coding sequence is operatively linked to regulatory components in a manner which permits transgene transcription, translation, and/or expression in a cell of a target tissue.
  • the AAV sequences of the vector typically comprise the cis-acting 5' and 3' inverted terminal repeat sequences (See, e.g., B. J. Carter, in “Handbook of Parvoviruses”, ed., P. Tijsser, CRC Press, pp. 155 168 (1990)).
  • the ITR sequences are about 145 bp in length.
  • substantially the entire sequences encoding the ITRs are used in the molecule, although some degree of minor modification of these sequences is permissible.
  • the ability to modify these ITR sequences is within the skill of the art. (See, e.g., texts such as Sambrook et al, “Molecular Cloning.
  • An example of such a molecule employed in the present invention is a “cis-acting” plasmid containing the transgene, in which the selected transgene sequence and associated regulatory elements are flanked by the 5' and 3' AAV ITR sequences.
  • the ITRs are the genetic elements responsible for the replication and packaging of the genome during vector production and are the only viral cis elements required to generate rAAV.
  • the ITRs are from an AAV different than that supplying a capsid.
  • ITRs from other AAV sources may be selected. Where the source of the ITRs is from AAV2 and the AAV capsid is from another AAV source, the resulting vector may be termed pseudotyped.
  • AAV vector genome comprises an AAV 5 ’ ITR, the nucleic acid sequences encoding the gene product(s) and any regulatory sequences, and an AAV 3’ ITR.
  • a self- complementary AAV is provided.
  • a shortened version of the 5’ ITR, termed AITR has been described in which the D-sequence and terminal resolution site (trs) are deleted.
  • the vector genome includes a shortened AAV2 ITR of 130 base pairs, wherein the external “a” element is deleted. The shortened ITR is reverted back to the wild-type length of 145 base pairs during vector DNA amplification using the internal A element as a template.
  • the full-length AAV 5’ and 3’ ITRs are used.
  • the vector in addition to the major elements identified above for the vector (e.g., an rAAV), the vector also includes conventional control elements necessary which are operably linked to the transgene in a manner which permits its transcription, translation and/or expression in a cell.
  • expression or “gene expression” refers to the process by which information from a gene is used in the synthesis of a functional gene product.
  • the gene product may be a protein, a peptide, or a nucleic acid polymer (such as an RNA, a DNA or a PNA).
  • regulatory sequence refers to nucleic acid sequences, such as initiator sequences, enhancer sequences, and promoter sequences, which induce, repress, or otherwise control the transcription of protein encoding nucleic acid sequences to which they are operably linked.
  • the regulatory control elements typically contain a promoter sequence as part of the expression control sequences, e.g., located between the selected 5’ ITR sequence and the coding sequence. In particularly desirable embodiments, a tissues specific promoter for the central nervous system is selected.
  • the promoter may be a neural cell promoter, e.g., gfaABC(l)D promoter (Addgene #50473)), or the human Syn promoter (the sequence is available from Addgene, Ref. #50465).
  • suitable promoters may include, e.g., constitutive promoters, regulatable promoters [see, e.g., WO 2011/126808 and WO 2013/04943], tissue specific promoters, or a promoter responsive to physiologic cues may be used may be utilized in the vectors described herein.
  • the promoter(s) can be selected from different sources, e.g., human cytomegalovirus (CMV) immediate-early enhancer/promoter, the SV40 early enhancer/promoter, the JC polymovirus promoter, myelin basic protein (MBP) or glial fibrillary acidic protein (GFAP) promoters, herpes simplex virus (HSV-1) latency associated promoter (LAP), rouse sarcoma virus (RSV) long terminal repeat (LTR) promoter, neuron-specific promoter (NSE), platelet derived growth factor (PDGF) promoter, hSYN, melanin-concentrating hormone (MCH) promoter, CBA, matrix metalloprotein promoter (MPP), and the chicken beta-actin promoter.
  • CMV human cytomegalovirus
  • MBP myelin basic protein
  • GFAP glial fibrillary acidic protein
  • HSV-1 herpes simplex virus
  • LAP rouse
  • a vector may contain one or more other appropriate transcription initiation, termination, enhancer sequences, efficient RNA processing signals such as splicing and polyadenylation (polyA) signals; sequences that stabilize cytoplasmic mRNA for example WPRE; sequences that enhance translation efficiency (i.e., Kozak consensus sequence); sequences that enhance protein stability; and when desired, sequences that enhance secretion of the encoded product.
  • RNA processing signals such as splicing and polyadenylation (polyA) signals
  • sequences that stabilize cytoplasmic mRNA for example WPRE sequences that enhance translation efficiency (i.e., Kozak consensus sequence); sequences that enhance protein stability; and when desired, sequences that enhance secretion of the encoded product.
  • An example of a suitable enhancer is the CMV enhancer.
  • Other suitable enhancers include those that are appropriate for desired target tissue indications.
  • the expression cassette comprises one or more expression enhancers.
  • the expression cassette contains two or more expression enhancers. These enhance
  • an enhancer may include a CMV immediate early (IE) enhancer.
  • an enhancer may include CMV IE enhancer (C4) comprising nucleic acid sequence of SEQ ID NO: 3. This enhancer may be present in two copies which are located adjacent to one another. Alternatively, the dual copies of the enhancer may be separated by one or more sequences.
  • the expression cassette further contains an intron, e.g., the chicken beta-actin intron.
  • an expression cassette comprises an intron which is a chicken beta actin intron comprising SEQ ID NO: 47.
  • suitable introns include those known in the art, e.g., such as are described in WO 2011/126808.
  • polyA sequences include, e.g., SV40, SV50, bovine growth hormone (bGH), human growth hormone, and synthetic polyAs.
  • the polyA is SV40 polyA.
  • the polyA is rabbit globin poly A (RBG).
  • the polyA is RBG polyA comprising SEQ ID NO: 10.
  • one or more sequences may be selected to stabilize mRNA.
  • An example of such a sequence is a modified WPRE sequence, which may be engineered upstream of the polyA sequence and downstream of the coding sequence [see, e.g., MA Zanta-Boussif, et al, Gene Therapy (2009) 16: 605-619.
  • the vector genome comprises a tissue specific promoter
  • the tissue specific promoter is a human synapsin promoter.
  • the human synapsin promoter comprises nucleic acid sequence of SEQ ID NO: 6.
  • the vector genome comprises a constitutive promoter, wherein the promoter is a CB7 promoter or a variant thereof, e.g., a CAG promoter.
  • CB7 or a variant thereof is a hybrid promoter (promoter element) comprising, at a minimum, a human cytomegalovirus (CMV) immediate early (IE) enhancer and a chicken [3- actin (CB or CBA) promoter.
  • a CB7 promoter or variant refers to a human cytomegalovirus (CMV) immediate early (IE) enhancer (C4), a chicken beta actin (CB) promoter, optionally an intron, and optional spacer sequences linking the elements of the hybrid promoter. See, e.g., chicken beta actin promoter with a cytomegalovirus enhancer.
  • a CB7 promoter or promoter element refers to a human cytomegalovirus (CMV) immediate early (IE) enhancer (C4), a chicken beta actin (CB) promoter, an intron, and optional spacer sequences linking the elements of the hybrid promoter.
  • a CB7 promoter or promoter element refers to a human cytomegalovirus (CMV) immediate early (IE) enhancer (C4), a chicken beta actin (CB) promoter, an intron which comprises chicken beta actin intron with rabbit beta globin splicing donor, and optional spacer sequences linking the elements of the hybrid promoter.
  • a CB7 promoter or promoter element refers to a human cytomegalovirus (CMV) immediate early (IE) enhancer (C4) (SEQ ID NO: 3), a chicken beta actin (CB) promoter (SEQ ID NO: 46), optionally an intron (SEQ ID NO: 47), and optional spacer sequences linking the elements of the hybrid promoter.
  • a CB7 promoter or promoter element refers to a human cytomegalovirus (CMV) immediate early (IE) enhancer (SEQ ID NO: 51), a chicken beta actin (CB) promoter (SEQ ID NO: 52), optionally an intron (SEQ ID NO: 53), and optional spacer sequences linking the elements of the hybrid promoter.
  • a CB7 promoter or promoter element comprises nucleic acid sequence of SEQ ID NO:4.
  • a CB7 promoter or promoter element comprises nucleic acid sequence of SEQ ID NO: 43.
  • a CB7 promoter or promoter element comprises nucleic acid sequence of SEQ ID NO: 48.
  • a CB7 promoter or promoter element comprises nucleic acid sequence of SEQ ID NO: 49. In certain embodiments, a CB7 promoter or promoter element comprises nucleic acid sequence of SEQ ID NO: 50.
  • the spacer sequences are non-coding and in certain embodiments, may be of different lengths.
  • the vector genome comprises: an AAV 5’ ITR, a promoter, an optional enhancer, an optional intron, a coding sequence for human C9orf72 (hC9orf72 or huC9orf72) comprising same, a poly A, and an AAV 3 ’ ITR.
  • the vector genome is an AAV2 5’ ITR, a CB7 promoter or variant thereof, an engineered C9orf72, a linker, a miR targeted to endogenous C9orf72 sequence, a rabbit beta globin poly A, and an AAV2 3’ ITR.
  • the vector genome is an AAV2 5’ ITR, a CB7 promoter or variant thereof, intron, C9orf72, a rabbit beta globin poly A, and an AAV2 3’ ITR.
  • the vector genome is an AAV2 5’ ITR, CB7 promoter or variant thereof, an engineered huC9orf72, a linker, a miR487 sequence, a rabbit beta globin poly A, and an AAV2 3’ ITR.
  • the huC9orf72 coding sequences are selected from those defined in the present specification. See, e.g., SEQ ID NO: 13 or a sequence at least 95% to 99.9% identical thereto, or a fragment thereof as defined herein.
  • other C9orf72 coding sequences may be combined with the miR487 provided herein.
  • Other elements of the vector genome or variations on these sequences may be selected for the vector genomes for certain embodiments of this invention.
  • the expression cassettes can be carried on any suitable vector, e.g., a plasmid, which is delivered to a packaging host cell.
  • a suitable vector e.g., a plasmid
  • the plasmids useful in this invention may be engineered such that they are suitable for replication and packaging in vitro in prokaryotic cells, insect cells, mammalian cells, among others. Suitable transfection techniques and packaging host cells are known and/or can be readily designed by one of skill in the art.
  • the production plasmid comprises a vector genome for packaging into a capsid which comprises: (a) an engineered nucleic acid sequence encoding human C9orf72; (b) a spacer sequence located between (a) and (c); (c) at least one miRNA sequence specific for endogenous human C9orf72 in a patient located 3’ to the sequence of (a) and (b); wherein the engineered nucleic acid sequence of (a) lacks the target site for the at least one miRNA, thereby preventing the miRNA from targeting the engineered human C9orf72 coding sequence; (c) regulatory sequences operably linked to (a) and (c).
  • the production plasmid comprises a vector genome comprising nucleic acid sequence of SEQ ID NO: 1, or an 5’ ITR - expression cassette of SEQ ID NO: 4 - 3’ ITR.
  • the expression cassettes described herein are engineered into a genetic element (e.g., a shuttle plasmid) which transfers the immunoglobulin construct sequences carried thereon into a packaging host cell for production a viral vector.
  • a genetic element e.g., a shuttle plasmid
  • the selected genetic element may be delivered to an AAV packaging cell by any suitable method, including transfection, electroporation, liposome delivery, membrane fusion techniques, high velocity DNA-coated pellets, viral infection and protoplast fusion. Stable AAV packaging cells can also be made.
  • the expression cassettes may be used to generate a viral vector other than AAV, or for production of mixtures of antibodies in vitro.
  • AAV intermediate or “AAV vector intermediate” refers to an assembled rAAV capsid which lacks the desired genomic sequences packaged therein. These may also be termed an “empty” capsid. Such a capsid may contain no detectable genomic sequences of an expression cassette, or only partially packaged genomic sequences which are insufficient to achieve expression of the gene product. These empty capsids are non-functional to transfer the gene of interest to a host cell.
  • the recombinant adeno-associated virus (AAV) described herein may be generated using techniques which are known. See, e.g., WO 2003/042397; WO 2005/033321, WO 2006/110689; US 7588772 B2.
  • AAV adeno-associated virus
  • Such a method involves culturing a host cell which contains a nucleic acid sequence encoding an AAV capsid protein; a functional rep gene; an expression cassette as described herein flanked by AAV inverted terminal repeats (ITRs) and a transgene; and sufficient helper functions to permit packaging of the expression cassette into the AAV capsid protein.
  • the host cell which contains a nucleic acid sequence encoding an AAV capsid; a functional rep gene; a vector genome as described; and sufficient helper functions to permit packaging of the vector genome into the AAV capsid protein.
  • the host cell is a HEK 293 cell.
  • a production cell culture useful for producing a recombinant AAV contains a nucleic acid which expresses the AAV capsid protein in the host cell; a nucleic acid molecule suitable for packaging into the AAV capsid, e.g., a vector genome which contains AAV ITRs and a non-AAV nucleic acid sequence encoding a gene product operably linked to sequences which direct expression of the product in a host cell; and sufficient AAV rep functions and adenovirus helper functions to permit packaging of the nucleic acid molecule into the recombinant AAV capsid.
  • the cell culture is composed of mammalian cells (e.g., human embryonic kidney 293 cells, among others) or insect cells (e.g., baculovirus).
  • the rep functions are from the same AAV source as the AAV providing the ITRs flanking the vector genome.
  • the AAV2 ITRs are selected and the AAV2 rep is used.
  • other rep sequences or another rep source may be selected.
  • the rep may be, but is not limited to, AAV1 rep protein, AAV2 rep protein; or rep 78, rep 68, rep 52, rep 40, rep68/78 and rep40/52; or a fragment thereof; or another source.
  • the rep and cap sequences are on the same genetic element in the cell culture. There may be a spacer between the rep sequence and cap gene. Any of these AAV or mutant AAV capsid sequences may be under the control of exogenous regulatory control sequences which direct expression thereof in a host cell.
  • cells are manufactured in a suitable cell culture (e.g., HEK 293) cells.
  • Methods for manufacturing the gene therapy vectors described herein include methods well known in the art such as generation of plasmid DNA used for production of the gene therapy vectors, generation of the vectors, and purification of the vectors.
  • the gene therapy vector is an AAV vector and the plasmids generated are an AAV cis-plasmid encoding the AAV genome and the gene of interest, an AAV trans-plasmid containing AAV rep and cap genes, and an adenovirus helper plasmid.
  • the vector generation process can include method steps such as initiation of cell culture, passage of cells, seeding of cells, transfection of cells with the plasmid DNA, post-transfection medium exchange to serum free medium, and the harvest of vector-containing cells and culture media.
  • the manufacturing process for rAAV.C9orf72.miR involves transient transfection of HEK293 cells with plasmid DNA.
  • a single batch or multiple batches are produced by PEI-mediated triple transfection of HEK293 cells in PALL iCELLis bioreactors.
  • Harvested AAV material are purified sequentially by clarification, TFF, affinity chromatography, and anion exchange chromatography in disposable, closed bioprocessing systems where possible.
  • the harvested vector-containing cells and culture media are referred to herein as crude cell harvest.
  • the gene therapy vectors are introduced into insect cells by infection with baculovirus-based vectors.
  • Zhang et al. 2009, “Adenovirus-adeno-associated virus hybrid for large-scale recombinant adeno-associated virus production,” Human Gene Therapy 20:922-929, the contents of each of which is incorporated herein by reference in its entirety. Methods of making and using these and other AAV production systems are also described in the following U.S.
  • the crude cell harvest may thereafter be subject to additional method steps such as concentration of the vector harvest, diafiltration of the vector harvest, microfluidization of the vector harvest, nuclease digestion of the vector harvest, filtration of microfluidized intermediate, crude purification by chromatography, crude purification by ultracentrifugation, buffer exchange by tangential flow filtration, and/or formulation and filtration to prepare bulk vector.
  • a two-step affinity chromatography purification at high salt concentration followed anion exchange resin chromatography are used to purify the vector drug product and to remove empty capsids. These methods are described in more detail in International Patent Application No. PCT/US2016/065970, filed December 9, 2016, which is incorporated by reference herein. Purification methods for AAV8, International Patent Application No. PCT/US2016/065976, filed December 9, 2016, and rhlO, International Patent Application No. PCT/US16/66013, filed December 9, 2016, entitled “Scalable Purification Method for AAVrhlO”, also filed December 11, 2015, and for AAV1, International Patent Application No. PCT/US2016/065974, filed December 9, 2016, for “Scalable Purification Method for AAV1”, filed December 11, 2015, are all incorporated by reference herein.
  • # of GC # of particles
  • the number of particles (pt) per 20 pL loaded is then multiplied by 50 to give particles (pt) /mL.
  • Pt/mL divided by GC/mL gives the ratio of particles to genome copies (pt/GC).
  • Pt/mL- GC/mL gives empty pt/mL.
  • Empty pt/mL divided by pt/mL and x 100 gives the percentage of empty particles.
  • the methods include subjecting the treated AAV stock to SDS-polyacrylamide gel electrophoresis, consisting of any gel capable of separating the three capsid proteins, for example, a gradient gel containing 3-8% Tris-acetate in the buffer, then running the gel until sample material is separated, and blotting the gel onto nylon or nitrocellulose membranes, preferably nylon.
  • Anti- AAV capsid antibodies are then used as the primary antibodies that bind to denatured capsid proteins, preferably an anti -AAV capsid monoclonal antibody, most preferably the B 1 anti- AAV-2 monoclonal antibody (Wobus et al., J. Virol. (2000) 74:9281-9293).
  • a secondary antibody is then used, one that binds to the primary antibody and contains a means for detecting binding with the primary antibody, more preferably an anti-IgG antibody containing a detection molecule covalently bound to it, most preferably a sheep anti-mouse IgG antibody covalently linked to horseradish peroxidase.
  • a method for detecting binding is used to semi- quantitatively determine binding between the primary and secondary antibodies, preferably a detection method capable of detecting radioactive isotope emissions, electromagnetic radiation, or colorimetric changes, most preferably a chemiluminescence detection kit.
  • a detection method capable of detecting radioactive isotope emissions, electromagnetic radiation, or colorimetric changes, most preferably a chemiluminescence detection kit.
  • samples from column fractions can be taken and heated in SDS- PAGE loading buffer containing reducing agent (e.g., DTT), and capsid proteins were resolved on pre-cast gradient polyacrylamide gels (e.g., Novex).
  • Silver staining may be performed using SilverXpress (Invitrogen, CA) according to the manufacturer's instructions or other suitable staining method, i.e., SYPRO ruby or coomassie stains.
  • the concentration of AAV vector genomes (vg) in column fractions can be measured by quantitative real time PCR (Q-PCR).
  • Samples are diluted and digested with DNase I (or another suitable nuclease) to remove exogenous DNA. After inactivation of the nuclease, the samples are further diluted and amplified using primers and a TaqManTM Anorogenic probe specific for the DNA sequence between the primers. The number of cycles required to reach a defined level of Auorescence (threshold cycle, Ct) is measured for each sample on an Applied Biosystems Prism 7700 Sequence Detection System. Plasmid DNA containing identical sequences to that contained in the AAV vector is employed to generate a standard curve in the Q-PCR reaction. The cycle threshold (Ct) values obtained from the samples are used to determine vector genome titer by normalizing it to the Ct value of the plasmid standard curve. End-point assays based on the digital PCR can also be used.
  • DNase I or another
  • an optimized q-PCR method which utilizes a broad-spectrum serine protease, e.g., proteinase K (such as is commercially available from Qiagen). More particularly, the optimized qPCR genome titer assay is similar to a standard assay, except that after the DNase I digestion, samples are diluted with proteinase K buffer and treated with proteinase K followed by heat inactivation. Suitably samples are diluted with proteinase K buffer in an amount equal to the sample size.
  • the proteinase K buffer may be concentrated to 2-fold or higher. Typically, proteinase K treatment is about 0.2 mg/mL, but may be varied from 0. 1 mg/mL to about 1 mg/mL.
  • the treatment step is generally conducted at about 55 °C for about 15 minutes, but may be performed at a lower temperature (e.g., about 37 °C to about 50 °C) over a longer time period (e.g., about 20 minutes to about 30 minutes), or a higher temperature (e.g., up to about 60 °C) for a shorter time period (e.g., about 5 to 10 minutes).
  • heat inactivation is generally at about 95 °C for about 15 minutes, but the temperature may be lowered (e.g., about 70 to about 90 °C) and the time extended (e.g., about 20 minutes to about 30 minutes). Samples are then diluted (e.g., 1000-fold) and subjected to TaqMan analysis as described in the standard assay.
  • droplet digital PCR may be used.
  • ddPCR droplet digital PCR
  • methods for determining single-stranded and self-complementary AAV vector genome titers by ddPCR have been described. See, e.g., M. Lock et al, Hu Gene Therapy Methods, Hum Gene Ther Methods. 2014 Apr;25(2): 115-25. doi: 10. 1089/hgtb.2013. 131. Epub 2014 Feb 14.
  • the method for separating rAAV particles having packaged genomic sequences from genome-deficient AAV intermediates involves subjecting a suspension comprising recombinant AAV viral particles and AAV capsid intermediates to fast performance liquid chromatography, wherein the AAV viral particles and AAV intermediates are bound to a strong anion exchange resin equilibrated at a high pH, and subjected to a salt gradient while monitoring eluate for ultraviolet absorbance at about 260 and about 280.
  • the pH may be adjusted depending upon the AAV selected.
  • the AAV full capsids are collected from a fraction which is eluted when the ratio of A260/A280 reaches an inflection point.
  • the diafiltered product may be applied to a Capture SelectTM Poros- AAV2/9 affinity resin (Life Technologies) that efficiently captures the AAV2 serotype. Under these ionic conditions, a significant percentage of residual cellular DNA and proteins flow through the column, while AAV particles are efficiently captured.
  • a “vector” as used herein is a biological or chemical moiety comprising a nucleic acid sequence which can be introduced into an appropriate target cell for replication or expression of said nucleic acid sequence.
  • a vector includes but not limited to a recombinant virus, a plasmid, Lipoplexes, a Polymersome, Polyplexes, a dendrimer, a cell penetrating peptide (CPP) conjugate, a magnetic particle, or a nanoparticle.
  • a vector is a nucleic acid molecule into which an exogenous or heterologous or engineered hC9orf72 coding sequence (and/or at least one miRNA) may be inserted, which can then be introduced into an appropriate target cell.
  • Such vectors preferably have one or more origin of replication, and one or more site into which the recombinant DNA can be inserted.
  • Vectors often have means by which cells with vectors can be selected from those without, e.g., they encode drug resistance genes.
  • Common vectors include plasmids, viral genomes, and "artificial chromosomes". Conventional methods of generation, production, characterization or quantification of the vectors are available to one of skill in the art.
  • the vector is a non-viral plasmid that comprises an expression cassette described thereof, e.g., “naked DNA”, “naked plasmid DNA”, RNA, mRNA, shRNA, RNAi, etc.
  • the plasmid or other nucleic acid sequence is delivered via a suitable device, e.g., via electrospray, electroporation.
  • the nucleic acid molecule is coupled with various compositions and nano particles, including, e.g., micelles, liposomes, cationic lipid - nucleic acid compositions, poly-glycan compositions and other polymers, lipid and/or cholesterol-based - nucleic acid conjugates, and other constructs such as are described herein.
  • a non-viral vector is used for delivery of an miRNA transcript targeting endogenous hC9orf72 at a site not present in the co-administered engineered hC9orf72 sequence.
  • the miRNA is delivered at an amount greater than about 0.5 mg/kg (e.g., greater than about 1.0 mg/kg, 1.5 mg/kg, 2.0 mg/kg, 2.5 mg/kg, 3.0 mg/kg, 4.0 mg/kg, 5.0 mg/kg, 6.0 mg/kg, 7.0 mg/kg, 8.0 mg/kg, 9.0 mg/kg, or 10.0 mg/kg) body weight of miRNA per dose.
  • the miRNA is delivered at an amount ranging from about 0.
  • the miRNA is delivered at an amount of or greater than about 1 mg, 5 mg, 10 mg, 15 mg, 20 mg, 25 mg, 30 mg, 35 mg, 40 mg, 45 mg, 50 mg, 55 mg, 60 mg, 65 mg, 70 mg, 75 mg, 80 mg, 85 mg, 90 mg, 95 mg, 100 mg, 150 mg, 200 mg, 250 mg, 300 mg, 350 mg, 400 mg, 450 mg, or 500 mg per dose.
  • miRNA transcripts are encapsulated in a lipid nanoparticle (LNP).
  • LNP lipid nanoparticle
  • the phrase "lipid nanoparticle” refers to a transfer vehicle comprising one or more lipids (e.g., cationic lipids, non- cationic lipids, and PEG-modified lipids).
  • the lipid nanoparticles are formulated to deliver one or more miRNA to one or more target cells (e.g., dorsal root ganglion, lower motor neurons and/or upper motor neurons, or the cell types identified above in the CNS).
  • lipids include, for example, the phosphatidyl compounds (e.g., phosphatidylglycerol, phosphatidylcholine, phosphatidylserine, phosphatidylethanolamine, sphingolipids, cerebrosides, and gangliosides). Also contemplated is the use of polymers as transfer vehicles, whether alone or in combination with other transfer vehicles.
  • phosphatidyl compounds e.g., phosphatidylglycerol, phosphatidylcholine, phosphatidylserine, phosphatidylethanolamine, sphingolipids, cerebrosides, and gangliosides.
  • polymers as transfer vehicles, whether alone or in combination with other transfer vehicles.
  • Suitable polymers may include, for example, polyacrylates, polyalkycyanoacrylates, polylactide, polylactide- polyglycolide copolymers, polycaprolactones, dextran, albumin, gelatin, alginate, collagen, chitosan, cyclodextrins, dendrimers and polyethylenimine.
  • the transfer vehicle is selected based upon its ability to facilitate the transfection of a miRNA to a target cell.
  • Useful lipid nanoparticles for miRNA comprise a cationic lipid to encapsulate and/or enhance the delivery of miRNA into the target cell that will act as a depot for protein production.
  • cationic lipid refers to any of a number of lipid species that carry a net positive charge at a selected pH, such as physiological pH.
  • the contemplated lipid nanoparticles may be prepared by including multi-component lipid mixtures of varying ratios employing one or more cationic lipids, non-cationic lipids and PEG- modified lipids.
  • Several cationic lipids have been described in the literature, many of which are commercially available. See, e.g., WO2014/089486, US 2018/0353616A1, and US 8,853,377B2, which are incorporated by reference.
  • LNP formulation is performed using routine procedures comprising cholesterol, ionizable lipid, helper lipid, PEG-lipid and polymer forming a lipid bilayer around encapsulated mRNA (Kowalski et al., 2019, Mol. Ther. 27(4):710-728).
  • LNP comprises a cationic lipids (i.e. N-[l-(2,3-dioleoyloxy)propyl]- N,N,N -trimethylammonium chloride (DOTMA), or l,2-dioleoyl-3-trimethylammonium- propane (DOTAP)) with helper lipid DOPE.
  • DOTMA N-[l-(2,3-dioleoyloxy)propyl]- N,N,N -trimethylammonium chloride
  • DOTAP l,2-dioleoyl-3-trimethylammonium- propane
  • LNP comprises an ionizable lipid Dlin-MC3-DMA ionizable lipids, or diketopiperazine-based ionizable lipids (cKK-E12).
  • polymer comprises a polyethyleneimine (PEI), or a poly(P- amino)esters (PBAEs). See, e.g., WO2014/089486, US 2018/0353616A1, US2013/0037977A1, WO2015/074085 Al, US9670152B2, and US 8,853,377B2, which are incorporated by reference.
  • the vector described herein is a “replication-defective virus” or a “viral vector” which refers to a synthetic or artificial viral particle in which an expression cassette containing a nucleic acid sequence encoding an engineered C9orf72 and/or at least one miRNA targeting endogenous C9orf72 at a site not present on the sequence of the engineered C9orf72.
  • Replication-defective viruses cannot generate progeny virions but retain the ability to infect target cells.
  • the genome of the viral vector does not include genes encoding the enzymes required to replicate (the genome can be engineered to be "gutless" - containing only the nucleic acid sequence encoding E2 flanked by the signals required for amplification and packaging of the artificial genome), but these genes may be supplied during production. Therefore, it is deemed safe for use in gene therapy since replication and infection by progeny virions cannot occur except in the presence of the viral enzyme required for replication.
  • a recombinant viral vector may be any suitable replication-defective viral vector, including, e.g., a recombinant adeno-associated virus (AAV), an adenovirus, a bocavirus, a hybrid AAV/bocavirus, a herpes simplex virus or a lentivirus.
  • AAV adeno-associated virus
  • the term “host cell” may refer to the packaging cell line in which a vector (e.g., a recombinant AAV) is produced.
  • a host cell may be a prokaryotic or eukaryotic cell (e.g., human, insect, or yeast) that contains exogenous or heterologous DNA that has been introduced into the cell by any means, e.g., electroporation, calcium phosphate precipitation, microinjection, transformation, viral infection, transfection, liposome delivery, membrane fusion techniques, high velocity DNA-coated pellets, viral infection and protoplast fusion.
  • host cells may include, but are not limited to an isolated cell, a cell culture, an Escherichia coli cell, a yeast cell, a human cell, a non-human cell, a mammalian cell, a nonmammalian cell, an insect cell, an HEK-293 cell, a liver cell, a kidney cell, a cell of the central nervous system, a neuron, a glial cell, or a stem cell.
  • target cell refers to any target cell in which expression of the hC9orf72 and/or miRNA is desired.
  • target cell is intended to reference the cells of the subject being treated for a C9orf72-associated disorder such as ALS. Examples of target cells may include, but are not limited to, cells within the central nervous system.
  • compositions containing at least one vector comprising C9orf72.miR e.g., an rAAV.C9orf72.miR stock
  • at least one vector comprising miR and/or at least one vector comprising stock e.g., an rAAV.C9orf72.miR stock
  • an optional carrier, excipient and/or preservative e.g., an rAAV.C9orf72.miR stock
  • a “stock” of rAAV refers to a population of rAAV. Despite heterogeneity in their capsid proteins due to deamidation, rAAV in a stock are expected to 5 share an identical vector genome.
  • a stock can include rAAV having capsids with, for example, heterogeneous deamidation patterns characteristic of the selected AAV capsid proteins and a selected production system. The stock may be produced from a single production system or pooled from multiple runs of the production system. A variety of production systems, including but not limited to those described herein, may be selected.
  • a composition comprises at least virus stock which is a recombinant AAV (rAAV) suitable for use in treating C9orf72-mediated ALS or FTD alone or in combination with other vector stock or composition.
  • rAAV recombinant AAV
  • the composition is suitable for use in preparing a medicament for treating patients.
  • a composition comprises a virus stock which is a recombinant AAV (rAAV) suitable for use in treating patients, said rAAV comprising: (a) an adeno-associated virus capsid, and (b) a vector genome packaged in the AAV capsid, said vector genome comprising AAV inverted terminal repeats, a coding sequence for an engineered C9orf72, a spacer sequence, a coding sequence for at least one miRNA specifically targeted to endogenous human C9orf72 at a site not present in the engineered human C9orf72 coding sequence, and regulatory sequences which direct expression of the encoded gene products.
  • rAAV recombinant AAV
  • a composition comprises separate vector stock comprising rAAV comprising: (a) an adeno-associated virus capsid, and (b) a vector genome packaged in the AAV capsid, said vector genome comprising AAV inverted terminal repeats, a coding sequence for an engineered human C9orf72, and regulatory sequences which direct expression of the encoded gene product and/or a separate vector stock comprising (a) an adeno-associated virus capsid, and (b) a vector genome packaged in the AAV capsid, said vector genome comprising AAV inverted terminal repeats, a coding sequence for at least one miRNA specifically targeted to endogenous human C9orf72 at a site not present in the engineered C9orf72 coding sequence, and regulatory sequences which direct expression of the encoded gene product.
  • the vector genome comprises a promoter, an enhancer, an intron, a human C9orf72 coding sequence, and a polyadenylation signal.
  • the intron consists of a chicken beta actin splice donor and a rabbit P splice acceptor element.
  • the vector genome further comprises an AAV2 5’ ITR and an AAV2 3’ ITR which flank all elements of the vector genome.
  • the rAAV.C9orf72.miR may be suspended in a physiologically compatible carrier to be administered to a human patient.
  • the vector is suitably suspended in an aqueous solution containing saline, a surfactant, and a physiologically compatible salt or mixture of salts.
  • the formulation is adjusted to a physiologically acceptable pH, e.g., in the range of pH 6 to 9, or pH 6.5 to 7.5, pH 7.0 to 7.7, or pH 7.2 to 7.8.
  • pH of the cerebrospinal fluid is about 7.28 to about 7.32, or a pH of 7.2 to 7.4, for intrathecal delivery, a pH within this range may be desired; whereas for intravenous delivery, a pH of about 6.8 to about 7.2 may be desired.
  • other pHs within the broadest ranges and these subranges may be selected for other route of delivery.
  • the formulation may contain a buffered saline aqueous solution not comprising sodium bicarbonate.
  • a buffered saline aqueous solution comprising one or more of sodium phosphate, sodium chloride, potassium chloride, calcium chloride, magnesium chloride and mixtures thereof, in water, such as a Harvard’s buffer.
  • the aqueous solution may further contain Kolliphor® P188, a poloxamer which is commercially available from BASF which was formerly sold under the trade name Lutrol® F68.
  • the aqueous solution may have a pH of 7.2 or a pH of 7.4.
  • the formulation may contain a buffered saline aqueous solution comprising 1 mM Sodium Phosphate (Na3PO4), 150 mM sodium chloride (NaCl), 3mM potassium chloride (KC1), 1.4 mM calcium chloride (CaC12), 0.8 mM magnesium chloride (MgC12), and 0.001% Kolliphor® 188. See, e.g., harvardapparatus.com/harvard- apparatus-perfusion-fluid.html. In certain embodiments, Harvard’s buffer is preferred.
  • the formulation may contain one or more permeation enhancers.
  • suitable permeation enhancers may include, e.g., mannitol, sodium glycocholate, sodium taurocholate, sodium deoxycholate, sodium salicylate, sodium caprylate, sodium caprate, sodium lauryl sulfate, polyoxyethylene-9-laurel ether, or EDTA.
  • the composition includes a carrier, diluent, excipient and/or adjuvant.
  • Suitable carriers may be readily selected by one of skill in the art in view of the indication for which the transfer virus is directed.
  • one suitable carrier includes saline, which may be formulated with a variety of buffering solutions (e.g., phosphate buffered saline).
  • Other exemplary carriers include sterile saline, lactose, sucrose, calcium phosphate, gelatin, dextran, agar, pectin, peanut oil, sesame oil, and water.
  • the buffer/carrier should include a component that prevents the rAAV, from sticking to the infusion tubing but does not interfere with the rAAV binding activity in vivo.
  • compositions may contain, in addition to the vector (e.g., rAAV) and carrier(s), other conventional pharmaceutical ingredients, such as preservatives, or chemical stabilizers.
  • preservatives include chlorobutanol, potassium sorbate, sorbic acid, sulfur dioxide, propyl gallate, the parabens, ethyl vanillin, glycerin, phenol, and parachlorophenol.
  • chemical stabilizers include gelatin and albumin.
  • “earner” includes any and all solvents, dispersion media, vehicles, coatings, diluents, antibacterial and antifungal agents, isotonic and absorption delaying agents, buffers, carrier solutions, suspensions, colloids, and the like. The use of such media and agents for pharmaceutical active substances is well known in the art. Supplementary active ingredients can also be incorporated into the compositions.
  • pharmaceutically- acceptable refers to molecular entities and compositions that do not produce an allergic or similar untoward reaction when administered to a host.
  • Delivery vehicles such as liposomes, nanocapsules, microparticles, microspheres, lipid particles, vesicles, and the like, may be used for the introduction of the compositions of the present invention into suitable host cells.
  • the rAAV vector delivered transgenes may be formulated for delivery either encapsulated in a lipid particle, a liposome, a vesicle, a nanosphere, or a nanoparticle or the like.
  • a composition in one embodiment, includes a final formulation suitable for delivery to a subject, e.g., is an aqueous liquid suspension buffered to a physiologically compatible pH and salt concentration.
  • a final formulation suitable for delivery to a subject e.g., is an aqueous liquid suspension buffered to a physiologically compatible pH and salt concentration.
  • one or more surfactants are present in the formulation.
  • the composition may be transported as a concentrate which is diluted for administration to a subject.
  • the composition may be lyophilized and reconstituted at the time of administration.
  • a suitable surfactant, or combination of surfactants may be selected from among nonionic surfactants that are nontoxic.
  • a difunctional block copolymer surfactant terminating in primary hydroxyl groups is selected, e.g., such as Pluronic® F68 [BASF], also known as Poloxamer 188, which has a neutral pH, has an average molecular weight of 8400.
  • Poloxamers may be selected, i.e., nonionic triblock copolymers composed of a central hydrophobic chain of polyoxypropylene (polypropylene oxide)) flanked by two hydrophilic chains of polyoxyethylene (polyethylene oxide)), SOLUTOL HS 15 (Macrogol-15 Hydroxystearate), LABRASOL (Polyoxy capryllic glyceride), poly oxy 10 oleyl ether, TWEEN (polyoxyethylene sorbitan fatty acid esters), ethanol and polyethylene glycol.
  • the formulation contains a poloxamer.
  • copolymers are commonly named with the letter "P" (for poloxamer) followed by three digits: the first two digits x 100 give the approximate molecular mass of the poly oxypropylene core, and the last digit x 10 gives the percentage polyoxyethylene content.
  • Poloxamer 188 is selected.
  • the surfactant may be present in an amount up to about 0.0005 % to about 0.001% of the suspension.
  • the vectors are administered in sufficient amounts to transfect the cells and to provide sufficient levels of gene transfer and expression to provide a therapeutic benefit without undue adverse effects, or with medically acceptable physiological effects, which can be determined by those skilled in the medical arts.
  • routes other than intrathecal administration may be used, such as, e.g., direct delivery to a desired organ e.g., the liver (optionally via the hepatic artery), lung, heart, eye, kidney), oral, inhalation, intranasal, intratracheal, intraarterial, intraocular, intravenous, intramuscular, subcutaneous, intradermal, and other parental routes of administration. Routes of administration may be combined, if desired.
  • a therapeutically effective human dosage of viral vector is generally in the range of from about 25 to about 1000 microliters to about 100 mL of solution containing concentrations of from about 1 x 10 9 to 1 x 10 16 genomes virus vector (to treat an average subject of 70 kg in body weight) including all integers or fractional amounts within the range, and preferably 1.0 x 10 12 GC to 1.0 x 10 14 GC for a human patient.
  • the compositions are formulated to contain at least IxlO 9 , 2xl0 9 , 3xl0 9 , 4xl0 9 , 5xl0 9 , 6xl0 9 , 7xl0 9 , 8xl0 9 , or 9xl0 9 GC per dose including all integers or fractional amounts within the range.
  • the compositions are formulated to contain at least IxlO 10 , 2xlO 10 , 3xl0 10 , 4xlO 10 , 5xl0 10 , 6xlO 10 , 7xlO 10 , 8xl0 10 , or 9xlO 10 GC per dose including all integers or fractional amounts within the range.
  • compositions are formulated to contain at least IxlO 11 , 2xlO n , 3xl0 n , 4xlO n , 5xl0 n , 6xlO n , 7xlO n , 8xl0 n , or 9x10“ GC per dose including all integers or fractional amounts within the range.
  • the compositions are formulated to contain at least IxlO 12 , 2xl0 12 , 3xl0 12 , 4xl0 12 , 5xl0 12 , 6xl0 12 , 7xl0 12 , 8xl0 12 , or 9x10 12 GC per dose including all integers or fractional amounts within the range.
  • compositions are formulated to contain at least IxlO 13 , 2xl0 13 , 3xl0 13 , 4xl0 13 , 5xl0 13 , 6xl0 13 , 7xl0 13 , 8xl0 13 , or 9xl0 13 GC per dose including all integers or fractional amounts within the range.
  • the compositions are formulated to contain at least IxlO 14 , 2xl0 14 , 3xl0 14 , 4xl0 14 , 5xl0 14 , 6xl0 14 , 7xl0 14 , 8xl0 14 , or 9x10 14 GC per dose including all integers or fractional amounts within the range.
  • compositions are formulated to contain at least IxlO 15 , 2xl0 15 , 3xl0 15 , 4xl0 15 , 5xl0 15 , 6xl0 15 , 7xl0 15 , 8xl0 15 , or 9xl0 15 GC per dose including all integers or fractional amounts within the range.
  • the dose can range from IxlO 10 to about IxlO 12 GC per dose including all integers or fractional amounts within the range.
  • the dose is in the range of about I x lO 9 GC/g brain mass to about I x lO 12 GC/g brain mass. In certain embodiments, the dose is in the range of about 1 x 10 10 GC/g brain mass to about 3.33 x 10 11 GC/g brain mass. In certain embodiments, the dose is in the range of about 3.33 x 10 11 GC/g brain mass to about 1. 1 x 10 12 GC/g brain mass. In certain embodiments, the dose is in the range of about 1. 1 x 10 12 GC/g brain mass to about 3.33 x 10 13 GC/g brain mass. In certain embodiments, the dose is lower than 3.33 x 10 11 GC/g brain mass.
  • the dose is lower than 1. 1 x 10 12 GC/g brain mass. In certain embodiments, the dose is lower than 3.33 x 10 13 GC/g brain mass. In certain embodiments, the dose is about I x lO 10 GC/g brain mass. In certain embodiments, the dose is about 2 x 10 10 GC/g brain mass. In certain embodiments, the dose is about 2 x 10 10 GC/g brain mass. In certain embodiments, the dose is about 3 x 10 10 GC/g brain mass. In certain embodiments, the dose is about 4 x IO 10 GC/g brain mass. In certain embodiments, the dose is about 5 x IO 10 GC/g brain mass.
  • the dose about 6 x IO 10 GC/g brain mass. In certain embodiments, the dose is about 7 x IO 10 GC/g brain mass. In certain embodiments, the dose about 8 x IO 10 GC/g brain mass. In certain embodiments, the dose is about 9 x IO 10 GC/g brain mass. In certain embodiments, the dose is about 1 x 10 11 GC/g brain mass. In certain embodiments, the dose is about 2 x 10 11 GC/g brain mass. In certain embodiments, the dose is about 3 x 10 11 GC/g brain mass. In certain embodiments, the dose is about 4 x 10 11 GC/g brain mass.
  • the dose is administered to humans as a flat dose in the range of about 1.44 x 10 13 to 4.33 x 10 14 GC of the rAAV. In certain embodiments, the dose is administered to humans as a flat dose in the range of about 1.44 x 10 13 to 2 x 10 14 GC of the rAAV. In certain embodiments, the dose is administered to humans as a flat dose in the range of about 3 x 10 13 to 1 x 10 14 GC of the rAAV. In certain embodiments, the dose is administered to humans as a flat dose in the range of about 5 x 10 13 to 1 x 10 14 GC of the rAAV.
  • the compositions can be formulated in dosage units to contain an amount of AAV that is in the range of about 1 x 10 13 to 8 x 10 14 GC of the rAAV. In some embodiments, the compositions can be formulated in dosage units to contain an amount of rAAV that is in the range of about 1.44 x 10 13 to 4.33 x 10 14 GC of the rAAV. In some embodiments, the compositions can be formulated in dosage units to contain an amount of rAAV that is in the range of about 3 x 10 13 to 1 x 10 14 GC of the rAAV. In some embodiments, the compositions can be formulated in dosage units to contain an amount of rAAV that is in the range of about 5 x 10 13 to 1 x 10 14 GC of the rAAV.
  • the vector is administered to a subject in a single dose.
  • vector may be delivered via multiple injections (for example 2 doses) is desired.
  • the dosage will be adjusted to balance the therapeutic benefit against any side effects and such dosages may vary depending upon the therapeutic application for which the recombinant vector is employed.
  • the levels of expression of the transgene can be monitored to determine the frequency of dosage resulting in viral vectors, preferably AAV vectors containing the minigene.
  • dosage regimens similar to those described for therapeutic purposes may be utilized for immunization using the compositions provided herein.
  • the terms “intrathecal delivery” or “intrathecal administration” refer to a route of administration via an injection into the spinal canal, more specifically into the subarachnoid space so that it reaches the cerebrospinal fluid (CSF).
  • CSF cerebrospinal fluid
  • Intrathecal delivery may include lumbar puncture, intraventricular (including intracerebroventricular (ICV)), suboccipital/intracistemal, and/or Cl -2 puncture.
  • material may be introduced for diffusion throughout the subarachnoid space by means of lumbar puncture.
  • injection may be into the cistema magna.
  • tracistemal delivery or “intracistemal administration” refer to a route of administration directly into the cerebrospinal fluid of the cistema magna cerebellomedularis, more specifically via a suboccipital puncture or by direct injection into the cistema magna or via permanently positioned tube.
  • Compositions comprising the miR target sequences described herein for repressing endogenous C9orf72 (e.g., in ALS patients) are generally targeted to one or more different cell types within the central nervous system, including, but not limited to, neurons (including, e.g., lower motor neurons and/or primary sensory neurons. These may include, e.g., pyramidal, purkinje, granule, spindle, and interneuron cells).
  • the vectors and compositions provided herein are useful for treating a patient having a C9orf72-associated disorder (e.g., ALS or FTD), neuropathy, or various symptoms associated therewith.
  • a C9orf72-associated disorder e.g., ALS or FTD
  • a combination regimen or co-therapy for treating a patient having ALS or FTD is provided.
  • this regimen or co-therapy comprises co-administering (a) a recombinant nucleic acid sequence encoding an engineered human C9orf72 coding sequence operably linked to regulatory sequences which direct expression thereof in a human target cell, wherein the human C9orf72 coding sequence has the sequence of SEQ ID NO: 13 or a sequence at least 95% identical thereto and which differs from endogenous human C9orf72 in the patient by having a mismatch in the miRNA target sequence of (b), and (b) a coding sequence for at least one miRNA specific for an endogenous human C9orf72 sequence in a human ALS subject, wherein the mRNA is operably linked to regulatory sequences which direct expression thereof in the subject.
  • the miR target sequence is the miR487, having the sequence of at least SEQ ID NO: 16, or at least SEQ ID NO: 15 in combination with a 5’ flanking region (e.g., SEQ ID NO: 5), linkers, and a 3’ flanking region (e.g., SEQ ID NO: 7).
  • the miR target sequences are the miR.NT sequence, having the sequence of at least SEQ ID NO: 6 with a 5’ flanking region, a linker, and a linker and 3’ flanking regions. See, e.g., SEQ ID NO: 8; or SEQ ID NO: 6 in combination with SEQ ID NO: 5 and/or SEQ ID NO: 7.
  • this regimen or co-therapy for treating a patient having C9orf72 comprises co-administering (a) a recombinant nucleic acid sequence encoding an engineered human C9orf72 coding sequence operably linked to regulatory sequences which direct expression thereof in a human target cell, wherein the human C9orf72 coding sequence is engineered to differs from endogenous human C9orf72 in the patient by having a mismatch in the miRNA target sequence of (b), and (b) a coding sequence for at least one miRNA specific for an endogenous human C9orf72 sequence in a human subject, wherein the miRNA coding sequence is operably linked to regulatory sequences which direct expression thereof in the subject, and wherein the at least one miRNA coding sequence has a sequence of one or more of: an miRNA coding sequence comprising SEQ ID NO: 16 (miR487 with flanking regions).
  • the nucleic acid molecule further comprises the miR target sequences are the miR.NT sequence, having the sequence of at least SEQ ID NO: 6 with a 5’ flanking region, a linker, and a linker and 3’ flanking regions. See, e.g., SEQ ID NO: 8; or SEQ ID NO: 6 in combination with SEQ ID NO: 5 and/or SEQ ID NO: 7.
  • a first vector comprises the nucleic acid (a) and a second, different vector, comprises at least one miRNA (b).
  • the first vector is a viral vector and/or the second vector is a viral vector and the first and the second viral vector may be from the same virus source or may be different.
  • the first vector is a non- viral vector
  • the second vector is a non-viral vector and the first and the second vectors may be same composition or may be different.
  • the vectors and compositions provided herein may be used in combination with one or more co-therapies selected from: Available approved treatments for the management of ALS that reduce morbidity in some patients include riluzole and edaravone Riluzole is an orally administered glutamate inhibitor that has been shown to delay the onset of ventilator dependence or tracheostomy in some people with ALS. Edaravone is an IV- administered neuroprotective agent that has shown modest success in slowing the loss of physical function in ALS patients. Patients with ALS may also benefit from multidisciplinary care including implementation of augmentative communication devices, nutritional support, ventilator assistance, medications to manage symptoms of the disease, psychological support, and physical, occupational, and speech therapy.
  • Suitable co-therapeutics may include acetaminophen, and/or nonsteroidal anti-inflammatory drugs (NSAIDs).
  • NSAIDs nonsteroidal anti-inflammatory drugs
  • the vectors may be delivered in a combination with an immunomodulatory regimen involving one or more steroids, e.g., prednisone.
  • Computed Tomography refers to radiography in which a three-dimensional image of a body structure is constructed by computer from a series of plane cross-sectional images made along an axis.
  • nucleic acid indicates that, when optimally aligned with appropriate nucleotide insertions or deletions with another nucleic acid (or its complementary strand), there is nucleotide sequence identity in at least about 95 to 99% of the aligned sequences.
  • the homology is over full-length sequence, or an open reading frame thereof, or another suitable fragment which is at least 15 nucleotides in length. Examples of suitable fragments are described herein.
  • sequence identity “percent sequence identity” or “percent identical” in the context of nucleic acid sequences refers to the residues in the two sequences which are the same when aligned for maximum correspondence.
  • the length of sequence identity comparison may be over the full-length of the genome, the full-length of a gene coding sequence, or a fragment of at least about 500 to 5000 nucleotides, is desired. However, identity among smaller fragments, e.g., of at least about nine nucleotides, usually at least about 20 to 24 nucleotides, at least about 28 to 32 nucleotides, at least about 36 or more nucleotides, may also be desired.
  • percent sequence identity may be readily determined for amino acid sequences, over the full-length of a protein, or a fragment thereof.
  • a fragment is at least about 8 amino acids in length and may be up to about 700 amino acids. Examples of suitable fragments are described herein.
  • highly conserved is meant at least 80% identity, preferably at least 90% identity, and more preferably, over 97% identity.
  • Identity is readily determined by one of skill in the art by resort to algorithms and computer programs known by those of skill in the art. Unless otherwise specified by an upper range, it will be understood that a percentage of identity is a minimum level of identity and encompasses all higher levels of identity up to 100% identity to the reference sequence. Unless otherwise specified, it will be understood that a percentage of identity is a minimum level of identity and encompasses all higher levels of identity up to 100% identity to the reference sequence. For example, “95% identity” and “at least 95% identity” may be used interchangeably and include 95, 96, 97, 98, 99 up to 100% identity to the referenced sequence, and all fractions therebetween.
  • aligned sequences or alignments refer to multiple nucleic acid sequences or protein (amino acids) sequences, often containing corrections for missing or additional bases or amino acids as compared to a reference sequence.
  • AAV alignments are performed using the published AAV9 sequences as a reference point. Alignments are performed using any of a variety of publicly or commercially available Multiple Sequence Alignment Programs.
  • Such programs include, “Clustal Omega”, “Clustal W”, “CAP Sequence Assembly”, “MAP”, and “MEME”, which are accessible through Web Servers on the internet. Other sources for such programs are known to those of skill in the art. Alternatively, Vector NTI utilities are also used. There are also a number of algorithms known in the art that can be used to measure nucleotide sequence identity, including those contained in the programs described above. As another example, polynucleotide sequences can be compared using FastaTM, a program in GCG Version 6.1. FastaTM provides alignments and percent sequence identity of the regions of the best overlap between the query and search sequences.
  • percent sequence identity between nucleic acid sequences can be determined using FastaTM with its default parameters (a word size of 6 and the NOPAM factor for the scoring matrix) as provided in GCG Version 6. 1, herein incorporated by reference.
  • Multiple sequence alignment programs are also available for amino acid sequences, e.g., the “Clustal Omega”, “Clustal X”, “MAP”, “PIMA”, “MSA”, “BLOCKMAKER”, “MEME”, and “Match-Box” programs. Generally, any of these programs are used at default settings, although one of skill in the art can alter these settings as needed.
  • one of skill in the art can utilize another algorithm or computer program which provides at least the level of identity or alignment as that provided by the referenced algorithms and programs. See, e.g., J. D. Thomson et al, Nucl. Acids. Res., “A comprehensive comparison of multiple sequence alignments”, 27(13):2682-2690 (1999).
  • the term “about” means a variability of 10 % ( ⁇ 10%, e.g., ⁇ 1, ⁇ 2, ⁇ 3, ⁇ 4, ⁇ 5, ⁇ 6, ⁇ 7, ⁇ 8, ⁇ 9, ⁇ 10, or values therebetween) from the reference given, unless otherwise specified.
  • disease As used herein, “disease”, “disorder” and “condition” are used interchangeably, to indicate an abnormal state in a subject.
  • C9orf72-related symptom(s)” or “symptom(s)” refers to symptom(s) found in patients with symptoms of ALS include, e.g., persistent weakness, which may have variable presentation with some patients having isolated weakness of one or more limbs, while others initially exhibit bulbar weakness, which affects the muscles that control speech, swallowing, and chewing. Other manifestations include abnormal muscle tone and tendon reflexes, signs of progressive muscle weakness, muscle wasting especially in the trunk and extremities, associated spasticity with an inability to control movement. Clinical symptoms range from fasciculations, muscle cramps, gait disturbances, loss of ambulation, loss of arm and hand function, to difficulty with speech and swallowing and breathlessness.
  • FTD frontotemporal dementia
  • “Patient” or “subject” as used herein means a male or female human, and animal models (including, e.g., dogs, non-human primates, rodents, or other suitable models) used for clinical research.
  • the subject of these methods and compositions is a human diagnosed with a C9orf72-associated disorder.
  • Such disorders may include a patient having a defect in the C9orf72 gene, e.g., such as associated with amyotrophic lateral sclerosis (ALS) or frontotemporal dementia (FTD), or both (C9FTD/ALS).
  • ALS amyotrophic lateral sclerosis
  • FTD frontotemporal dementia
  • C9orf72 repeat expansions have also been identified as a rare cause of other neurodegenerative diseases, including Parkinson disease, progressive supranuclear palsy, ataxia, corticobasal syndrome, Huntington disease-like syndrome, Creutzfeldt-Jakob disease and Alzheimer disease.
  • the human subject of these methods and compositions is a prenatal, a newborn, an infant, a toddler, a preschool, a grade-schooler, a teen, a young adult or an adult.
  • the subject of these methods and compositions is a pediatric patient.
  • a therapeutic level means an C9orf72 activity at least about 5%, about 8%, about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, about 100%, more than 100%, about 2-fold, about 3 -fold, or about 5 -fold of a healthy control.
  • Suitable assays for measuring the activity of an hC9orf72 are known in the art.
  • such therapeutic levels of the one or more subunit protein may result in alleviation of the C9orf72-associated ALS or FTD symptom(s); reversal of certain C9orf72-related symptoms and/or prevention of progression of ALS or FTD - related certain symptoms; or any combination thereof.
  • therapeutic efficacy is measured by trachesotomy-free survival, improved lung function measures, e.g., as measured by forced vital capacity (FVC) or slow viral capacity (SVC).
  • FVC forced vital capacity
  • SVC slow viral capacity
  • ALSFRS-R ALS functional rating scale
  • suitable biomarkers may be measured to assess efficacy.
  • suitable biomarkers include, e.g., the neurofilament heavy chain (NFH) and neurofilament light chain (NFL), dipeptide repeat proteins, tau protein, and/or neuroimaging.
  • the human C9orf72 delivered by the compositions and regimens provided herein has the amino acid sequence of a functional endogenous wild-type protein.
  • the sequence is the amino acid sequence of SEQ ID NO: 14 or 45 or a functional protein which is at about 95 to 100% identity to functional, human C9orf72 protein.
  • RNA Ribonucleic acid
  • expression is used herein in its broadest meaning and comprises the production of RNA or of RNA and protein.
  • expression or “translation” relates in particular to the production of peptides or proteins. Expression may be transient or may be stable.
  • an expression cassette (and a vector genome) may comprise one or more dorsal root ganglion (drg)- miRNA targeting sequences in the UTR, e.g., to reduce drg toxicity and/or axonopathy.
  • drg dorsal root ganglion
  • an expression cassette may be delivered via a genetic element (e.g., a plasmid) to a packaging host cell and packaged into the capsid of a viral vector (e.g., a viral particle).
  • a genetic element e.g., a plasmid
  • a viral vector e.g., a viral particle
  • operably linked refers to both expression control sequences that are contiguous with the gene of interest and expression control sequences that act in trans or at a distance to control the gene of interest.
  • heterologous when used with reference to a protein or a nucleic acid indicates that the protein or the nucleic acid comprises two or more sequences or subsequences which are not found in the same relationship to each other in nature.
  • the nucleic acid is typically recombinantly produced, having two or more sequences from unrelated genes arranged to make a new functional nucleic acid.
  • the nucleic acid has a promoter from one gene arranged to direct the expression of a coding sequence from a different gene.
  • the promoter is heterologous.
  • regulatory elements comprise but not limited to: promoter; enhancer; transcription factor; transcription terminator; efficient RNA processing signals such as splicing and polyadenylation signals (poly A); sequences that stabilize cytoplasmic mRNA, for example Woodchuck Hepatitis Virus (WHP) Posttranscriptional Regulatory Element (WPRE); sequences that enhance translation efficiency (i.e., Kozak consensus sequence).
  • promoter enhancer
  • transcription factor transcription terminator
  • efficient RNA processing signals such as splicing and polyadenylation signals (poly A)
  • poly A polyadenylation signals
  • sequences that stabilize cytoplasmic mRNA for example Woodchuck Hepatitis Virus (WHP) Posttranscriptional Regulatory Element (WPRE); sequences that enhance translation efficiency (i.e., Kozak consensus sequence).
  • WPRE Woodchuck Hepatitis Virus
  • WPRE Posttranscriptional Regulatory Element
  • translation in the context of the present invention relates to a process at the ribosome, wherein an mRNA strand controls the assembly of an amino acid sequence to generate a protein or a peptide.
  • a vector genome for a packaging plasmid comprises SEQ ID NO: 17, includes a shortened AAV2 - 5’ ITR, the expression cassette comprising a C4 enhancer, a CB7 promoter, an engineered C9orf72 coding sequences and the C9miR487 target sequences, WPRE element, and a polyA signal (e.g., the expression cassette of SEQ ID NO: 18 or a sequence at least 97% identical thereto), and a shortened AAV2- 3’ AAV.
  • the vector genome comprises a full-length 5 ’ ITR and a full-length 3 ’ ITR.
  • the vector genome comprises the vector elements above, without the WPRE element.
  • the vector genome comprises a scAAV.
  • an rAAV or another vector may contain an expression cassettes containing the miR487 targeting sequences and the C9orf72 coding sequences in a separate vector [see, e.g., SEQ ID NO: 19] or separate expression cassette.
  • the WPRE element may be eliminated from the expression cassette and/or replaced with another genome element.
  • rAAV comprising (1) expression cassettes comprising a miR sequences targeted to endogenous C9orf72, (2) an expression cassette comprising a combination these miR sequences and an engineered C9orf72 cDNA which has modifications in the regions of C9orf72 targeted by the miR in the expression cassette so that it is not also targeted by the miR.
  • rAAV having vector genomes expressing various miRNA sequences were examined: miR.NT (negative control), miR32-101 (positive control), and miR487.
  • Vectors were constructed using convention triple transfection methods in a 293 HEK cell line transfected with a cis plasmid comprising the vector genome to be packaged composed of a 5’ ITR, a spacer sequence, the expression cassette, a spacer sequence, and the 3’ ITR. Shortened (130 bp) 5’- and 3’ ITRs are in this cis plasmid; during replication and packaging, these revert to the full-length 145 bp 5’ and 3’ ITRs.
  • This cis plasmid is cotransfected with a trans plasmid comprising Ad helper genes needed for transfection and packaging, and a trans plasmid comprising the VP 1 gene encoding the AAV capsid.
  • Ad helper genes needed for transfection and packaging
  • trans plasmid comprising the VP 1 gene encoding the AAV capsid.
  • an AAV9 mutant termed AAV9-eB was used.
  • rAAV constructs described herein to knockdown mutant C9orf72 RNA and DPRs is evaluated in a Tg(C9orf72_3) line 112 mouse model.
  • rAAV is administered to adult Tg(C9orf72_3) line 112 mice via a single intracerebroventricular (ICV) injection.
  • ICV intracerebroventricular
  • the dose range was selected to evaluate half-log increments beginning with the maximum feasible dose.
  • Vehicle-treated transgenic and non-transgenic mice serve as controls. Thirty days after injection, mice are sacrificed, and the brain and spinal cord collected for analysis. The 30 day time point is selected to allow sufficient time to reach steady-state levels of C9orf72 RNA and DPR protein.
  • Total C9orf72 mRNA is measured using exon-specific primers by quantitative rtPCR and normalized to GAPDH expression.
  • the abnormal repeat-containing transcript is quantified by rtPCR using primers specific to the first intron of C9orf72.
  • DPRs poly-GP are measured by immunoassay using the Mesoscale Discovery platform.
  • rAAV is administered to adult Tg(C9orf72_3) line 112 mice via a single intracerebroventricular (ICV) injection by trained personnel.
  • ICV intracerebroventricular
  • Vehicle-treated transgenic and non-transgenic mice serve as controls.
  • Clinical observations will be performed twice daily, and body weights are measured weekly. For all unscheduled deaths, comprehensive gross pathology and histopathology on a complete list of tissues and other analyses as appropriate are performed to determine a possible cause of death.
  • mice are sacrificed.
  • the 90 day time point is selected to assess durability of knockdown of the mutant transcript.
  • the brain, spinal cord, heart, lung, liver, spleen, kidneys, esophagus, stomach, large and small intestines, mesenteric and cervical lymph nodes, adrenal glands, and gonads are collected, examined for gross pathology, and processed for histopathology. Applicable immunohistochemistry staining for immune cell infiltrates is performed in the event of histopathology findings. Blood is collected for serum chemistry panels and complete blood counts. Intron-containing C9orf72 RNA and DPRs are measured in brain and spinal cord as described above. The lowest dose significantly reducing mutant C9orf72 mRNA and DPR expression levels is considered the MED. Significance will be determined by appropriate statistical comparisons to the vehicle control group. Portions of the brain and spinal cord and all other tissues collected are fixed and embedded in paraffin for analysis of histopathology.
  • FIGs 1A to ID provide qPCR results from spinal cord of 11-14 week old mice (C9 LI 12 Het) injected (iv-tail vein) with a 3 x 10 11 GC/100 pl of rAAV-PHP.eb- CB7.CLC9miR.WPRE.rBG, the miR is NT or PBS, miR487, miR32, or miR32-101.
  • FIG1A provides the results in spinal cord for a C9 intron spliced primer.
  • FIG IB provides the results in spinal cord for C9 intron retained primers.
  • FIGs 1C and ID provide qPCR results from brain for C9 intron spliced primers (FIG 1C) or C9 intron retained primers (FIG ID).
  • FIGs 2A-2D provides the results of DPR protein pathology assessment in a poly(GP) Meso Scale Discovery (MSD)-Immunoassay, soluble fraction.
  • MSD Meso Scale Discovery
  • C57BL/6J- Tg(C9orf72_i3)l 12Lutzy/J (JR: 023099) mice show significant increases in poly(GP) soluble fraction in brain lysates: at 1, and 3 months of age and spinal cord lysate: at 12 months of age compared to NCAR, controls.
  • As mice age decrease of DPRs in the soluble fraction in mice in brain as observed in (GrC2)149 mice. Data represented as mean ⁇ SD.
  • FIG 2A shows (G4C2) 149 mice show significant increases in poly(GP) soluble fraction in brain lysates at 6, 9 & 12 months of age compared to (0462)149 controls.
  • FIGs 2B and 2C show that as mice age, decrease of DPRs in the soluble fraction in (6462)149 mice is expected (FIG 2B), as they accumulate in the insoluble fraction (FIG 26).
  • FIG 3 provides a survival curve with percent survival graphed over age in weeks to 14 weeks for various groups of wild-type control (WT/NGAR) female or male mice or Hemizygous/TG mice receiving PBS only (VEH) or receiving 3x10 11 one of two different rAAV:
  • AAV-1 is an AAV PHP.eB capsid with a vector genome of GB7.GI.69miR487.WPRE.rBG
  • AAV-2 is an AAV PHP.eB capsid with a vector genome of GB7.GI.G9miR487.WPRE.rBG, via tail vein injection at 4 weeks of age.
  • FIG 4 provides body weights by group (male and female together) from the animals study described in FIG 3, as studied from inception (4 weeks of age) through termination.
  • FIG 5 provides body weights for the females by group from the animals study described in FIG 3, as studied from inception (4 weeks of age) through termination.
  • FIG 6 provides body weights for the males by group from the animals study described in FIG 3, as studied from inception (4 weeks of age) through termination.
  • FIGs 7A and 7B provides the poly(GP) response in brain for a wild-type mouse (WT/NGAR vehicle) (Group 1), hemizygous/TG mice receiving PBS only (Vehicle) and two treatment groups receiving 3xl0 n one of two different rAAV: AAV-1 is an AAV PHP.eB capsid with a vector genome of GB7.GI.G9miR487.WPRE.rBG and AAV-2 is an AAV PHP.eB capsid with a vector genome of GB7.GI.G9miR487.WPRE.rBG, via tail vein injection at 4 weeks of age.
  • FIG 7A is corrected for background and FIG 7B is uncorrected for background.
  • Control cells are treated with an rAAV vector having the same capsid as the rAAV test vector that does not carry the miRNA or will receive no treatment.
  • Cells are harvested for RNA isolation and RNA-seq analysis.
  • Transcripts downregulated by the rAAV test vector are identified.
  • potential miRNA target sequences are identified by sequence homology, and the degree of homology between the corresponding target sequence in rhesus monkeys will be evaluated in order to predict the likelihood that toxicity related to the off-target gene knockdown could be predicted by the NHP toxicology study.
  • a 90 day GLP-compliant safety study is conducted in adult rhesus macaques (approximately 3-10 years old) to investigate the toxicology of rAAV test vector following ICM administration.
  • the 90 day evaluation period was selected because this allows sufficient time for transgene expression to reach a stable plateau.
  • the age of the animals is selected to be representative of the intended adult patient population.
  • the study design is outlined in the .
  • Dose levels are selected to be equivalent to those that will be evaluated in the planned MED when scaled by brain mass (assuming 0.4 g for the adult mouse brain and 90 g for the adult rhesus macaque brain), and these doses bracket the proposed clinical dose level range.
  • NHPs are dosed using the same vector delivery device as that intended for clinical trials. The vector delivery device and administration procedure are optimized prior to the start of the toxicology study to ensure reproducible and accurate vector delivery. The actual administered vector dose level and any device-related vector loss will be provided in the study report.
  • Baseline neurologic examinations complete physical exam, body weight, and daily observations, including assessment of appetite, clinical pathology (cell counts with differentials, clinical chemistries, and a coagulation panel), CSF chemistry, and CSF cytology will be performed.
  • clinical pathology cell counts with differentials, clinical chemistries, and a coagulation panel
  • CSF chemistry CSF cytology
  • CSF cytology CSF cytology
  • rAAV test vector or vehicle administration the animals are monitored daily for signs of distress and abnormal behavior.
  • Blood and CSF clinical pathology assessments and neurologic examinations are performed on a weekly basis for 30 days following rAAV test vector or vehicle administration, followed by every 30 days thereafter.
  • anti-AAV NAbs and cytotoxic T lymphocyte (CTL) responses to the rAAV are assessed by an interferon gamma (IFN-y) enzyme-linked immunospot (ELISpot) assay.
  • IFN-y interferon gamma enzyme-linked immunospot
  • mice Ninety days after rAAV or vehicle administration, animals will be euthanized.
  • tissues (brain, spinal cord, DRG, peripheral nerves, heart, lung, liver, spleen, kidneys, esophagus, stomach, large and small intestines, mesenteric and cervical lymph nodes, adrenal glands, and gonads) are harvested, weighed as appropriate, and analyzed for histopathology.
  • lymphocytes are harvested from the liver, spleen, and bone marrow to evaluate the presence of T cells reactive to the vector capsid in these organs at the time of necropsy.
  • Vector biodistribution is evaluated by qPCR in tissue samples.
  • Vector genomes are also be quantified in serum and CSF samples.
  • Vector excretion is be evaluated by analysis of vector genomes detected in urine and feces.
  • CSF cerebrospinal fluid
  • F female
  • GLP good laboratory practice
  • GC genome copies
  • ICM intra-cistema magna
  • ITFFB intrathecal final formulation buffer
  • M male
  • N number of animals
  • N/A not applicable
  • ROA route of administration.

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Abstract

Provided herein are rAAV and other vectors and compositions useful for treating a patient having C9orf72 comprising an engineered hC9orf72 coding sequence and the at least one miRNA coding sequence, wherein the engineered human C9orf72 coding sequence has a sequence which differs from endogenous human C9orf72 in the patient in the target site of the encoded miRNA. Also provided are methods for treating C9orf72-associated ALS, FTD, and related disorders.

Description

COMPOSITIONS AND METHODS USEFUL FOR TREATMENT OF
C9ORF72-MEDIATED DISORDERS
REFERENCE TO AN ELECTRONIC SEQUENCE LISTING
The electronic sequence listing filed herewith named “UPN-18-8536PCT.xml” with size of 157,533 bytes, created on date of January 5, 2023, and the contents of the electronic sequence listing (e.g., the sequences and text therein) are incorporated herein by reference in entirety.
BACKGROUND OF THE INVENTION
Amyotrophic lateral sclerosis (ALS) is a chronic progressive and fatal neurodegenerative disease caused by the degeneration of upper and lower motor neurons. It is characterized by progressive muscle weakness and atrophy, eventually leading to respiratory failure. Approximately 5-50% of ALS patients have clinical symptoms of frontotemporal dementia (FTD) (Hudson, 1981, Amyotrophic lateral sclerosis and its association with dementia, parkinsonism and other neurological disorders: a review. Brain 104, 217-247. doi: 10.1093/brain/104.2.217; Lomen-Hoerth et al., 2003, Are amyotrophic lateral sclerosis patients cognitively normal? Neurology 60, 1094-1097. doi:
10. 1212/OLwnl.0000055861.95202.8d). FTD is the second most common form of early-onset dementia, manifesting as frontal and/or temporal lobe atrophy, accompanied by personality and behavioral changes as well as language dysfunction. In fact, a proportion of patients with FTD also develop ALS. In addition to clinical overlapping, ubiquitin-positive tau-negative inclusion bodies (TDP-43), were considered to be a major pathological protein in ALS and FTD pathological studies (Neumann et al., 2006, Ubiquitinated TDP-43 in frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Science 314, 130-133. doi:
10. 1126/science. 1134108). In 2011, a major discovery connecting ALS and FTD was made that the expanded GGGGCC hexanucleotide repeat of the C9orf72 gene is an important genetic cause for ALS/FTD, accounting for roughly 40% of familial ALS patients, 25% of familial FTD patients and as high as 88% in familial ALS/FTD patients (DeJesus-Hemandez et al., 2011, Expanded GGGGCC hexanucleotide repeat in noncoding region of C9ORF72 causes chromosome 9p-linked FTD and ALS. Neuron 72, 245-256. doi:
10. 1016/j.neuron.2011.09.011). ALS and FTD present significant clinical, genetic, and histopathological overlaps; therefore, they are considered as two extremes of the same disease continuum.
What are needed are treatments useful for reducing the symptoms, severity and/or progression of C9orf72-associated ALS, FTD and related disorders.
Summary of the Invention
Viral and non-viral vectors and compositions useful for treating patients having symptoms associated with defects in human C9ORF72 expression and/or patients having ALS or FTD, are provided herein.
In certain embodiments, a recombinant adeno-associated virus (rAAV) comprising an AAV capsid and a vector genome is provided. The rAAV comprises: (a) an engineered nucleic acid sequence encoding human C9orf72; (b) a spacer sequence located between (a) and (c); (c) a nucleic acid sequence encoding at least one miRNA sequence specific for endogenous human C9orf72 in an ALS or FTD patient located 3’ to the sequence of (a) and (b); wherein the engineered nucleic acid sequence of (a) lacks the target site for the encoded at least one miRNA, thereby preventing the encoded miRNA from targeting the engineered human C9orf72 coding sequence; and (c) regulatory sequences operably linked to (a) and (c). In certain embodiments, the AAV capsid is selected from AAV9, AAVhu68, AAV1 or AAVrh91. In certain embodiments, the spacer is 75 nucleotides to about 250 nucleotides in length. In one aspect, a vector is provided which comprises an engineered human C9orf72 coding sequence operably linked to regulatory sequences which direct expression thereof in a human target cell. In certain embodiments, a vector is provided which comprises a nucleic acid sequence encoding at least one hairpin miRNA, wherein the encoded miRNA is specific for endogenous human C9orf72 in a human subject operably linked to regulatory sequences which direct expression thereof in the subject. In certain embodiments, a vector or other composition comprises both the engineered human C9orf72 coding sequence and the at least one miRNA coding sequence. In such an embodiment, the engineered C9orf72 coding sequence lacks the target site for the at least one miRNA, thereby preventing the miRNA from targeting the engineered human C9orf72 coding sequence. In certain embodiments, the vector is a replication-defective viral vector which comprises a vector genome comprising the human C9orf72 coding sequences, the coding sequence for the at least one miRNA and the regulatory sequences. In certain embodiments, the viral vector is a recombinant adeno-associated virus (rAAV) particle having an AAV capsid which has the packaged therein the vector genome. In certain embodiments, the AAV capsid is AAVhu68, AAV1 or AAVrh91.
In certain embodiments, a vector is provided which comprises a engineered C9orf72 coding sequence has the nucleic acid sequence of SEQ ID NO: 13 or a sequence at least 90% identical thereto, provided that the nucleic acid sequences targeted by the encoded miRNA are different from the endogenous human C9orf72 sequence.
In certain embodiments, the composition comprises a recombinant nucleic acid sequence encoding an engineered human C9orf72 coding sequence operably linked to regulatory sequences which direct expression thereof in a human target cell and a nucleic acid sequence encoding at least one miRNA specific for endogenous human C9orf72 in a patient operably linked to regulatory sequences which direct expression thereof in the subject, wherein the engineered C9orf72 coding sequence lacks a target site for the encoded at least one miRNA, thereby preventing the miRNA from targeting the engineered C9orf72 coding sequence.
In certain embodiments, a pharmaceutical composition comprising the vector, rAAV, or a composition, and a pharmaceutically acceptable aqueous suspending liquid, excipient, and/or diluent.
In certain embodiments, a method for treating a patient having a C9orf72-associated disorder (e.g., ALS or FTD) is provided comprising delivering an effective amount of the vector, a recombinant AAV, or a composition to a patient in need thereof.
In certain embodiments, a combination regimen for treating a patient having a C9orf72- associated disorder is provided which comprises co-administering (a) a recombinant nucleic acid sequence encoding an engineered human C9orf72 coding sequence operably linked to regulatory sequences which direct expression thereof in a human target cell, wherein the human c9orf72 coding sequence has the sequence of SEQ ID NO: 13 or a sequence at least 95% identical thereto and which differs from endogenous human c9 in the patient by having a mismatch in the miRNA target sequence of (b), (b) at least one miRNA specific for an endogenous human c9 sequence in a human subject, wherein the mRNA is operably linked to regulatory sequences which direct expression thereof in the subject.
These and other advantages will be apparent from the Detailed Description of the Invention which follows.
Brief Description of the Drawings
FIGs 1A to ID provide qPCR results from spinal cord of 11-14 week old mice (09 LI 12 Het) injected (iv-tail vein) with a 3 x 1011 GC/100 pl of rAAV-PHP.eb- CB7.CLC9miR.WPRE.rBG, the miR is NT or PBS, miR487, miR32, or miR32-101. FIG1A provides the results in spinal cord for a C9 intron spliced primer. FIG IB provides the results in spinal cord for C9 intron retained primers. FIGs 1C and ID provide qPCR results from brain for C9 intron spliced primers (FIG 1C) or C9 intron retained primers (FIG ID).
FIGs 2A-2D provides the results of DPR protein pathology assessment in a poly(GP) Meso Scale Discovery (MSD)-Immunoassay, soluble fraction. C57BL/6J- Tg(C9orf72_i3)l 12Lutzy/J (JR: 023099) mice show significant increases in poly(GP) soluble fraction in brain lysates: at 1, and 3 months of age and spinal cord lysate: at 12 months of age compared to NCAR, controls. As mice age, decrease of DPRs in the soluble fraction in mice in brain as observed in (GrC2)149 mice. Data represented as mean ± SD. poly(GP) response in C9-deficient mice treated with rAAV and vehicle or rAAV comprising miRNA. FIG 2A shows (G4C2) 149 mice show significant increases in poly(GP) soluble fraction in brain lysates at 6, 9 & 12 months of age compared to (0462)149 controls. FIGs 2B and 2C show that as mice age, decrease of DPRs in the soluble fraction in (6462)149 mice is expected (FIG 2B), as they accumulate in the insoluble fraction (FIG 26).
FIG 3 provides a survival curve with percent survival graphed over age in weeks to 14 weeks for various groups of wild-type control (WT/NGAR) female or male mice or Hemizygous/TG mice receiving PBS only (VEH) or receiving 3x1011 one of two different rAAV: AAV-1 is an AAV PHP.eB capsid with a vector genome of GB7.GI.69miR487.WPRE.rBG and AAV-2 is an AAV PHP.eB capsid with a vector genome of GB7.GI.G9miR487.WPRE.rBG, via tail vein injection at 4 weeks of age.
FIG 4 provides body weights by group (male and female together) from the animals study described in FIG 3, as studied from inception (4 weeks of age) through termination. FIG 5 provides body weights for the females by group from the animals study described in FIG 3, as studied from inception (4 weeks of age) through termination.
FIG 6 provides body weights for the males by group from the animals study described in FIG 3, as studied from inception (4 weeks of age) through termination.
FIGs 7A and 7B provides the poly(GP) response in brain for a wild-type mouse (WT/N CAR vehicle) (Group 1), hemizygous/TG mice receiving PBS only (Vehicle) and two treatment groups receiving 3xl0n one of two different rAAV: AAV-1 is an AAV PHP.eB capsid with a vector genome of CB7.CI.C9miR487.WPRE.rBG and AAV-2 is an AAV PHP.eB capsid with a vector genome of CB7.CI.C9miR487.WPRE.rBG, via tail vein injection at 4 weeks of age. FIG 7A is corrected for background and FIG 7B is uncorrected for background.
Detailed Description of the Invention
Sequences, vectors and compositions are provided here for co-administering to a patient a nucleic acid sequence which expresses human c9orf72 protein and a nucleic acid sequence encoding at least one miRNA which specifically targets a site in the endogenous hexanucleotide repeat expansion in the first intron of the human C9orf72 gene which target site is not present on the engineered C9orf72 coding sequence. Suitably, the engineered c9orf72 coding sequence is engineered to remove the specific target site for the miRNA. Novel engineered C9orf72 and novel miRNA target sequences are provided herein. These may be used alone or in combination with each other and/or other therapeutics for the treatment of C9orf72-associated ALS, FTD, and related disorders.
As used herein the term “endogenous C9orf72” refers to the C9orf72 gene (chromosome 9 open reading frame 72) which encodes the C9 protein in humans. The human C9orf72 gene is located on the short (p) arm of chromosome 9 open reading frame 72, from base pair 27,546,546 to base pair 27,573,866 (GRCh38). Its cytogenetic location is at 9p21. 2. This has also been termed C9orf72, chromosome 9 open reading frame 72, ALSFTD, FTD ALS, FTDALS1, DENNL72, C9orf72-SMCR8 complex subunit, DENND9. Dysfunction in C9orf72 is associated with ALS, familial FTD, or related disorders. In certain embodiments, functional C9 proteins having the sequence of SEQ NO: 14. However, in certain embodiments, the protein has less than 100% identity to the amino acid sequence of SEQ ID NO: 14 may be delivered by the compositions provided herein (e.g., an ORF a protein having 97% to 100% identity to SEQ ID NO: 14).
In one embodiment, an engineered C9orf72 coding sequence is provided which has the nucleic acid sequence of SEQ ID NO: 13 or a sequence of about 90%, at least 95% identical, at least 97% identical, at least 98% identical, or 99% to 100% identical to SEQ ID NO: 13 and which expresses the human C9 protein found in non-C9orf72-associated ALS and FTD patients. See, e.g., SEQ ID NO: 14.
In certain embodiments, an engineered C9orf72 coding sequence is provided which has the nucleic acid sequence of SEQ ID NO: 13 or a sequence at least 90% identical when the engineered coding sequence is co-administered with the miR487 sequence comprising at least a 5’ flanking region, at least SEQ ID NO: 15 (miR487) or a sequence at least 99% identical to SEQ ID NO: 15, and a 3’ flanking region, wherein the at least one miRNA does not bind to the engineered C9orf72 coding sequence of (a) or its encoded messenger RNA (mRNA). In certain embodiments, the 5’ flank is selected from a sequence of SEQ ID NO: 5 or SEQ ID NO: 22. Suitably, the sequence having identity to SEQ ID NO: 13 expresses the same protein.
A “5’ UTR” is upstream of the initiation codon for a gene product coding sequence. The 5’ UTR is generally shorter than the 3’ UTR. Generally, the 5’ UTR is about 3 nucleotides to about 200 nucleotides in length, but may optionally be longer.
A “3 ’ UTR” is downstream of the coding sequence for a gene product and is generally longer than the 5’ UTR. In certain embodiments, the 3’ UTR is about 200 nucleotides to about 800 nucleotides in length, but may optionally be longer or shorter.
As used herein, an “miRNA” refers to a microRNA which is a small non-coding RNA molecule which regulates mRNA and stops it from being translated to protein. Generally, hairpin-forming RNAs have a self-complementary “stem-loop” structure that includes a single nucleic acid encoding a stem portion having a duplex comprising a sense strand (e.g., passenger strand) connected to an antisense strand (e.g., guide strand) by a loop sequence. The passenger strand and the guide strand share complementarity. In some embodiments, the passenger strand and guide strand share 100% complementarity. In some embodiments, the passenger strand and guide strand share at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or at least 99% complementarity. A passenger strand and a guide strand may lack complementarity due to a base-pair mismatch. In some embodiments, the passenger strand and guide strand of a hairpin-forming RNA have at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7 at least 8, at least 9, or at least 10 mismatches. Generally, the first 2-8 nucleotides of the stem (relative to the loop) are referred to as “seed” residues and play an important role in target recognition and binding. The first residue of the stem (relative to the loop) is referred to as the “anchor” residue. In some embodiments, hairpin-forming RNA have a mismatch at the anchor residue. As used herein, the miRNA contains a “seed sequence” which is a region of nucleotides which specifically binds to mRNA (e.g., in the endogenous C9orf72) by complementary base pairing, leading to destruction or silencing of the mRNA. Such silencing may result in downregulation rather than complete extinguishing of the endogenous hC9orf72. Unless otherwise specified, the term “miRNA” encompasses artificial microRNA (amiRNA), which are artificially designed.
A “self-complementary nucleic acid” refers to a nucleic acid capable of hybridizing with itself (i.e., folding back upon itself) to form a single-stranded duplex structure, due to the complementarity (e.g., base-pairing) of the nucleotides within the nucleic acid strand. Self- complementary nucleic acids can form a variety of secondary structures, such as hairpin loops, loops, bulges, junctions and internal bulges. Certain self-complementary nucleic acids (e.g., miRNA or AmiRNA) perform regulatory functions, such as gene silencing.
The encoded miRNA provided herein have been designed to specifically target the endogenous human C9orf72 gene in patients having a C9ORF72-associated disorder such as ALS or FTD. In certain embodiments the miRNA coding sequence comprises an anti-sense sequence.
In certain embodiments, the seed sequence is 100% identical to the antisense sequence describe in the table. In certain embodiments, the seed sequence is located on the mature miRNA (5’ to 3’) and is generally starts at position 2 to 7, 2 to 8, or about 6 nucleotides from the 5’ end of the miRNA sense strand (from the 5’ end of the sense (+) strand) of the miRNA, although it may be longer than in length. In certain embodiments, the length of the seed sequence is no less than about 30% of the length of the miRNA sequence, which may be at least 7 nucleotides to about 28 nucleotides in length, at least 8 nucleotides to about 28 nucleotides in length, 7 nucleotides to 28 nucleotides, 8 nucleotides to 18 nucleotides, 12 nucleotides to 28 nucleotides in length, about 20 to about 26 nucleotides, about 21 nucleotides, about 24 nucleotides, or about 26 nucleotides. In the examples provided herein, the miRNA is delivered in the form of a stem-loop miRNA precursor sequences, e.g., about 50 to about 80 nucleotides in length, or about 55 nucleotides to about 70 nucleotides, or 60 to 65 nucleotides in length. In certain embodiments, this miRNA precursor comprises about 5 nucleotides, about a 21 -nucleotide seed sequence, about a 19 nucleotide stem loop and about a 19 nucleotide sense sequence, wherein the sense sequence corresponds to the anti-sense sequence with one or two nucleotides being mismatched. An example of a suitable miRNA coding sequence is the miR487 sequence (see, e.g., in the vector genome of SEQ ID NO: 17: The 5’ flank (nt 3438)..(nt 3460) (1-23 of SEQ ID NO: 5), miR487 (nt 3461)..(nt 3524), antisense (nt 3466)..(nt 3486), loop (nt 3487)..(nt 3505), sense (nt 3506)..(nt 3524), and 3’ flank (nt 3525).. (nt 3568). See, also SEQ ID NO:9.
In certain embodiments, the nucleic acid molecules (e.g., an expression cassette or vector genome) may contain at least one, or more than one miRNA coding sequence. In certain embodiments, the nucleic acid molecules (e.g., an expression cassette or vector genome) may contain one, two or more miRNA coding sequence of SEQ ID NO: 15 (miR487), or miR487 further comprising flanking regions (e.g., SE QID NO: 16). In certain embodiments, the nucleic acid molecules (e.g., an expression cassette or vector genome) may contain one, two or more miRNA coding sequence of SEQ ID NO: 15 (miR487, 64 nt) or SEQ ID NO: 16.
As used herein, an “miRNA target sequence” is a sequence located on the DNA positive strand (5’ to 3’) (e.g., of C9orf72) and is at least partially complementary to a miRNA sequence, including the miRNA seed sequence. The miRNA target sequence is exogenous to the untranslated region of the encoded transgene product and is designed to be specifically targeted by miRNA in cells in which repression of transgene expression is desired. Without wishing to be bound by theory, because hC9orf72 is a ubiquitous protein and excess expression may be associated with toxicity and/or other negative side effects, the miRNA preferentially target the endogenous hC9orf72 gene while avoiding targeting the engineered hC9orf72 gene which is delivered to the patient. More particularly, the sequences encoding the hC9orf72 which are delivered via a vector are designed to contain altered codon sequences at the target site.
Typically, the miRNA target sequence is at least 7 nucleotides to about 28 nucleotides in length, at least 8 nucleotides to about 28 nucleotides in length, 7 nucleotides to 28 nucleotides, 8 nucleotides to 18 nucleotides, 12 nucleotides to 28 nucleotides in length, about 20 to about 26 nucleotides, about 22 nucleotides, about 24 nucleotides, or about 26 nucleotides, and which contains at least one consecutive region (e.g., 7 or 8 nucleotides) which is complementary to the miRNA seed sequence. In certain embodiments, the target sequence comprises a sequence with exact complementarity (100%) or partial complementarity to the miRNA seed sequence with some mismatches. In certain embodiments, the target sequence comprises at least 7 to 8 nucleotides which are 100% complementary to the miRNA seed sequence. In certain embodiments, the target sequence consists of a sequence which is 100% complementary to the miRNA seed sequence. In certain embodiments, the target sequence contains multiple copies (e.g., two or three copies) of the sequence which is 100% complementary to the seed sequence. In certain embodiments, the region of 100% complementarity comprises at least 30% of the length of the target sequence. In certain embodiments, the remainder of the target sequence has at least about 80 % to about 99% complementarity to the miRNA. In certain embodiments, in an expression cassette containing a DNA positive strand, the miRNA target sequence is the reverse complement of the miRNA.
Thus, the sequences provided herein which are 95% to 99.9% identical to the mutant C9 coding sequences of SEQ ID NO: 13, are designed to avoid reverting to a native human sequence to which a selected miRNA in the construct is targeted. Preferably, these sequence encode native functional human C9 protein which is not associated with any disorder. For example, the protein may have the sequence of SEQ ID NO: 14 or a sequence about 95 to about 100% identical, or at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 14.
In certain embodiments, the miRNA preferentially targets the endogenous hC9 gene while avoiding targeting the engineered hc9 gene, wherein the endogenous C9orf72 isoform 2 nucleic acid sequence is reproduced in SEQ ID NO: 44 and the encoded protein is reproduced in SEQ ID NO: 45. [See, e.g., NCBI NM_018325.4 (C9orf72 Variant 2) and Ensembl ENST00000380003.8 (C9orf72-203)]. In certain embodiments, the miRNA coding sequence comprises one or more of : (i) 15 or 16. In certain embodiments, the engineered hC9 nucleic acid sequence is of SEQ ID NO: 13. In certain embodiments the engineered hC9 nucleic acid sequence is of SEQ ID NO: 13 wherein 1, 2, 3, or 4 nucleotide mismatches are present.
In certain embodiments, a single nucleic acid (e.g., an expression cassette or vector genome containing same) contains both the engineered hC9 coding sequence and at least one miRNA coding sequence, wherein the miRNA is specifically targeted to a region of the endogenous human C9 sequence not present in the engineered hC9 sequence. In certain embodiments, the human C9 coding sequence is upstream (5’) of the at least one miRNA and these two elements are separated by a spacer or linker sequence. In certain embodiments, there is at least 75 nucleotides between the stop codon of the hC9 coding sequence and the start of the most 5’ miRNA coding sequence. In certain embodiments, the spacer is about 75 nucleotides to about 300 nucleotides, or about 75 nucleotides to about 250 nucleotides, or about 75 nucleotides to about 200 nucleotides, or about 75 nucleotides to about 150 nucleotides, or about 75 nucleotides to about 100 nucleotides, or about 80 nucleotides to about 300 nucleotides, or about 80 nucleotides to about 250 nucleotides, or about 80 nucleotides to about 200 nucleotides, or about 80 nucleotides to about 150 nucleotides, or about 80 nucleotides to about 100 nucleotides,. Optionally, the engineered hC9 coding sequence and the at least one miRNA coding sequence are separated by about 75 nucleotides. Suitably, the spacer sequence is a non-coding sequence which lacks any restriction enzyme sites. Optionally, the spacer may include one or more intron sequences. In certain embodiments, one or more of the miRNA sequences may be located within the intron.
In certain embodiments, the engineered hC9 coding sequence and the miRNA coding sequence(s) are delivered via different nucleic acid sequences, e.g., two or more different vectors, a combination comprising a vector and an LNP, etc. In certain embodiments, the two different vectors are AAV vectors. In certain embodiments, these vectors have different expression cassettes. In other embodiments, these vectors have the same capsid. In other embodiments, the vectors have different embodiments. In certain embodiments, the miRNA coding sequence(s) are delivered via an LNP or another non-viral delivery system. In certain embodiments, the engineered hC9 sequence is delivered via an LNP or another non-viral delivery system. In certain embodiments, combinations of two or more different delivery systems (e.g., viral and non-viral, two different non-viral) are used. In these and other embodiments, the two or more different vectors or other delivery systems may be administered substantially simultaneously, or one or more of these systems may be delivered before the other. In certain embodiments, the engineered hC9 sequence is SEQ ID NO: 13, or a sequence 90% to 100% identical thereto which encodes an mRNA which is not bound by the miR with which it is co-administered and which encodes functional human C9orf72.
As used herein, the terms “AAV ,C9orf72” or “rAAV.h9ORF72” are used to refer to a recombinant adeno-associated virus which has an AAV capsid having therewithin a vector genome comprising a human C9orf72 coding sequence (e.g., a cDNA) under the control of regulatory sequences. As used herein, the terms “AAV.C9orf72.miRXXX” or “rAAV.C9orf72.miRXXX” are used to refer to a recombinant adeno-associated virus which has an AAV capsid having therewithin a vector genome comprising an miR targeting an endogenous human C9ORF72 coding sequence.
Specific capsid types may be specified, such as, e.g., AAV.C9orf72 or rAAVl.C9orf72, which refers to a recombinant AAV having an AAV1 capsid; AAVhu68.C9orf72 or AAVhu68.C9orf72, which refers to recombinant AAV having an AAVhu68 capsid. AAVrh91.C9orf72 or AAVrh91.C9orf72, which refers to recombinant AAV having an AAVrh91 capsid.
A “recombinant AAV” or “rAAV” is a DNAse-resistant viral particle containing two elements, an AAV capsid and a vector genome containing at least non-AAV coding sequences packaged within the AAV capsid. Unless otherwise specified, this term may be used interchangeably with the phrase “rAAV vector”. The rAAV is a “replication-defective virus” or “viral vector”, as it lacks any functional AAV rep gene or functional AAV cap gene and cannot generate progeny. In certain embodiments, the only AAV sequences are the AAV inverted terminal repeat sequences (ITRs), typically located at the extreme 5’ and 3’ ends of the vector genome in order to allow the gene and regulatory sequences located between the ITRs to be packaged within the AAV capsid. Generally, an AAV capsid is composed of 60 capsid (cap) protein subunits, VP1, VP2, and VP3, that are arranged in an icosahedral symmetry in a ratio of approximately 1: 1: 10 to 1: 1:20, depending upon the selected AAV. Various AAVs may be selected as sources for capsids of AAV viral vectors as identified above. In one embodiment, the AAV capsid is an AAV9 capsid or an engineered variant thereof. See, SEQ ID NO: 30 and 31. In certain embodiments, the variant AAV9 capsid is an AAV9.PhP.eB capsid. In certain embodiments, the PhP.eB capsid is selected for use in mouse studies and is a suitable model for a clade F vector (e.g., AAVhu68) in humans. In certain embodiments, the capsid protein is designated by a number or a combination of numbers and letters following the term “AAV” in the name of the rAAV vector.
Unless otherwise specified, the AAV capsid, ITRs, and other selected AAV components described herein, may be readily selected from among any AAV, including, without limitation, the AAVs identified as AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAVrhlO, AAVhu37, AAVrh32.33, AAV8bp, AAV7M8 and AAVAnc80, AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9.47, AAV9(hul4), AAV10, AAV11, AAV12, AAVrh8, AAVrh74, AAV-DJ8, AAV-DJ, AAVhu68, AAV9 variants (e.g., PCT/US21/61312, filed December 1, 2021 and US Provisional Application No. 63/119,863, filed December 1, 2020; and US Provisional Patent Application No. 63/178,881, filed April 23, 2021), AAVhu95 and AAVhu96 (see, US Provisional Application No. 63/251,599, filed October 2, 2021), without limitation. See, e.g., WO 2019/168961 and WO 2019/169004, both for Novel AAV Vectors Having Reduced Capsid Deamidation and Uses Therefor; US Published Patent Application No. 2007-0036760- Al; US Published Patent Application No. 2009-0197338-Al; EP 1310571. See also, WO 2003/042397 (AAV7 and other simian AAV), US Patent 7790449 and US Patent 7282199 (AAV8), WO 2005/033321 and US 7,906,111 (AAV9), and WO 2006/110689, and WO 2003/042397 (rh.10), WO 2005/033321, WO 2018/160582 (AAVhu68), which are incorporated herein by reference. See, also WO 2019/168961 and WO 2019/169004, describing deamidation profiles for these and other AAV capsids. In certain embodiments, the capsid, has two encoded amino acid differences as compared to another Clade F capsid, AAV9, with differences at positions 67 and 157, based on the numbering of the VP1 protein, shown in SEQ ID NO: 34 (see, SEQ ID NO: 32 and 33 for nucleotide sequence). In contrast, the other Clade F AAV (AAV9, hu31, hu31) have an Ala at position 67 and an Ala at position 157. See, e.g., WO 2022/082109, providing engineered AAVhu68 coding sequences, WO 2018/160582; WO 2019/169004; and WO 2019/168961, all of which are incorporated herein by reference in their entireties.
In certain embodiments, an AAVhu68 capsid is further characterized by one or more of the following. AAVhu68 capsid proteins comprise: AAVhu68 vpl proteins produced by expression from a nucleic acid sequence which encodes the amino acid sequence of 1 to 736 of SEQ ID NO: 34, vpl proteins produced from SEQ ID NO: 32 or 33, or vpl proteins produced from a nucleic acid sequence at least 70% identical to SEQ ID NO: 33 which encodes the predicted amino acid sequence of 1 to 736 of SEQ ID NO: 34; AAVhu68 vp2 proteins produced by expression from a nucleic acid sequence which encodes the amino acid sequence of at least about amino acids 138 to 736 of SEQ ID NO: 34, vp2 proteins produced from a sequence comprising at least nucleotides 412 to 2211 of SEQ ID NO: 32 or 33, or vp2 proteins produced from a nucleic acid sequence at least 70% identical to at least nucleotides 412 to 2211 of SEQ ID NO: 32 or 33 which encodes the predicted amino acid sequence of at least about amino acids 138 to 736 of SEQ ID NO: 34; and/or AAVhu68 vp3 proteins produced by expression from a nucleic acid sequence which encodes the predicted amino acid sequence of at least about amino acids 203 to 736 of SEQ ID NO: 34, vp3 proteins produced from a sequence comprising at least nucleotides 607 to 2211 of SEQ ID NO: 32 or 33, or vp3 proteins produced from a nucleic acid sequence at least 70% identical to at least nucleotides 607 to 2211 of SEQ ID NO: 32 or 33 which encodes the amino acid sequence of at least about amino acids 203 to 736 of SEQ ID NO: 34. In certain embodiments, an AAVhu68 capsid comprises: (i) heterogenous populations of AAVhu68 vpl proteins, AAVhu68 vp2 proteins, and AAVhu68 vp3 proteins produced from a nucleic acid sequence encoding SEQ ID NO: 34, wherein the AAVhu68vp 1 proteins comprise a glutamic acid at position 67 and a valine at position 157 and the AAVhu68vp2 proteins comprise a valine at position 157 based on the numbering of SEQ ID NO: 34; or (ii) heterogenous populations of AAVhu68 vpl, AAVhu68 vp2 and AAVhu68 vp3 proteins, wherein the AAVhu68 vpl proteins are amino acids 1 to 736 of SEQ ID NO: 34 (vpl) which comprise a glutamic acid at position 67 and a valine at position 157 and further comprise subpopulations of vpl proteins comprising modified amino acids based on the amino acids positions in SEQ ID NO: 34, wherein the AAVhu68 vp2 proteins are amino acids 138 to 736 of SEQ ID NO: 34 (vp2) which comprise a valine at position 157 and further comprise subpopulations of vp2 proteins comprising modified amino acids based on the amino acid positions in SEQ ID NO: 34, and wherein the AAVhu68 vp3 proteins are amino acids 203 to 736 of SEQ ID NO: 34 (vp3), which comprise subpopulations of vp3 proteins comprising modified amino acids based on the amino acid positions in SEQ ID NO: 34, wherein the AAVhu68 vpl, AAVhu68 vp2 and AAV hu68 vp3 proteins in (i) and (ii) comprise at least 50% to 100% deamidated asparagines (N) in asparagine - glycine pairs at each of positions 57, 329, 452, 512, relative to the amino acids in SEQ ID NO: 34, wherein the deamidated asparagines are deamidated to aspartic acid, isoaspartic acid, an interconverting aspartic acid/isoaspartic acid pair, or combinations thereof, as determined using mass spectrometry. In certain embodiments, the AAVhu68 capsid comprises: (a) a subpopulation of vpl proteins in which 75% to 100% of the N at position 57 of the vpl proteins are deamidated, as determined using mass spectrometry; and/or (b) subpopulations of vpl proteins, vp2 proteins, and/or vp3 proteins in which 75% to 100% of the N at position 329, based on the numbering of SEQ ID NO:34, are deamidated as determined using mass spectrometry; and/or (c) subpopulations of vpl proteins, vp2 proteins, and/or vp3 proteins in which 75% to 100% of the N at position 452, based on the numbering of SEQ ID NO:34, are deamidated as determined using mass spectrometry; and/or (d) subpopulations of vpl proteins, vp2 proteins, and/or vp3 proteins in which 75% to 100% of the N at position 512, based on the numbering of SEQ ID NO:34, are deamidated as determined using mass spectrometry.
Other suitable sequences may include, e.g., AAVhu95 [engineered VP1 nucleic acid sequence SEQ ID NO: 26; amino acid sequence SEQ ID NO: 1 and 35]; AAVhu96 [engineered AAVhu96 VP1 nucleic acid sequence, SEQ ID NO: 28; AAV hu96 VP1 amino acid sequence, SEQ ID NO: 29],
Other suitable AAVs may include, without limitation, AAVrh90 [PCT/US20/30273, fded April 28, 2020], AAVrh91 [see, SEQ ID NO: 37 and 38; PCT/US20/30266, filed April 28, 2020 and US Provisional Patent Applications No. 63/109,734, filed November 4, 2020 and US Provisional Patent Application No. 63/065,616, filed August 14, 2020] AAVrh92, AAVrh93, AAVrh91.93 [PCT/US20/30281, filed April 28, 2020], which are incorporated by reference herein. Other suitable AAV include AAV3B variants which are described in PCT/US20/56511, filed October 20, 2020, describing AAV3B.AR2.01, AAV3B.AR2.02, AAV3B.AR2.03, AAV3B.AR2.04, AAV3B.AR2.05, AAV3B.AR2.06, AAV3B.AR2.07, AAV3B.AR2.08, AAV3B.AR2. 10, AAV3B.AR2. 11, AAV3B.AR2. 12, AAV3B.AR2. 13, AAV3B.AR2. 14, AAV3B.AR2. 15, AAV3B.AR2. 16, or AAV3B.AR2. 17, which are incorporated herein by reference. These documents also describe other AAV capsids which may be selected for generating rAAV and are incorporated by reference. Among the AAVs isolated or engineered from human or non-human primates (NHP) and well characterized, human AAV2 is the first AAV that was developed as a gene transfer vector; it has been widely used for efficient gene transfer experiments in different target tissues and animal models.
As used herein, a “vector genome” refers to the nucleic acid sequence packaged inside a parvovirus (e.g., rAAV) capsid which forms a viral particle. Such a nucleic acid sequence contains AAV inverted terminal repeat sequences (ITRs). In the examples herein, a vector genome contains, at a minimum, from 5’ to 3’, an AAV 5’ ITR, coding sequence(s) (i.e., transgene(s)), and an AAV 3’ ITR. ITRs from AAV2, a different source AAV than the capsid, or other than full-length ITRs may be selected. In certain embodiments, the ITRs are from the same AAV source as the AAV which provides the rep function during production or a transcomplementing AAV. Further, other ITRs, e.g., self-complementary (scAAV) ITRs, may be used. Both single-stranded AAV and self-complementary (sc) AAV are encompassed with the rAAV. The transgene is a nucleic acid coding sequence, heterologous to the vector sequences, which encodes a polypeptide, protein, functional RNA molecule (e.g., miRNA, miRNA inhibitor) or other gene product, of interest. The nucleic acid coding sequence is operatively linked to regulatory components in a manner which permits transgene transcription, translation, and/or expression in a cell of a target tissue. Suitable components of a vector genome are discussed in more detail herein.
In one example, a “vector genome” contains, at a minimum, from 5’ to 3’, a vectorspecific sequence, a nucleic acid sequence comprising an engineered human C9orf72 coding sequence and optionally an miRNA sequences targeting the endogenous C9orf72 operably linked to regulatory control sequences (which direct their expression in a target cell), where the vector-specific sequence may be a terminal repeat sequence which specifically packages the vector genome into a viral vector capsid or envelope protein. For example, AAV inverted terminal repeats are utilized for packaging into AAV and certain other parvovirus capsids.
In certain embodiments, a composition is provided which comprises an aqueous liquid suitable for intrathecal injection and a stock of vector (e.g., rAAV having a AAV capsid which preferentially targets cells in the central nervous system and/or the dorsal root ganglia (e.g., CNS, including, e.g., nerve cells (such as, pyramidal, purkinje, granule, spindle, and interneuron cells) and glia cells (such as astrocytes, oligodendrocytes, microglia, and ependymal cells), wherein the vector having an engineered hC9orf72 coding sequence and/or an at least one miRNA specific endogenous hC9orf72 for delivery to the central nervous system (CNS). In certain embodiments, the composition comprising one or more vectors as described herein is formulated for sub-occipital injection into the cistema magna (intra- cistema magna). In certain embodiments, the composition is administered via a computed tomography- (CT-) rAAV injection. In certain embodiments, the composition is administered using Ommaya reservoir. In certain embodiments, the patient is administered a single dose of the composition.
As used herein, an “expression cassette” refers to a nucleic acid molecule which comprises a biologically useful nucleic acid sequence (e.g., a gene cDNA encoding a protein, enzyme or other useful gene product, mRNA, etc.) and regulatory sequences operably linked thereto which direct or modulate transcription, translation, and/or expression of the nucleic acid sequence and its gene product. As used herein, “operably linked” sequences include both regulatory sequences that are contiguous or non-contiguous with the nucleic acid sequence and regulatory sequences that act in trans or cis nucleic acid sequence. Such regulatory sequences typically include, e.g., one or more of a promoter, an enhancer, an intron, a Kozak sequence, a polyadenylation sequence, and a TATA signal. The expression cassette may contain regulatory sequences upstream (5’ to) of the gene sequence, e.g., one or more of a promoter, an enhancer, an intron, etc., and one or more of an enhancer, or regulatory sequences downstream (3’ to) a gene sequence, e.g., 3’ untranslated region (3’ UTR) comprising a polyadenylation site, among other elements. In certain embodiments, the regulatory sequences are operably linked to the nucleic acid sequence of a gene product, wherein the regulatory sequences are separated from nucleic acid sequence of a gene product by an intervening nucleic acid sequences, i.e., 5 ’-untranslated regions (5’UTR). In certain embodiments, the expression cassette comprises nucleic acid sequence of one or more of gene products. In some embodiments, the expression cassette can be a monocistronic or a bicistronic expression cassette. In other embodiments, the term “transgene” refers to one or more DNA sequences from an exogenous source which are inserted into a target cell.
Typically, such an expression cassette can be used for generating a viral vector and contains the coding sequence for the gene product described herein flanked by packaging signals of the viral genome and other expression control sequences such as those described herein. In certain embodiments, a vector genome may contain two or more expression cassettes. In certain embodiment expression cassette comprises the C9orf72 coding sequences and miRNA sequences targeting the endogenous C9orf72), promoter, and may include other regulatory sequences therefor, which cassette may be packaged into a vector (e.g., rAAV, lentivirus, retrovirus, etc.).
AAV
Recombinant parvoviruses are particularly well suited as vectors. As described herein, recombinant parvoviruses may contain an AAV capsid (or bocavirus capsid). In certain embodiments, the capsid targets cells within the dorsal root ganglion and/or cells within the lower motor neurons and/or primary sensory neurons. In certain embodiments, compositions provided herein may have a single rAAV stock which comprises an rAAV comprising an engineered hC9orf72 and an miRNA specifically targeting endogenous hC9orf72 in order to downregulate the endogenous hC9orf72 levels and to reduce any toxicity associated with overexpression of hC9orf72. In other embodiments, an rAAV may be comprise the hC9orf72 and may be co-administered with a different vector comprising an miRNA which downregulates endogenous hC9orf72. In other embodiments, an rAAV may be comprise the at least one miRNA which downregulates endogenous hC9orf72 and a second vector (or other composition) delivers the hC9orf72.
For example, vectors generated using AAV capsids from Clade F (e.g., AAVhu68 or AAV9) can be used to produce vectors which target and express hC9orf72 in the CNS. Alternatively, vectors generated using AAV capsids from Clade A (e.g., AAV1, AAVrh91) may be selected. In still other embodiments, other parvovirus or other AAV viruses may be suitable sources of AAV capsids.
An AAV 1 capsid refers to a capsid having AAV vp 1 proteins, AAV vp2 proteins and AAV vp3 proteins. In particular embodiments, the AAV 1 capsid comprises a pre-determined ratio of AAV vpl proteins, AAV vp2 proteins and AAV vp3 proteins of about 1: 1: 10 assembled into a T1 icosahedron capsid of 60 total vp proteins. An AAV1 capsid is capable of packaging genomic sequences to form an AAV particle (e.g., a recombinant AAV where the genome is a vector genome). Typically, the capsid nucleic acid sequences encoding the longest of the vp proteins, i.e., VP1, is expressed in trans during production of an rAAV having an AAV1 capsid are described in, e.g., US Patent 6,759,237, US Patent 7,105,345, US Patent 7,186,552, US Patent 8,637,255, and US Patent 9,567,607, which are incorporated herein by reference. See, also, WO 2018/168961, which is incorporated by reference. In certain embodiments, AAV 1 is characterized by a capsid composition of a heterogenous population of VP isoforms which are deamidated as defined in WO 2018/160582, incorporated herein by reference in its entirety, based on the total amount of VP proteins in the capsid, as determined using mass spectrometry. In certain embodiments, the AAV capsid is modified at one or more of the following positions, in the ranges provided below, as determined using mass spectrometry. Suitable modifications include those described in the paragraph above labelled modulation of deamidation, which is incorporated herein. In certain embodiments, one or more of the following positions, or the glycine following the N is modified as described herein. In certain embodiments, an AAV 1 mutant is constructed in which the glycine following the N at position 57, 383, 512 and/or 718 are preserved (i.e., remain unmodified). In certain embodiments, the NG at the four positions identified in the preceding sentence are preserved with the native sequence. In certain embodiments, an artificial NG is introduced into a different position than one of the positions as defined and identified in WO 2018/160582, incorporated herein by reference.
As used herein, an AAVhu68 capsid refers to a capsid as defined in WO 2018/160582, incorporated herein by reference. As described herein, a rAAVhu68 has a rAAVhu68 capsid produced in a production system expressing capsids from an AAVhu68 nucleic acid. In certain embodiments, the AAVhu68 nucleic acid sequence is SEQ ID NO: 32 or 33, encoding and for an amino acid sequence of SEQ ID NO 34. In certain embodiments, the AAVhu68 nucleic acid sequence is SEQ ID NO: 32 or 33, encoding for an amino acid sequence of SEQ ID NO: 34. The rAAVhu68 resulting from production using a single nucleic acid sequence vpl produces the heterogenous populations of vpl proteins, vp2 proteins and vp3 proteins. These subpopulations include, at a minimum, deamidated asparagine (N or Asn) residues. For example, asparagines in asparagine - glycine pairs are highly deamidated. In certain embodiments, the vp2 and/or vp3 proteins may be expressed additionally or alternatively from different nucleic acid sequences than the vpl, e.g., to alter the ratio of the vp proteins in a selected expression system.
Genomic sequences which are packaged into an AAV capsid and delivered to a host cell are typically composed of, at a minimum, a transgene and its regulatory sequences, and AAV inverted terminal repeats (ITRs). Both single-stranded AAV and self-complementary (sc) AAV are encompassed with the rAAV. The transgene is a nucleic acid coding sequence, heterologous to the vector sequences, which encodes a polypeptide, protein, functional RNA molecule (e.g., miRNA, miRNA inhibitor) or other gene product, of interest. The nucleic acid coding sequence is operatively linked to regulatory components in a manner which permits transgene transcription, translation, and/or expression in a cell of a target tissue.
The AAV sequences of the vector typically comprise the cis-acting 5' and 3' inverted terminal repeat sequences (See, e.g., B. J. Carter, in “Handbook of Parvoviruses”, ed., P. Tijsser, CRC Press, pp. 155 168 (1990)). The ITR sequences are about 145 bp in length. Preferably, substantially the entire sequences encoding the ITRs are used in the molecule, although some degree of minor modification of these sequences is permissible. The ability to modify these ITR sequences is within the skill of the art. (See, e.g., texts such as Sambrook et al, “Molecular Cloning. A Laboratory Manual”, 2d ed., Cold Spring Harbor Laboratory, New York (1989); and K. Fisher et al., J. Virol., 70:520 532 (1996)). An example of such a molecule employed in the present invention is a “cis-acting” plasmid containing the transgene, in which the selected transgene sequence and associated regulatory elements are flanked by the 5' and 3' AAV ITR sequences.
The ITRs are the genetic elements responsible for the replication and packaging of the genome during vector production and are the only viral cis elements required to generate rAAV. In one embodiment, the ITRs are from an AAV different than that supplying a capsid. In a preferred embodiment, the ITR sequences from AAV2, or the deleted version thereof (AITR), which may be used for convenience and to accelerate regulatory approval. However, ITRs from other AAV sources may be selected. Where the source of the ITRs is from AAV2 and the AAV capsid is from another AAV source, the resulting vector may be termed pseudotyped. Typically, AAV vector genome comprises an AAV 5 ’ ITR, the nucleic acid sequences encoding the gene product(s) and any regulatory sequences, and an AAV 3’ ITR. However, other configurations of these elements may be suitable. In one embodiment, a self- complementary AAV is provided. A shortened version of the 5’ ITR, termed AITR, has been described in which the D-sequence and terminal resolution site (trs) are deleted. In certain embodiments, the vector genome includes a shortened AAV2 ITR of 130 base pairs, wherein the external “a” element is deleted. The shortened ITR is reverted back to the wild-type length of 145 base pairs during vector DNA amplification using the internal A element as a template. In other embodiments, the full-length AAV 5’ and 3’ ITRs are used.
In addition to the major elements identified above for the vector (e.g., an rAAV), the vector also includes conventional control elements necessary which are operably linked to the transgene in a manner which permits its transcription, translation and/or expression in a cell. As used herein, the term “expression” or “gene expression” refers to the process by which information from a gene is used in the synthesis of a functional gene product. The gene product may be a protein, a peptide, or a nucleic acid polymer (such as an RNA, a DNA or a PNA).
As used herein, the term "regulatory sequence", or "expression control sequence" refers to nucleic acid sequences, such as initiator sequences, enhancer sequences, and promoter sequences, which induce, repress, or otherwise control the transcription of protein encoding nucleic acid sequences to which they are operably linked. The regulatory control elements typically contain a promoter sequence as part of the expression control sequences, e.g., located between the selected 5’ ITR sequence and the coding sequence. In particularly desirable embodiments, a tissues specific promoter for the central nervous system is selected. For example, the promoter may be a neural cell promoter, e.g., gfaABC(l)D promoter (Addgene #50473)), or the human Syn promoter (the sequence is available from Addgene, Ref. #50465).
Other suitable promoters may include, e.g., constitutive promoters, regulatable promoters [see, e.g., WO 2011/126808 and WO 2013/04943], tissue specific promoters, or a promoter responsive to physiologic cues may be used may be utilized in the vectors described herein. The promoter(s) can be selected from different sources, e.g., human cytomegalovirus (CMV) immediate-early enhancer/promoter, the SV40 early enhancer/promoter, the JC polymovirus promoter, myelin basic protein (MBP) or glial fibrillary acidic protein (GFAP) promoters, herpes simplex virus (HSV-1) latency associated promoter (LAP), rouse sarcoma virus (RSV) long terminal repeat (LTR) promoter, neuron-specific promoter (NSE), platelet derived growth factor (PDGF) promoter, hSYN, melanin-concentrating hormone (MCH) promoter, CBA, matrix metalloprotein promoter (MPP), and the chicken beta-actin promoter. In addition to a promoter a vector may contain one or more other appropriate transcription initiation, termination, enhancer sequences, efficient RNA processing signals such as splicing and polyadenylation (polyA) signals; sequences that stabilize cytoplasmic mRNA for example WPRE; sequences that enhance translation efficiency (i.e., Kozak consensus sequence); sequences that enhance protein stability; and when desired, sequences that enhance secretion of the encoded product. An example of a suitable enhancer is the CMV enhancer. Other suitable enhancers include those that are appropriate for desired target tissue indications. In one embodiment, the expression cassette comprises one or more expression enhancers. In one embodiment, the expression cassette contains two or more expression enhancers. These enhancers may be the same or may differ from one another. For example, an enhancer may include a CMV immediate early (IE) enhancer. In certain embodiments, an enhancer may include CMV IE enhancer (C4) comprising nucleic acid sequence of SEQ ID NO: 3. This enhancer may be present in two copies which are located adjacent to one another. Alternatively, the dual copies of the enhancer may be separated by one or more sequences. In still another embodiment, the expression cassette further contains an intron, e.g., the chicken beta-actin intron. In certain embodiments, an expression cassette comprises an intron which is a chicken beta actin intron comprising SEQ ID NO: 47. Other suitable introns include those known in the art, e.g., such as are described in WO 2011/126808. Examples of suitable polyA sequences include, e.g., SV40, SV50, bovine growth hormone (bGH), human growth hormone, and synthetic polyAs. In certain embodiments, the polyA is SV40 polyA. In certain embodiments, the polyA is rabbit globin poly A (RBG). In certain embodiments, the polyA is RBG polyA comprising SEQ ID NO: 10. Optionally, one or more sequences may be selected to stabilize mRNA. An example of such a sequence is a modified WPRE sequence, which may be engineered upstream of the polyA sequence and downstream of the coding sequence [see, e.g., MA Zanta-Boussif, et al, Gene Therapy (2009) 16: 605-619.
In certain embodiments, the vector genome comprises a tissue specific promoter In some embodiments, the tissue specific promoter is a human synapsin promoter. In certain embodiments, the human synapsin promoter comprises nucleic acid sequence of SEQ ID NO: 6. In certain embodiments, the vector genome comprises a constitutive promoter, wherein the promoter is a CB7 promoter or a variant thereof, e.g., a CAG promoter. In certain embodiments, CB7 or a variant thereof is a hybrid promoter (promoter element) comprising, at a minimum, a human cytomegalovirus (CMV) immediate early (IE) enhancer and a chicken [3- actin (CB or CBA) promoter. In certain embodiments, a CB7 promoter or variant refers to a human cytomegalovirus (CMV) immediate early (IE) enhancer (C4), a chicken beta actin (CB) promoter, optionally an intron, and optional spacer sequences linking the elements of the hybrid promoter. See, e.g., chicken beta actin promoter with a cytomegalovirus enhancer. In certain embodiments, a CB7 promoter or promoter element refers to a human cytomegalovirus (CMV) immediate early (IE) enhancer (C4), a chicken beta actin (CB) promoter, an intron, and optional spacer sequences linking the elements of the hybrid promoter. In certain embodiments, a CB7 promoter or promoter element refers to a human cytomegalovirus (CMV) immediate early (IE) enhancer (C4), a chicken beta actin (CB) promoter, an intron which comprises chicken beta actin intron with rabbit beta globin splicing donor, and optional spacer sequences linking the elements of the hybrid promoter. In certain embodiments, a CB7 promoter or promoter element refers to a human cytomegalovirus (CMV) immediate early (IE) enhancer (C4) (SEQ ID NO: 3), a chicken beta actin (CB) promoter (SEQ ID NO: 46), optionally an intron (SEQ ID NO: 47), and optional spacer sequences linking the elements of the hybrid promoter. In certain embodiments, a CB7 promoter or promoter element refers to a human cytomegalovirus (CMV) immediate early (IE) enhancer (SEQ ID NO: 51), a chicken beta actin (CB) promoter (SEQ ID NO: 52), optionally an intron (SEQ ID NO: 53), and optional spacer sequences linking the elements of the hybrid promoter. In certain embodiments, a CB7 promoter or promoter element comprises nucleic acid sequence of SEQ ID NO:4. In certain embodiments, a CB7 promoter or promoter element comprises nucleic acid sequence of SEQ ID NO: 43. In certain embodiments, a CB7 promoter or promoter element comprises nucleic acid sequence of SEQ ID NO: 48. In certain embodiments, a CB7 promoter or promoter element comprises nucleic acid sequence of SEQ ID NO: 49. In certain embodiments, a CB7 promoter or promoter element comprises nucleic acid sequence of SEQ ID NO: 50. Preferably, the spacer sequences are non-coding and in certain embodiments, may be of different lengths.
In one embodiment, the vector genome comprises: an AAV 5’ ITR, a promoter, an optional enhancer, an optional intron, a coding sequence for human C9orf72 (hC9orf72 or huC9orf72) comprising same, a poly A, and an AAV 3 ’ ITR. In certain embodiment, the vector genome is an AAV2 5’ ITR, a CB7 promoter or variant thereof, an engineered C9orf72, a linker, a miR targeted to endogenous C9orf72 sequence, a rabbit beta globin poly A, and an AAV2 3’ ITR. In certain embodiment, the vector genome is an AAV2 5’ ITR, a CB7 promoter or variant thereof, intron, C9orf72, a rabbit beta globin poly A, and an AAV2 3’ ITR. In certain embodiment, the vector genome is an AAV2 5’ ITR, CB7 promoter or variant thereof, an engineered huC9orf72, a linker, a miR487 sequence, a rabbit beta globin poly A, and an AAV2 3’ ITR. The huC9orf72 coding sequences are selected from those defined in the present specification. See, e.g., SEQ ID NO: 13 or a sequence at least 95% to 99.9% identical thereto, or a fragment thereof as defined herein. In certain embodiments, other C9orf72 coding sequences may be combined with the miR487 provided herein. Other elements of the vector genome or variations on these sequences may be selected for the vector genomes for certain embodiments of this invention.
Vector Production
For use in producing an AAV viral vector (e.g., a recombinant (r) AAV), the expression cassettes can be carried on any suitable vector, e.g., a plasmid, which is delivered to a packaging host cell. The plasmids useful in this invention may be engineered such that they are suitable for replication and packaging in vitro in prokaryotic cells, insect cells, mammalian cells, among others. Suitable transfection techniques and packaging host cells are known and/or can be readily designed by one of skill in the art.
In certain embodiments, the production plasmid comprises a vector genome for packaging into a capsid which comprises: (a) an engineered nucleic acid sequence encoding human C9orf72; (b) a spacer sequence located between (a) and (c); (c) at least one miRNA sequence specific for endogenous human C9orf72 in a patient located 3’ to the sequence of (a) and (b); wherein the engineered nucleic acid sequence of (a) lacks the target site for the at least one miRNA, thereby preventing the miRNA from targeting the engineered human C9orf72 coding sequence; (c) regulatory sequences operably linked to (a) and (c). In certain embodiments, the production plasmid comprises a vector genome comprising nucleic acid sequence of SEQ ID NO: 1, or an 5’ ITR - expression cassette of SEQ ID NO: 4 - 3’ ITR.
Methods for generating and isolating AAVs suitable for use as vectors are known in the art. See generally, e.g., Grieger & Samulski, 2005, “Adeno-associated virus as a gene therapy vector: Vector development, production and clinical applications,” Adv. Biochem. Engin/Biotechnol. 99: 119-145; Buning et al., 2008, “Recent developments in adeno- associated virus vector technology,” J. Gene Med. 10:717-733; and the references cited below, each of which is incorporated herein by reference in its entirety. For packaging a transgene into virions, the ITRs are the only AAV components required in cis in the same construct as the nucleic acid molecule containing the expression cassettes. The cap and rep genes can be supplied in trans.
In one embodiment, the expression cassettes described herein are engineered into a genetic element (e.g., a shuttle plasmid) which transfers the immunoglobulin construct sequences carried thereon into a packaging host cell for production a viral vector. In one embodiment, the selected genetic element may be delivered to an AAV packaging cell by any suitable method, including transfection, electroporation, liposome delivery, membrane fusion techniques, high velocity DNA-coated pellets, viral infection and protoplast fusion. Stable AAV packaging cells can also be made. Alternatively, the expression cassettes may be used to generate a viral vector other than AAV, or for production of mixtures of antibodies in vitro. The methods used to make such constructs are known to those with skill in nucleic acid manipulation and include genetic engineering, recombinant engineering, and synthetic techniques. See, e.g., Molecular Cloning: A Laboratory Manual, ed. Green and Sambrook, Cold Spring Harbor Press, Cold Spring Harbor, NY (2012).
The term “AAV intermediate” or “AAV vector intermediate” refers to an assembled rAAV capsid which lacks the desired genomic sequences packaged therein. These may also be termed an “empty” capsid. Such a capsid may contain no detectable genomic sequences of an expression cassette, or only partially packaged genomic sequences which are insufficient to achieve expression of the gene product. These empty capsids are non-functional to transfer the gene of interest to a host cell.
The recombinant adeno-associated virus (AAV) described herein may be generated using techniques which are known. See, e.g., WO 2003/042397; WO 2005/033321, WO 2006/110689; US 7588772 B2. Such a method involves culturing a host cell which contains a nucleic acid sequence encoding an AAV capsid protein; a functional rep gene; an expression cassette as described herein flanked by AAV inverted terminal repeats (ITRs) and a transgene; and sufficient helper functions to permit packaging of the expression cassette into the AAV capsid protein. Also provided herein is the host cell which contains a nucleic acid sequence encoding an AAV capsid; a functional rep gene; a vector genome as described; and sufficient helper functions to permit packaging of the vector genome into the AAV capsid protein. In one embodiment, the host cell is a HEK 293 cell. These methods are described in more detail in W02017160360 A2, which is incorporated by reference herein. Methods of generating the capsid, coding sequences therefor, and methods for production of rAAV viral vectors have been described. See, e.g., Gao, et al, Proc. Natl. Acad. Sci. U.S.A. 100 (10), 6081-6086 (2003) and US 2013/0045186A1.
In one embodiment, a production cell culture useful for producing a recombinant AAV is provided. Such a cell culture contains a nucleic acid which expresses the AAV capsid protein in the host cell; a nucleic acid molecule suitable for packaging into the AAV capsid, e.g., a vector genome which contains AAV ITRs and a non-AAV nucleic acid sequence encoding a gene product operably linked to sequences which direct expression of the product in a host cell; and sufficient AAV rep functions and adenovirus helper functions to permit packaging of the nucleic acid molecule into the recombinant AAV capsid. In one embodiment, the cell culture is composed of mammalian cells (e.g., human embryonic kidney 293 cells, among others) or insect cells (e.g., baculovirus).
Typically, the rep functions are from the same AAV source as the AAV providing the ITRs flanking the vector genome. In the examples herein, the AAV2 ITRs are selected and the AAV2 rep is used. Optionally, other rep sequences or another rep source (and optionally another ITR source) may be selected. For example, the rep may be, but is not limited to, AAV1 rep protein, AAV2 rep protein; or rep 78, rep 68, rep 52, rep 40, rep68/78 and rep40/52; or a fragment thereof; or another source. Optionally, the rep and cap sequences are on the same genetic element in the cell culture. There may be a spacer between the rep sequence and cap gene. Any of these AAV or mutant AAV capsid sequences may be under the control of exogenous regulatory control sequences which direct expression thereof in a host cell.
In one embodiment, cells are manufactured in a suitable cell culture (e.g., HEK 293) cells. Methods for manufacturing the gene therapy vectors described herein include methods well known in the art such as generation of plasmid DNA used for production of the gene therapy vectors, generation of the vectors, and purification of the vectors. In some embodiments, the gene therapy vector is an AAV vector and the plasmids generated are an AAV cis-plasmid encoding the AAV genome and the gene of interest, an AAV trans-plasmid containing AAV rep and cap genes, and an adenovirus helper plasmid. The vector generation process can include method steps such as initiation of cell culture, passage of cells, seeding of cells, transfection of cells with the plasmid DNA, post-transfection medium exchange to serum free medium, and the harvest of vector-containing cells and culture media.
In certain embodiments, the manufacturing process for rAAV.C9orf72.miR involves transient transfection of HEK293 cells with plasmid DNA. A single batch or multiple batches are produced by PEI-mediated triple transfection of HEK293 cells in PALL iCELLis bioreactors. Harvested AAV material are purified sequentially by clarification, TFF, affinity chromatography, and anion exchange chromatography in disposable, closed bioprocessing systems where possible.
The harvested vector-containing cells and culture media are referred to herein as crude cell harvest. In yet another system, the gene therapy vectors are introduced into insect cells by infection with baculovirus-based vectors. For reviews on these production systems, see generally, e.g., Zhang et al., 2009, “Adenovirus-adeno-associated virus hybrid for large-scale recombinant adeno-associated virus production,” Human Gene Therapy 20:922-929, the contents of each of which is incorporated herein by reference in its entirety. Methods of making and using these and other AAV production systems are also described in the following U.S. patents, the contents of each of which is incorporated herein by reference in its entirety: 5,139,941; 5,741,683; 6,057,152; 6,204,059; 6,268,213; 6,491,907; 6,660,514; 6,951,753; 7,094,604; 7,172,893; 7,201,898; 7,229,823; and 7,439,065, which are incorporated herein by reference. See, also, US Provisional Patent Application No. 63/371,597, filed August 16, 2022, entitled “Scalable Methods for Producing rAAV with Packaged Vector Genomes, and US Provisional Patent Application No. 63/371,592, filed August 16, 2022, entitled "Scalable Methods for Downstream Purification of Recombinant Adeno-associated Virus”, both incorporated by reference in their entirety. The crude cell harvest may thereafter be subject to additional method steps such as concentration of the vector harvest, diafiltration of the vector harvest, microfluidization of the vector harvest, nuclease digestion of the vector harvest, filtration of microfluidized intermediate, crude purification by chromatography, crude purification by ultracentrifugation, buffer exchange by tangential flow filtration, and/or formulation and filtration to prepare bulk vector.
A two-step affinity chromatography purification at high salt concentration followed anion exchange resin chromatography are used to purify the vector drug product and to remove empty capsids. These methods are described in more detail in International Patent Application No. PCT/US2016/065970, filed December 9, 2016, which is incorporated by reference herein. Purification methods for AAV8, International Patent Application No. PCT/US2016/065976, filed December 9, 2016, and rhlO, International Patent Application No. PCT/US16/66013, filed December 9, 2016, entitled “Scalable Purification Method for AAVrhlO”, also filed December 11, 2015, and for AAV1, International Patent Application No. PCT/US2016/065974, filed December 9, 2016, for “Scalable Purification Method for AAV1”, filed December 11, 2015, are all incorporated by reference herein.
To calculate empty and full particle content, VP3 band volumes for a selected sample {e.g., in examples herein an iodixanol gradient-purified preparation where # of GC = # of particles) are plotted against GC particles loaded. The resulting linear equation (y = mx+c) is used to calculate the number of particles in the band volumes of the test article peaks. The number of particles (pt) per 20 pL loaded is then multiplied by 50 to give particles (pt) /mL. Pt/mL divided by GC/mL gives the ratio of particles to genome copies (pt/GC). Pt/mL- GC/mL gives empty pt/mL. Empty pt/mL divided by pt/mL and x 100 gives the percentage of empty particles.
Generally, methods for assaying for empty capsids and AAV vector particles with packaged genomes have been known in the art. See, e.g., Grimm et al., Gene Therapy (1999) 6: 1322-1330; Sommer et al., Molec. Ther. (2003) 7: 122-128. To test for denatured capsid, the methods include subjecting the treated AAV stock to SDS-polyacrylamide gel electrophoresis, consisting of any gel capable of separating the three capsid proteins, for example, a gradient gel containing 3-8% Tris-acetate in the buffer, then running the gel until sample material is separated, and blotting the gel onto nylon or nitrocellulose membranes, preferably nylon. Anti- AAV capsid antibodies are then used as the primary antibodies that bind to denatured capsid proteins, preferably an anti -AAV capsid monoclonal antibody, most preferably the B 1 anti- AAV-2 monoclonal antibody (Wobus et al., J. Virol. (2000) 74:9281-9293). A secondary antibody is then used, one that binds to the primary antibody and contains a means for detecting binding with the primary antibody, more preferably an anti-IgG antibody containing a detection molecule covalently bound to it, most preferably a sheep anti-mouse IgG antibody covalently linked to horseradish peroxidase. A method for detecting binding is used to semi- quantitatively determine binding between the primary and secondary antibodies, preferably a detection method capable of detecting radioactive isotope emissions, electromagnetic radiation, or colorimetric changes, most preferably a chemiluminescence detection kit. For example, for SDS-PAGE, samples from column fractions can be taken and heated in SDS- PAGE loading buffer containing reducing agent (e.g., DTT), and capsid proteins were resolved on pre-cast gradient polyacrylamide gels (e.g., Novex). Silver staining may be performed using SilverXpress (Invitrogen, CA) according to the manufacturer's instructions or other suitable staining method, i.e., SYPRO ruby or coomassie stains. In one embodiment, the concentration of AAV vector genomes (vg) in column fractions can be measured by quantitative real time PCR (Q-PCR). Samples are diluted and digested with DNase I (or another suitable nuclease) to remove exogenous DNA. After inactivation of the nuclease, the samples are further diluted and amplified using primers and a TaqMan™ Anorogenic probe specific for the DNA sequence between the primers. The number of cycles required to reach a defined level of Auorescence (threshold cycle, Ct) is measured for each sample on an Applied Biosystems Prism 7700 Sequence Detection System. Plasmid DNA containing identical sequences to that contained in the AAV vector is employed to generate a standard curve in the Q-PCR reaction. The cycle threshold (Ct) values obtained from the samples are used to determine vector genome titer by normalizing it to the Ct value of the plasmid standard curve. End-point assays based on the digital PCR can also be used.
In one aspect, an optimized q-PCR method is used which utilizes a broad-spectrum serine protease, e.g., proteinase K (such as is commercially available from Qiagen). More particularly, the optimized qPCR genome titer assay is similar to a standard assay, except that after the DNase I digestion, samples are diluted with proteinase K buffer and treated with proteinase K followed by heat inactivation. Suitably samples are diluted with proteinase K buffer in an amount equal to the sample size. The proteinase K buffer may be concentrated to 2-fold or higher. Typically, proteinase K treatment is about 0.2 mg/mL, but may be varied from 0. 1 mg/mL to about 1 mg/mL. The treatment step is generally conducted at about 55 °C for about 15 minutes, but may be performed at a lower temperature (e.g., about 37 °C to about 50 °C) over a longer time period (e.g., about 20 minutes to about 30 minutes), or a higher temperature (e.g., up to about 60 °C) for a shorter time period (e.g., about 5 to 10 minutes). Similarly, heat inactivation is generally at about 95 °C for about 15 minutes, but the temperature may be lowered (e.g., about 70 to about 90 °C) and the time extended (e.g., about 20 minutes to about 30 minutes). Samples are then diluted (e.g., 1000-fold) and subjected to TaqMan analysis as described in the standard assay.
Additionally, or alternatively, droplet digital PCR (ddPCR) may be used. For example, methods for determining single-stranded and self-complementary AAV vector genome titers by ddPCR have been described. See, e.g., M. Lock et al, Hu Gene Therapy Methods, Hum Gene Ther Methods. 2014 Apr;25(2): 115-25. doi: 10. 1089/hgtb.2013. 131. Epub 2014 Feb 14.
In brief, the method for separating rAAV particles having packaged genomic sequences from genome-deficient AAV intermediates involves subjecting a suspension comprising recombinant AAV viral particles and AAV capsid intermediates to fast performance liquid chromatography, wherein the AAV viral particles and AAV intermediates are bound to a strong anion exchange resin equilibrated at a high pH, and subjected to a salt gradient while monitoring eluate for ultraviolet absorbance at about 260 and about 280. The pH may be adjusted depending upon the AAV selected. See, e.g., W02017/160360 (AAV9), W02017/100704 (AAVrhlO), WO 2017/100676 (e.g., AAV8), and WO 2017/100674 (AAV1), which are incorporated by reference herein. In this method, the AAV full capsids are collected from a fraction which is eluted when the ratio of A260/A280 reaches an inflection point. In one example, for the Affinity Chromatography step, the diafiltered product may be applied to a Capture Select™ Poros- AAV2/9 affinity resin (Life Technologies) that efficiently captures the AAV2 serotype. Under these ionic conditions, a significant percentage of residual cellular DNA and proteins flow through the column, while AAV particles are efficiently captured.
NON-AAV AND NON-VIRAL VECTORS
A “vector” as used herein is a biological or chemical moiety comprising a nucleic acid sequence which can be introduced into an appropriate target cell for replication or expression of said nucleic acid sequence. Examples of a vector includes but not limited to a recombinant virus, a plasmid, Lipoplexes, a Polymersome, Polyplexes, a dendrimer, a cell penetrating peptide (CPP) conjugate, a magnetic particle, or a nanoparticle. In one embodiment, a vector is a nucleic acid molecule into which an exogenous or heterologous or engineered hC9orf72 coding sequence (and/or at least one miRNA) may be inserted, which can then be introduced into an appropriate target cell. Such vectors preferably have one or more origin of replication, and one or more site into which the recombinant DNA can be inserted. Vectors often have means by which cells with vectors can be selected from those without, e.g., they encode drug resistance genes. Common vectors include plasmids, viral genomes, and "artificial chromosomes". Conventional methods of generation, production, characterization or quantification of the vectors are available to one of skill in the art.
In one embodiment, the vector is a non-viral plasmid that comprises an expression cassette described thereof, e.g., “naked DNA”, “naked plasmid DNA”, RNA, mRNA, shRNA, RNAi, etc. Optionally the plasmid or other nucleic acid sequence is delivered via a suitable device, e.g., via electrospray, electroporation. In other embodiments, the nucleic acid molecule is coupled with various compositions and nano particles, including, e.g., micelles, liposomes, cationic lipid - nucleic acid compositions, poly-glycan compositions and other polymers, lipid and/or cholesterol-based - nucleic acid conjugates, and other constructs such as are described herein. See, e.g., WO2014/089486, US 2018/0353616A1, US2013/0037977A1, W02015/074085A1, US9670152B2, and US 8,853,377B2, X. Su et al, Mol. Pharmaceutics, 2011, 8 (3), pp 774-787; web publication: March 21, 2011; WO2013/182683, WO 2010/053572 and WO 2012/170930, all of which are incorporated herein by reference.
In certain embodiment, a non-viral vector is used for delivery of an miRNA transcript targeting endogenous hC9orf72 at a site not present in the co-administered engineered hC9orf72 sequence. In some embodiments, the miRNA is delivered at an amount greater than about 0.5 mg/kg (e.g., greater than about 1.0 mg/kg, 1.5 mg/kg, 2.0 mg/kg, 2.5 mg/kg, 3.0 mg/kg, 4.0 mg/kg, 5.0 mg/kg, 6.0 mg/kg, 7.0 mg/kg, 8.0 mg/kg, 9.0 mg/kg, or 10.0 mg/kg) body weight of miRNA per dose. In some embodiments, the miRNA is delivered at an amount ranging from about 0. 1-100 mg/kg (e.g., about 0. 1-90 mg/kg, 0. 1-80 mg/kg, 0. 1-70 mg/kg, 0. 1-60 mg/kg, 0. 1-50 mg/kg, 0. 1-40 mg/kg, 0. 1-30 mg/kg, 0. 1-20 mg/kg, 0.1-10 mg/kg) body weight of miRNA per dose. In some embodiments, the miRNA is delivered at an amount of or greater than about 1 mg, 5 mg, 10 mg, 15 mg, 20 mg, 25 mg, 30 mg, 35 mg, 40 mg, 45 mg, 50 mg, 55 mg, 60 mg, 65 mg, 70 mg, 75 mg, 80 mg, 85 mg, 90 mg, 95 mg, 100 mg, 150 mg, 200 mg, 250 mg, 300 mg, 350 mg, 400 mg, 450 mg, or 500 mg per dose.
In certain embodiments, miRNA transcripts are encapsulated in a lipid nanoparticle (LNP). As used herein, the phrase "lipid nanoparticle" refers to a transfer vehicle comprising one or more lipids (e.g., cationic lipids, non- cationic lipids, and PEG-modified lipids). Preferably, the lipid nanoparticles are formulated to deliver one or more miRNA to one or more target cells (e.g., dorsal root ganglion, lower motor neurons and/or upper motor neurons, or the cell types identified above in the CNS). Examples of suitable lipids include, for example, the phosphatidyl compounds (e.g., phosphatidylglycerol, phosphatidylcholine, phosphatidylserine, phosphatidylethanolamine, sphingolipids, cerebrosides, and gangliosides). Also contemplated is the use of polymers as transfer vehicles, whether alone or in combination with other transfer vehicles. Suitable polymers may include, for example, polyacrylates, polyalkycyanoacrylates, polylactide, polylactide- polyglycolide copolymers, polycaprolactones, dextran, albumin, gelatin, alginate, collagen, chitosan, cyclodextrins, dendrimers and polyethylenimine. In one embodiment, the transfer vehicle is selected based upon its ability to facilitate the transfection of a miRNA to a target cell. Useful lipid nanoparticles for miRNA comprise a cationic lipid to encapsulate and/or enhance the delivery of miRNA into the target cell that will act as a depot for protein production. As used herein, the phrase "cationic lipid" refers to any of a number of lipid species that carry a net positive charge at a selected pH, such as physiological pH. The contemplated lipid nanoparticles may be prepared by including multi-component lipid mixtures of varying ratios employing one or more cationic lipids, non-cationic lipids and PEG- modified lipids. Several cationic lipids have been described in the literature, many of which are commercially available. See, e.g., WO2014/089486, US 2018/0353616A1, and US 8,853,377B2, which are incorporated by reference. In certain embodiments, LNP formulation is performed using routine procedures comprising cholesterol, ionizable lipid, helper lipid, PEG-lipid and polymer forming a lipid bilayer around encapsulated mRNA (Kowalski et al., 2019, Mol. Ther. 27(4):710-728). In some embodiments, LNP comprises a cationic lipids (i.e. N-[l-(2,3-dioleoyloxy)propyl]- N,N,N -trimethylammonium chloride (DOTMA), or l,2-dioleoyl-3-trimethylammonium- propane (DOTAP)) with helper lipid DOPE. In some embodiments, LNP comprises an ionizable lipid Dlin-MC3-DMA ionizable lipids, or diketopiperazine-based ionizable lipids (cKK-E12). In some embodiments, polymer comprises a polyethyleneimine (PEI), or a poly(P- amino)esters (PBAEs). See, e.g., WO2014/089486, US 2018/0353616A1, US2013/0037977A1, WO2015/074085 Al, US9670152B2, and US 8,853,377B2, which are incorporated by reference. In certain embodiments, the vector described herein is a “replication-defective virus" or a “viral vector” which refers to a synthetic or artificial viral particle in which an expression cassette containing a nucleic acid sequence encoding an engineered C9orf72 and/or at least one miRNA targeting endogenous C9orf72 at a site not present on the sequence of the engineered C9orf72. Replication-defective viruses cannot generate progeny virions but retain the ability to infect target cells. In one embodiment, the genome of the viral vector does not include genes encoding the enzymes required to replicate (the genome can be engineered to be "gutless" - containing only the nucleic acid sequence encoding E2 flanked by the signals required for amplification and packaging of the artificial genome), but these genes may be supplied during production. Therefore, it is deemed safe for use in gene therapy since replication and infection by progeny virions cannot occur except in the presence of the viral enzyme required for replication.
As used herein, a recombinant viral vector may be any suitable replication-defective viral vector, including, e.g., a recombinant adeno-associated virus (AAV), an adenovirus, a bocavirus, a hybrid AAV/bocavirus, a herpes simplex virus or a lentivirus.
As used herein, the term “host cell” may refer to the packaging cell line in which a vector (e.g., a recombinant AAV) is produced. A host cell may be a prokaryotic or eukaryotic cell (e.g., human, insect, or yeast) that contains exogenous or heterologous DNA that has been introduced into the cell by any means, e.g., electroporation, calcium phosphate precipitation, microinjection, transformation, viral infection, transfection, liposome delivery, membrane fusion techniques, high velocity DNA-coated pellets, viral infection and protoplast fusion. Examples of host cells may include, but are not limited to an isolated cell, a cell culture, an Escherichia coli cell, a yeast cell, a human cell, a non-human cell, a mammalian cell, a nonmammalian cell, an insect cell, an HEK-293 cell, a liver cell, a kidney cell, a cell of the central nervous system, a neuron, a glial cell, or a stem cell.
As used herein, the term "target cell" refers to any target cell in which expression of the hC9orf72 and/or miRNA is desired. In certain embodiments, the term "target cell" is intended to reference the cells of the subject being treated for a C9orf72-associated disorder such as ALS. Examples of target cells may include, but are not limited to, cells within the central nervous system. Compositions
Provided herein are compositions containing at least one vector comprising C9orf72.miR (e.g., an rAAV.C9orf72.miR stock) and/or at least one vector comprising miR and/or at least one vector comprising stock, and an optional carrier, excipient and/or preservative.
As used herein, a “stock” of rAAV refers to a population of rAAV. Despite heterogeneity in their capsid proteins due to deamidation, rAAV in a stock are expected to 5 share an identical vector genome. A stock can include rAAV having capsids with, for example, heterogeneous deamidation patterns characteristic of the selected AAV capsid proteins and a selected production system. The stock may be produced from a single production system or pooled from multiple runs of the production system. A variety of production systems, including but not limited to those described herein, may be selected.
In certain embodiments, a composition comprises at least virus stock which is a recombinant AAV (rAAV) suitable for use in treating C9orf72-mediated ALS or FTD alone or in combination with other vector stock or composition. In certain embodiments, the composition is suitable for use in preparing a medicament for treating patients. In certain embodiments, a composition comprises a virus stock which is a recombinant AAV (rAAV) suitable for use in treating patients, said rAAV comprising: (a) an adeno-associated virus capsid, and (b) a vector genome packaged in the AAV capsid, said vector genome comprising AAV inverted terminal repeats, a coding sequence for an engineered C9orf72, a spacer sequence, a coding sequence for at least one miRNA specifically targeted to endogenous human C9orf72 at a site not present in the engineered human C9orf72 coding sequence, and regulatory sequences which direct expression of the encoded gene products. In certain embodiments, a composition comprises separate vector stock comprising rAAV comprising: (a) an adeno-associated virus capsid, and (b) a vector genome packaged in the AAV capsid, said vector genome comprising AAV inverted terminal repeats, a coding sequence for an engineered human C9orf72, and regulatory sequences which direct expression of the encoded gene product and/or a separate vector stock comprising (a) an adeno-associated virus capsid, and (b) a vector genome packaged in the AAV capsid, said vector genome comprising AAV inverted terminal repeats, a coding sequence for at least one miRNA specifically targeted to endogenous human C9orf72 at a site not present in the engineered C9orf72 coding sequence, and regulatory sequences which direct expression of the encoded gene product. In certain embodiments, the vector genome comprises a promoter, an enhancer, an intron, a human C9orf72 coding sequence, and a polyadenylation signal. In certain embodiments, the intron consists of a chicken beta actin splice donor and a rabbit P splice acceptor element. In certain embodiments, the vector genome further comprises an AAV2 5’ ITR and an AAV2 3’ ITR which flank all elements of the vector genome.
The rAAV.C9orf72.miR (rAAV.hC9orf72 or another vector) may be suspended in a physiologically compatible carrier to be administered to a human patient. In certain embodiments, for administration to a human patient, the vector is suitably suspended in an aqueous solution containing saline, a surfactant, and a physiologically compatible salt or mixture of salts. Suitably, the formulation is adjusted to a physiologically acceptable pH, e.g., in the range of pH 6 to 9, or pH 6.5 to 7.5, pH 7.0 to 7.7, or pH 7.2 to 7.8. As the pH of the cerebrospinal fluid is about 7.28 to about 7.32, or a pH of 7.2 to 7.4, for intrathecal delivery, a pH within this range may be desired; whereas for intravenous delivery, a pH of about 6.8 to about 7.2 may be desired. However, other pHs within the broadest ranges and these subranges may be selected for other route of delivery.
In certain embodiments, the formulation may contain a buffered saline aqueous solution not comprising sodium bicarbonate. Such a formulation may contain a buffered saline aqueous solution comprising one or more of sodium phosphate, sodium chloride, potassium chloride, calcium chloride, magnesium chloride and mixtures thereof, in water, such as a Harvard’s buffer. The aqueous solution may further contain Kolliphor® P188, a poloxamer which is commercially available from BASF which was formerly sold under the trade name Lutrol® F68. The aqueous solution may have a pH of 7.2 or a pH of 7.4.
In another embodiment, the formulation may contain a buffered saline aqueous solution comprising 1 mM Sodium Phosphate (Na3PO4), 150 mM sodium chloride (NaCl), 3mM potassium chloride (KC1), 1.4 mM calcium chloride (CaC12), 0.8 mM magnesium chloride (MgC12), and 0.001% Kolliphor® 188. See, e.g., harvardapparatus.com/harvard- apparatus-perfusion-fluid.html. In certain embodiments, Harvard’s buffer is preferred.
In other embodiments, the formulation may contain one or more permeation enhancers. Examples of suitable permeation enhancers may include, e.g., mannitol, sodium glycocholate, sodium taurocholate, sodium deoxycholate, sodium salicylate, sodium caprylate, sodium caprate, sodium lauryl sulfate, polyoxyethylene-9-laurel ether, or EDTA.
In another embodiment, the composition includes a carrier, diluent, excipient and/or adjuvant. Suitable carriers may be readily selected by one of skill in the art in view of the indication for which the transfer virus is directed. For example, one suitable carrier includes saline, which may be formulated with a variety of buffering solutions (e.g., phosphate buffered saline). Other exemplary carriers include sterile saline, lactose, sucrose, calcium phosphate, gelatin, dextran, agar, pectin, peanut oil, sesame oil, and water. The buffer/carrier should include a component that prevents the rAAV, from sticking to the infusion tubing but does not interfere with the rAAV binding activity in vivo.
Optionally, the compositions may contain, in addition to the vector (e.g., rAAV) and carrier(s), other conventional pharmaceutical ingredients, such as preservatives, or chemical stabilizers. Suitable exemplary preservatives include chlorobutanol, potassium sorbate, sorbic acid, sulfur dioxide, propyl gallate, the parabens, ethyl vanillin, glycerin, phenol, and parachlorophenol. Suitable chemical stabilizers include gelatin and albumin.
As used herein, “earner” includes any and all solvents, dispersion media, vehicles, coatings, diluents, antibacterial and antifungal agents, isotonic and absorption delaying agents, buffers, carrier solutions, suspensions, colloids, and the like. The use of such media and agents for pharmaceutical active substances is well known in the art. Supplementary active ingredients can also be incorporated into the compositions. The phrase “pharmaceutically- acceptable” refers to molecular entities and compositions that do not produce an allergic or similar untoward reaction when administered to a host. Delivery vehicles such as liposomes, nanocapsules, microparticles, microspheres, lipid particles, vesicles, and the like, may be used for the introduction of the compositions of the present invention into suitable host cells. In particular, the rAAV vector delivered transgenes may be formulated for delivery either encapsulated in a lipid particle, a liposome, a vesicle, a nanosphere, or a nanoparticle or the like.
In one embodiment, a composition includes a final formulation suitable for delivery to a subject, e.g., is an aqueous liquid suspension buffered to a physiologically compatible pH and salt concentration. Optionally, one or more surfactants are present in the formulation. In another embodiment, the composition may be transported as a concentrate which is diluted for administration to a subject. In other embodiments, the composition may be lyophilized and reconstituted at the time of administration.
A suitable surfactant, or combination of surfactants, may be selected from among nonionic surfactants that are nontoxic. In one embodiment, a difunctional block copolymer surfactant terminating in primary hydroxyl groups is selected, e.g., such as Pluronic® F68 [BASF], also known as Poloxamer 188, which has a neutral pH, has an average molecular weight of 8400. Other surfactants and other Poloxamers may be selected, i.e., nonionic triblock copolymers composed of a central hydrophobic chain of polyoxypropylene (polypropylene oxide)) flanked by two hydrophilic chains of polyoxyethylene (polyethylene oxide)), SOLUTOL HS 15 (Macrogol-15 Hydroxystearate), LABRASOL (Polyoxy capryllic glyceride), poly oxy 10 oleyl ether, TWEEN (polyoxyethylene sorbitan fatty acid esters), ethanol and polyethylene glycol. In one embodiment, the formulation contains a poloxamer. These copolymers are commonly named with the letter "P" (for poloxamer) followed by three digits: the first two digits x 100 give the approximate molecular mass of the poly oxypropylene core, and the last digit x 10 gives the percentage polyoxyethylene content. In one embodiment Poloxamer 188 is selected. The surfactant may be present in an amount up to about 0.0005 % to about 0.001% of the suspension.
The vectors are administered in sufficient amounts to transfect the cells and to provide sufficient levels of gene transfer and expression to provide a therapeutic benefit without undue adverse effects, or with medically acceptable physiological effects, which can be determined by those skilled in the medical arts. Optionally, routes other than intrathecal administration may be used, such as, e.g., direct delivery to a desired organ e.g., the liver (optionally via the hepatic artery), lung, heart, eye, kidney), oral, inhalation, intranasal, intratracheal, intraarterial, intraocular, intravenous, intramuscular, subcutaneous, intradermal, and other parental routes of administration. Routes of administration may be combined, if desired.
Dosages of the vector will depend primarily on factors such as the condition being treated, the age, weight and health of the patient, and may thus vary among patients. For example, a therapeutically effective human dosage of viral vector is generally in the range of from about 25 to about 1000 microliters to about 100 mL of solution containing concentrations of from about 1 x 109 to 1 x 1016 genomes virus vector (to treat an average subject of 70 kg in body weight) including all integers or fractional amounts within the range, and preferably 1.0 x 1012 GC to 1.0 x 1014 GC for a human patient. In one embodiment, the compositions are formulated to contain at least IxlO9, 2xl09, 3xl09, 4xl09, 5xl09, 6xl09, 7xl09, 8xl09, or 9xl09 GC per dose including all integers or fractional amounts within the range. In another embodiment, the compositions are formulated to contain at least IxlO10, 2xlO10, 3xl010, 4xlO10, 5xl010, 6xlO10, 7xlO10, 8xl010, or 9xlO10 GC per dose including all integers or fractional amounts within the range. In another embodiment, the compositions are formulated to contain at least IxlO11, 2xlOn, 3xl0n, 4xlOn, 5xl0n, 6xlOn, 7xlOn, 8xl0n, or 9x10“ GC per dose including all integers or fractional amounts within the range. In another embodiment, the compositions are formulated to contain at least IxlO12, 2xl012, 3xl012, 4xl012, 5xl012, 6xl012, 7xl012, 8xl012, or 9x1012 GC per dose including all integers or fractional amounts within the range. In another embodiment, the compositions are formulated to contain at least IxlO13, 2xl013, 3xl013, 4xl013, 5xl013, 6xl013, 7xl013, 8xl013, or 9xl013 GC per dose including all integers or fractional amounts within the range. In another embodiment, the compositions are formulated to contain at least IxlO14, 2xl014, 3xl014, 4xl014, 5xl014, 6xl014, 7xl014, 8xl014, or 9x1014 GC per dose including all integers or fractional amounts within the range. In another embodiment, the compositions are formulated to contain at least IxlO15, 2xl015, 3xl015, 4xl015, 5xl015, 6xl015, 7xl015, 8xl015, or 9xl015 GC per dose including all integers or fractional amounts within the range. In one embodiment, for human application the dose can range from IxlO10 to about IxlO12 GC per dose including all integers or fractional amounts within the range.
In certain embodiments, the dose is in the range of about I x lO9 GC/g brain mass to about I x lO12 GC/g brain mass. In certain embodiments, the dose is in the range of about 1 x 1010 GC/g brain mass to about 3.33 x 1011 GC/g brain mass. In certain embodiments, the dose is in the range of about 3.33 x 1011 GC/g brain mass to about 1. 1 x 1012 GC/g brain mass. In certain embodiments, the dose is in the range of about 1. 1 x 1012 GC/g brain mass to about 3.33 x 1013 GC/g brain mass. In certain embodiments, the dose is lower than 3.33 x 1011 GC/g brain mass. In certain embodiments, the dose is lower than 1. 1 x 1012 GC/g brain mass. In certain embodiments, the dose is lower than 3.33 x 1013 GC/g brain mass. In certain embodiments, the dose is about I x lO10 GC/g brain mass. In certain embodiments, the dose is about 2 x 1010 GC/g brain mass. In certain embodiments, the dose is about 2 x 1010 GC/g brain mass. In certain embodiments, the dose is about 3 x 1010 GC/g brain mass. In certain embodiments, the dose is about 4 x IO10 GC/g brain mass. In certain embodiments, the dose is about 5 x IO10 GC/g brain mass. In certain embodiments, the dose about 6 x IO10 GC/g brain mass. In certain embodiments, the dose is about 7 x IO10 GC/g brain mass. In certain embodiments, the dose about 8 x IO10 GC/g brain mass. In certain embodiments, the dose is about 9 x IO10 GC/g brain mass. In certain embodiments, the dose is about 1 x 1011 GC/g brain mass. In certain embodiments, the dose is about 2 x 1011 GC/g brain mass. In certain embodiments, the dose is about 3 x 1011 GC/g brain mass. In certain embodiments, the dose is about 4 x 1011 GC/g brain mass. In certain embodiments, the dose is administered to humans as a flat dose in the range of about 1.44 x 1013 to 4.33 x 1014 GC of the rAAV. In certain embodiments, the dose is administered to humans as a flat dose in the range of about 1.44 x 1013 to 2 x 1014 GC of the rAAV. In certain embodiments, the dose is administered to humans as a flat dose in the range of about 3 x 1013 to 1 x 1014 GC of the rAAV. In certain embodiments, the dose is administered to humans as a flat dose in the range of about 5 x 1013 to 1 x 1014 GC of the rAAV. In some embodiments, the compositions can be formulated in dosage units to contain an amount of AAV that is in the range of about 1 x 1013 to 8 x 1014 GC of the rAAV. In some embodiments, the compositions can be formulated in dosage units to contain an amount of rAAV that is in the range of about 1.44 x 1013 to 4.33 x 1014 GC of the rAAV. In some embodiments, the compositions can be formulated in dosage units to contain an amount of rAAV that is in the range of about 3 x 1013 to 1 x 1014 GC of the rAAV. In some embodiments, the compositions can be formulated in dosage units to contain an amount of rAAV that is in the range of about 5 x 1013 to 1 x 1014 GC of the rAAV.
In certain embodiments, the vector is administered to a subject in a single dose. In certain embodiments, vector may be delivered via multiple injections (for example 2 doses) is desired.
The dosage will be adjusted to balance the therapeutic benefit against any side effects and such dosages may vary depending upon the therapeutic application for which the recombinant vector is employed. The levels of expression of the transgene can be monitored to determine the frequency of dosage resulting in viral vectors, preferably AAV vectors containing the minigene. Optionally, dosage regimens similar to those described for therapeutic purposes may be utilized for immunization using the compositions provided herein. As used herein, the terms “intrathecal delivery” or “intrathecal administration” refer to a route of administration via an injection into the spinal canal, more specifically into the subarachnoid space so that it reaches the cerebrospinal fluid (CSF). Intrathecal delivery may include lumbar puncture, intraventricular (including intracerebroventricular (ICV)), suboccipital/intracistemal, and/or Cl -2 puncture. For example, material may be introduced for diffusion throughout the subarachnoid space by means of lumbar puncture. In another example, injection may be into the cistema magna.
As used herein, the terms “intracistemal delivery” or “intracistemal administration” refer to a route of administration directly into the cerebrospinal fluid of the cistema magna cerebellomedularis, more specifically via a suboccipital puncture or by direct injection into the cistema magna or via permanently positioned tube.
Compositions comprising the miR target sequences described herein for repressing endogenous C9orf72 (e.g., in ALS patients) are generally targeted to one or more different cell types within the central nervous system, including, but not limited to, neurons (including, e.g., lower motor neurons and/or primary sensory neurons. These may include, e.g., pyramidal, purkinje, granule, spindle, and interneuron cells).
Uses
The vectors and compositions provided herein are useful for treating a patient having a C9orf72-associated disorder (e.g., ALS or FTD), neuropathy, or various symptoms associated therewith. A combination regimen or co-therapy for treating a patient having ALS or FTD is provided. In certain embodiments, this regimen or co-therapy comprises co-administering (a) a recombinant nucleic acid sequence encoding an engineered human C9orf72 coding sequence operably linked to regulatory sequences which direct expression thereof in a human target cell, wherein the human C9orf72 coding sequence has the sequence of SEQ ID NO: 13 or a sequence at least 95% identical thereto and which differs from endogenous human C9orf72 in the patient by having a mismatch in the miRNA target sequence of (b), and (b) a coding sequence for at least one miRNA specific for an endogenous human C9orf72 sequence in a human ALS subject, wherein the mRNA is operably linked to regulatory sequences which direct expression thereof in the subject. In certain embodiments, the miR target sequence is the miR487, having the sequence of at least SEQ ID NO: 16, or at least SEQ ID NO: 15 in combination with a 5’ flanking region (e.g., SEQ ID NO: 5), linkers, and a 3’ flanking region (e.g., SEQ ID NO: 7). In certain embodiments, the miR target sequences are the miR.NT sequence, having the sequence of at least SEQ ID NO: 6 with a 5’ flanking region, a linker, and a linker and 3’ flanking regions. See, e.g., SEQ ID NO: 8; or SEQ ID NO: 6 in combination with SEQ ID NO: 5 and/or SEQ ID NO: 7.
In certain embodiments, this regimen or co-therapy for treating a patient having C9orf72 comprises co-administering (a) a recombinant nucleic acid sequence encoding an engineered human C9orf72 coding sequence operably linked to regulatory sequences which direct expression thereof in a human target cell, wherein the human C9orf72 coding sequence is engineered to differs from endogenous human C9orf72 in the patient by having a mismatch in the miRNA target sequence of (b), and (b) a coding sequence for at least one miRNA specific for an endogenous human C9orf72 sequence in a human subject, wherein the miRNA coding sequence is operably linked to regulatory sequences which direct expression thereof in the subject, and wherein the at least one miRNA coding sequence has a sequence of one or more of: an miRNA coding sequence comprising SEQ ID NO: 16 (miR487 with flanking regions). In certain embodiments, the nucleic acid molecule further comprises the miR target sequences are the miR.NT sequence, having the sequence of at least SEQ ID NO: 6 with a 5’ flanking region, a linker, and a linker and 3’ flanking regions. See, e.g., SEQ ID NO: 8; or SEQ ID NO: 6 in combination with SEQ ID NO: 5 and/or SEQ ID NO: 7. In certain embodiments, a first vector comprises the nucleic acid (a) and a second, different vector, comprises at least one miRNA (b). In certain embodiments, the first vector is a viral vector and/or the second vector is a viral vector and the first and the second viral vector may be from the same virus source or may be different. In certain embodiments, the first vector is a non- viral vector, the second vector is a non-viral vector and the first and the second vectors may be same composition or may be different.
Optionally, the vectors and compositions provided herein may be used in combination with one or more co-therapies selected from: Available approved treatments for the management of ALS that reduce morbidity in some patients include riluzole and edaravone Riluzole is an orally administered glutamate inhibitor that has been shown to delay the onset of ventilator dependence or tracheostomy in some people with ALS. Edaravone is an IV- administered neuroprotective agent that has shown modest success in slowing the loss of physical function in ALS patients. Patients with ALS may also benefit from multidisciplinary care including implementation of augmentative communication devices, nutritional support, ventilator assistance, medications to manage symptoms of the disease, psychological support, and physical, occupational, and speech therapy. Other suitable co-therapeutics may include acetaminophen, and/or nonsteroidal anti-inflammatory drugs (NSAIDs). In certain embodiments, the vectors may be delivered in a combination with an immunomodulatory regimen involving one or more steroids, e.g., prednisone.
As used herein, the term Computed Tomography (CT) refers to radiography in which a three-dimensional image of a body structure is constructed by computer from a series of plane cross-sectional images made along an axis.
The term “substantial homology” or “substantial similarity,” when referring to a nucleic acid, or fragment thereof, indicates that, when optimally aligned with appropriate nucleotide insertions or deletions with another nucleic acid (or its complementary strand), there is nucleotide sequence identity in at least about 95 to 99% of the aligned sequences. Preferably, the homology is over full-length sequence, or an open reading frame thereof, or another suitable fragment which is at least 15 nucleotides in length. Examples of suitable fragments are described herein.
The terms “sequence identity” “percent sequence identity” or “percent identical” in the context of nucleic acid sequences refers to the residues in the two sequences which are the same when aligned for maximum correspondence. The length of sequence identity comparison may be over the full-length of the genome, the full-length of a gene coding sequence, or a fragment of at least about 500 to 5000 nucleotides, is desired. However, identity among smaller fragments, e.g., of at least about nine nucleotides, usually at least about 20 to 24 nucleotides, at least about 28 to 32 nucleotides, at least about 36 or more nucleotides, may also be desired. Similarly, “percent sequence identity” may be readily determined for amino acid sequences, over the full-length of a protein, or a fragment thereof. Suitably, a fragment is at least about 8 amino acids in length and may be up to about 700 amino acids. Examples of suitable fragments are described herein.
By the term “highly conserved” is meant at least 80% identity, preferably at least 90% identity, and more preferably, over 97% identity. Identity is readily determined by one of skill in the art by resort to algorithms and computer programs known by those of skill in the art. Unless otherwise specified by an upper range, it will be understood that a percentage of identity is a minimum level of identity and encompasses all higher levels of identity up to 100% identity to the reference sequence. Unless otherwise specified, it will be understood that a percentage of identity is a minimum level of identity and encompasses all higher levels of identity up to 100% identity to the reference sequence. For example, “95% identity” and “at least 95% identity” may be used interchangeably and include 95, 96, 97, 98, 99 up to 100% identity to the referenced sequence, and all fractions therebetween.
Unless otherwise specified, numerical values will be understood to be subject to conventional mathematic rounding rules.
Generally, when referring to “identity”, “homology”, or “similarity” between two different adeno-associated viruses, “identity”, “homology” or “similarity” is determined in reference to “aligned” sequences. “Aligned” sequences or “alignments” refer to multiple nucleic acid sequences or protein (amino acids) sequences, often containing corrections for missing or additional bases or amino acids as compared to a reference sequence. In the examples, AAV alignments are performed using the published AAV9 sequences as a reference point. Alignments are performed using any of a variety of publicly or commercially available Multiple Sequence Alignment Programs. Examples of such programs include, “Clustal Omega”, “Clustal W”, “CAP Sequence Assembly”, “MAP”, and “MEME”, which are accessible through Web Servers on the internet. Other sources for such programs are known to those of skill in the art. Alternatively, Vector NTI utilities are also used. There are also a number of algorithms known in the art that can be used to measure nucleotide sequence identity, including those contained in the programs described above. As another example, polynucleotide sequences can be compared using Fasta™, a program in GCG Version 6.1. Fasta™ provides alignments and percent sequence identity of the regions of the best overlap between the query and search sequences. For instance, percent sequence identity between nucleic acid sequences can be determined using Fasta™ with its default parameters (a word size of 6 and the NOPAM factor for the scoring matrix) as provided in GCG Version 6. 1, herein incorporated by reference. Multiple sequence alignment programs are also available for amino acid sequences, e.g., the “Clustal Omega”, “Clustal X”, “MAP”, “PIMA”, “MSA”, “BLOCKMAKER”, “MEME”, and “Match-Box” programs. Generally, any of these programs are used at default settings, although one of skill in the art can alter these settings as needed. Alternatively, one of skill in the art can utilize another algorithm or computer program which provides at least the level of identity or alignment as that provided by the referenced algorithms and programs. See, e.g., J. D. Thomson et al, Nucl. Acids. Res., “A comprehensive comparison of multiple sequence alignments”, 27(13):2682-2690 (1999).
It is to be noted that the term “a” or “an” refers to one or more. As such, the terms “a (or “an”), “one or more,” and “at least one” are used interchangeably herein.
The words “comprise”, “comprises”, and “comprising” are to be interpreted inclusively rather than exclusively. The words “consist”, “consisting”, and its variants, are to be interpreted exclusively, rather than inclusively. While various embodiments in the specification are presented using “comprising” language, under other circumstances, a related embodiment is also intended to be interpreted and described using “consisting of’ or “consisting essentially of’ language.
As used herein, the term “about” means a variability of 10 % (±10%, e.g., ±1, ±2, ±3, ±4, ±5, ±6, ±7, ±8, ±9, ±10, or values therebetween) from the reference given, unless otherwise specified.
As used herein, “disease”, “disorder” and “condition” are used interchangeably, to indicate an abnormal state in a subject.
As used herein, the term “C9orf72-related symptom(s)” or “symptom(s)” refers to symptom(s) found in patients with symptoms of ALS include, e.g., persistent weakness, which may have variable presentation with some patients having isolated weakness of one or more limbs, while others initially exhibit bulbar weakness, which affects the muscles that control speech, swallowing, and chewing. Other manifestations include abnormal muscle tone and tendon reflexes, signs of progressive muscle weakness, muscle wasting especially in the trunk and extremities, associated spasticity with an inability to control movement. Clinical symptoms range from fasciculations, muscle cramps, gait disturbances, loss of ambulation, loss of arm and hand function, to difficulty with speech and swallowing and breathlessness. Aspiration pneumonia and respiratory insufficiency are common causes of death in these patients. Approximately 29% of C9orf72 repeat expansion carriers do not present with symptoms of ALS. Instead, they are diagnosed with frontotemporal dementia (FTD), which is a progressive brain disorder that affects personality, behavior, language, and cognition. Some individuals even develop features of both conditions and are diagnosed as having the ALS- FTD variant.
“Patient” or “subject” as used herein means a male or female human, and animal models (including, e.g., dogs, non-human primates, rodents, or other suitable models) used for clinical research. In one embodiment, the subject of these methods and compositions is a human diagnosed with a C9orf72-associated disorder. Such disorders may include a patient having a defect in the C9orf72 gene, e.g., such as associated with amyotrophic lateral sclerosis (ALS) or frontotemporal dementia (FTD), or both (C9FTD/ALS). C9orf72 repeat expansions have also been identified as a rare cause of other neurodegenerative diseases, including Parkinson disease, progressive supranuclear palsy, ataxia, corticobasal syndrome, Huntington disease-like syndrome, Creutzfeldt-Jakob disease and Alzheimer disease. In certain embodiments, the human subject of these methods and compositions is a prenatal, a newborn, an infant, a toddler, a preschool, a grade-schooler, a teen, a young adult or an adult. In a further embodiment, the subject of these methods and compositions is a pediatric patient.
As used herein, the term “a therapeutic level” means an C9orf72 activity at least about 5%, about 8%, about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, about 100%, more than 100%, about 2-fold, about 3 -fold, or about 5 -fold of a healthy control. Suitable assays for measuring the activity of an hC9orf72 are known in the art. In some embodiments, such therapeutic levels of the one or more subunit protein may result in alleviation of the C9orf72-associated ALS or FTD symptom(s); reversal of certain C9orf72-related symptoms and/or prevention of progression of ALS or FTD - related certain symptoms; or any combination thereof. In certain embodiments, therapeutic efficacy is measured by trachesotomy-free survival, improved lung function measures, e.g., as measured by forced vital capacity (FVC) or slow viral capacity (SVC). Other suitable measures of therapeutic effect may be determined using a ALS functional rating scale (ALSFRS-R) which assesses gross motor tasks (turning in bed, walking and climbing stairs), fine motor tasks (cutting food, handwriting and dressing/hygiene), bulbar function (speech, swallowing and salivation), and breathing function (dyspnea, orthopnea and need for ventilatory support) (Cedarbaum et al., (1999). "The ALSFRS-R: a revised ALS functional rating scale that incorporates assessments of respiratory function. BDNF ALS Study Group (Phase III)." J Neurol Sei. 169(1-2): 13-21). Accurate Test of Limb Isometric Strength (ATLIS), Amyotrophic Lateral Sclerosis-Specific Quality of Life-Short Form (ALSSQOL-SF). Additionally or alternatively, suitable biomarkers may be measured to assess efficacy. Suitable biomarkers include, e.g., the neurofilament heavy chain (NFH) and neurofilament light chain (NFL), dipeptide repeat proteins, tau protein, and/or neuroimaging.
In certain embodiments, the human C9orf72 delivered by the compositions and regimens provided herein has the amino acid sequence of a functional endogenous wild-type protein. In certain embodiments, the sequence is the amino acid sequence of SEQ ID NO: 14 or 45 or a functional protein which is at about 95 to 100% identity to functional, human C9orf72 protein.
The term “expression” is used herein in its broadest meaning and comprises the production of RNA or of RNA and protein. With respect to RNA, the term “expression” or “translation” relates in particular to the production of peptides or proteins. Expression may be transient or may be stable.
Additionally optionally, an expression cassette (and a vector genome) may comprise one or more dorsal root ganglion (drg)- miRNA targeting sequences in the UTR, e.g., to reduce drg toxicity and/or axonopathy. See, e.g., PCT/US2019/67872, filed December 20, 2019 and now published as WO 2020/132455, PCT/US2021/032002, now published as WO2021/231579, US Provisional Patent Application No. 63/023593, filed May 12, 2020, and US Provisional Patent Application No. 63/038488, filed June 12, 2020, and US Provisional Application No. 63/279,561, all entitled “Compositions for Drg-Specific Reduction of Transgene Expression”, which are incorporated herein in their entireties. In some embodiments, an expression cassette may be delivered via a genetic element (e.g., a plasmid) to a packaging host cell and packaged into the capsid of a viral vector (e.g., a viral particle).
As used herein, the term “operably linked” refers to both expression control sequences that are contiguous with the gene of interest and expression control sequences that act in trans or at a distance to control the gene of interest.
The term “heterologous” when used with reference to a protein or a nucleic acid indicates that the protein or the nucleic acid comprises two or more sequences or subsequences which are not found in the same relationship to each other in nature. For instance, the nucleic acid is typically recombinantly produced, having two or more sequences from unrelated genes arranged to make a new functional nucleic acid. For example, in one embodiment, the nucleic acid has a promoter from one gene arranged to direct the expression of a coding sequence from a different gene. Thus, with reference to the coding sequence, the promoter is heterologous.
As described herein, regulatory elements comprise but not limited to: promoter; enhancer; transcription factor; transcription terminator; efficient RNA processing signals such as splicing and polyadenylation signals (poly A); sequences that stabilize cytoplasmic mRNA, for example Woodchuck Hepatitis Virus (WHP) Posttranscriptional Regulatory Element (WPRE); sequences that enhance translation efficiency (i.e., Kozak consensus sequence).
The term “translation” in the context of the present invention relates to a process at the ribosome, wherein an mRNA strand controls the assembly of an amino acid sequence to generate a protein or a peptide.
In one embodiment, a vector genome for a packaging plasmid is provided herein comprises SEQ ID NO: 17, includes a shortened AAV2 - 5’ ITR, the expression cassette comprising a C4 enhancer, a CB7 promoter, an engineered C9orf72 coding sequences and the C9miR487 target sequences, WPRE element, and a polyA signal (e.g., the expression cassette of SEQ ID NO: 18 or a sequence at least 97% identical thereto), and a shortened AAV2- 3’ AAV. In certain embodiments, e.g.., a packaged rAAV vector, the vector genome comprises a full-length 5 ’ ITR and a full-length 3 ’ ITR. In certain embodiments, the vector genome comprises the vector elements above, without the WPRE element. In certain embodiments, the vector genome comprises a scAAV.
In certain embodiments, an rAAV or another vector may contain an expression cassettes containing the miR487 targeting sequences and the C9orf72 coding sequences in a separate vector [see, e.g., SEQ ID NO: 19] or separate expression cassette. In certain embodiments, the WPRE element may be eliminated from the expression cassette and/or replaced with another genome element.
Unless defined otherwise in this specification, technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art and by reference to published texts, which provide one skilled in the art with a general guide to many of the terms used in the present application. The following examples are illustrative only and are not intended to limit the present invention.
EXAMPLES
The following examples are illustrative and are not intended to limit the present invention.
EXAMPLE 1 : C9orf72 Vector Strategy
We generated rAAV comprising (1) expression cassettes comprising a miR sequences targeted to endogenous C9orf72, (2) an expression cassette comprising a combination these miR sequences and an engineered C9orf72 cDNA which has modifications in the regions of C9orf72 targeted by the miR in the expression cassette so that it is not also targeted by the miR. To knock down endogenous C9orf72, rAAV having vector genomes expressing various miRNA sequences were examined: miR.NT (negative control), miR32-101 (positive control), and miR487.
Vectors were constructed using convention triple transfection methods in a 293 HEK cell line transfected with a cis plasmid comprising the vector genome to be packaged composed of a 5’ ITR, a spacer sequence, the expression cassette, a spacer sequence, and the 3’ ITR. Shortened (130 bp) 5’- and 3’ ITRs are in this cis plasmid; during replication and packaging, these revert to the full-length 145 bp 5’ and 3’ ITRs. This cis plasmid is cotransfected with a trans plasmid comprising Ad helper genes needed for transfection and packaging, and a trans plasmid comprising the VP 1 gene encoding the AAV capsid. In certain of the mouse studies, an AAV9 mutant termed AAV9-eB was used.
EXAMPLE 2: Proof-of-Concept Study in the Tg(C9orf72_3) Line 112 Mouse Model
The ability of the rAAV constructs described herein to knockdown mutant C9orf72 RNA and DPRs is evaluated in a Tg(C9orf72_3) line 112 mouse model. rAAV is administered to adult Tg(C9orf72_3) line 112 mice via a single intracerebroventricular (ICV) injection. The dose range was selected to evaluate half-log increments beginning with the maximum feasible dose. Vehicle-treated transgenic and non-transgenic mice serve as controls. Thirty days after injection, mice are sacrificed, and the brain and spinal cord collected for analysis. The 30 day time point is selected to allow sufficient time to reach steady-state levels of C9orf72 RNA and DPR protein. Total C9orf72 mRNA is measured using exon-specific primers by quantitative rtPCR and normalized to GAPDH expression. The abnormal repeat-containing transcript is quantified by rtPCR using primers specific to the first intron of C9orf72. DPRs (poly-GP) are measured by immunoassay using the Mesoscale Discovery platform.
EXAMPLE 3: Identification of the Minimum Effective Dose (MED) in the Tg(C9orf72_3) Line 112 Mouse Model
Multiple doses of selected rAAV vectors are evaluated in the Tg(C9orf72_3) line 112 mouse model. The doses include the maximum feasible dose and half-log increments over a 30-fold dose range. rAAV is administered to adult Tg(C9orf72_3) line 112 mice via a single intracerebroventricular (ICV) injection by trained personnel. Vehicle-treated transgenic and non-transgenic mice serve as controls. Clinical observations will be performed twice daily, and body weights are measured weekly. For all unscheduled deaths, comprehensive gross pathology and histopathology on a complete list of tissues and other analyses as appropriate are performed to determine a possible cause of death. Ninety days after injection, mice are sacrificed. The 90 day time point is selected to assess durability of knockdown of the mutant transcript. The brain, spinal cord, heart, lung, liver, spleen, kidneys, esophagus, stomach, large and small intestines, mesenteric and cervical lymph nodes, adrenal glands, and gonads are collected, examined for gross pathology, and processed for histopathology. Applicable immunohistochemistry staining for immune cell infiltrates is performed in the event of histopathology findings. Blood is collected for serum chemistry panels and complete blood counts. Intron-containing C9orf72 RNA and DPRs are measured in brain and spinal cord as described above. The lowest dose significantly reducing mutant C9orf72 mRNA and DPR expression levels is considered the MED. Significance will be determined by appropriate statistical comparisons to the vehicle control group. Portions of the brain and spinal cord and all other tissues collected are fixed and embedded in paraffin for analysis of histopathology.
FIGs 1A to ID provide qPCR results from spinal cord of 11-14 week old mice (C9 LI 12 Het) injected (iv-tail vein) with a 3 x 1011 GC/100 pl of rAAV-PHP.eb- CB7.CLC9miR.WPRE.rBG, the miR is NT or PBS, miR487, miR32, or miR32-101. FIG1A provides the results in spinal cord for a C9 intron spliced primer. FIG IB provides the results in spinal cord for C9 intron retained primers. FIGs 1C and ID provide qPCR results from brain for C9 intron spliced primers (FIG 1C) or C9 intron retained primers (FIG ID).
FIGs 2A-2D provides the results of DPR protein pathology assessment in a poly(GP) Meso Scale Discovery (MSD)-Immunoassay, soluble fraction. C57BL/6J- Tg(C9orf72_i3)l 12Lutzy/J (JR: 023099) mice show significant increases in poly(GP) soluble fraction in brain lysates: at 1, and 3 months of age and spinal cord lysate: at 12 months of age compared to NCAR, controls. As mice age, decrease of DPRs in the soluble fraction in mice in brain as observed in (GrC2)149 mice. Data represented as mean ± SD. poly(GP) response in C9-deficient mice treated with rAAV and vehicle or rAAV comprising miRNA. FIG 2A shows (G4C2) 149 mice show significant increases in poly(GP) soluble fraction in brain lysates at 6, 9 & 12 months of age compared to (0462)149 controls. FIGs 2B and 2C show that as mice age, decrease of DPRs in the soluble fraction in (6462)149 mice is expected (FIG 2B), as they accumulate in the insoluble fraction (FIG 26).
FIG 3 provides a survival curve with percent survival graphed over age in weeks to 14 weeks for various groups of wild-type control (WT/NGAR) female or male mice or Hemizygous/TG mice receiving PBS only (VEH) or receiving 3x1011 one of two different rAAV: AAV-1 is an AAV PHP.eB capsid with a vector genome of GB7.GI.69miR487.WPRE.rBG and AAV-2 is an AAV PHP.eB capsid with a vector genome of GB7.GI.G9miR487.WPRE.rBG, via tail vein injection at 4 weeks of age.
FIG 4 provides body weights by group (male and female together) from the animals study described in FIG 3, as studied from inception (4 weeks of age) through termination.
FIG 5 provides body weights for the females by group from the animals study described in FIG 3, as studied from inception (4 weeks of age) through termination.
FIG 6 provides body weights for the males by group from the animals study described in FIG 3, as studied from inception (4 weeks of age) through termination.
FIGs 7A and 7B provides the poly(GP) response in brain for a wild-type mouse (WT/NGAR vehicle) (Group 1), hemizygous/TG mice receiving PBS only (Vehicle) and two treatment groups receiving 3xl0n one of two different rAAV: AAV-1 is an AAV PHP.eB capsid with a vector genome of GB7.GI.G9miR487.WPRE.rBG and AAV-2 is an AAV PHP.eB capsid with a vector genome of GB7.GI.G9miR487.WPRE.rBG, via tail vein injection at 4 weeks of age. FIG 7A is corrected for background and FIG 7B is uncorrected for background.
EXAMPLE 4: Off-Target Analysis in Human iPSC-Derived Motor Neuron-Like Cells
This study evaluates off-target gene knockdown following rAAV transduction of human motor neuron-like cells. Motor neuron-like cells will be differentiated from induced pluripotent stem cells (iPSCs) according to standard protocols (Bianchi et al, 2018, Rapid and efficient differentiation of functional motor neurons from human iPSC for neural injury modelling. Stem Cell Res. 2018 Oct;32: 126-134. doi: 10.1016/j.scr.2018.09.006. Epub 2018 Sep 26. PMID: 30278374.). The phenotype is confirmed by morphology and choline acetyltransferase staining. Cells are transduced with rAAV. Control cells are treated with an rAAV vector having the same capsid as the rAAV test vector that does not carry the miRNA or will receive no treatment. Cells are harvested for RNA isolation and RNA-seq analysis. Transcripts downregulated by the rAAV test vector are identified. For each downregulated transcript, potential miRNA target sequences are identified by sequence homology, and the degree of homology between the corresponding target sequence in rhesus monkeys will be evaluated in order to predict the likelihood that toxicity related to the off-target gene knockdown could be predicted by the NHP toxicology study.
EXAMPLE 5: Toxicology Study in Nonhuman Primates
A 90 day GLP-compliant safety study is conducted in adult rhesus macaques (approximately 3-10 years old) to investigate the toxicology of rAAV test vector following ICM administration. The 90 day evaluation period was selected because this allows sufficient time for transgene expression to reach a stable plateau. The age of the animals is selected to be representative of the intended adult patient population. The study design is outlined in the . Rhesus macaques receive one of three dose levels of rAAV.C9orf72.MiR (3.00 x 1012 GC total, 1.00 x 1013 GC total, or 3.00 x 1013 GC total; N=3 per dose) or vehicle (ITFFB; N=2). Dose levels are selected to be equivalent to those that will be evaluated in the planned MED when scaled by brain mass (assuming 0.4 g for the adult mouse brain and 90 g for the adult rhesus macaque brain), and these doses bracket the proposed clinical dose level range. NHPs are dosed using the same vector delivery device as that intended for clinical trials. The vector delivery device and administration procedure are optimized prior to the start of the toxicology study to ensure reproducible and accurate vector delivery. The actual administered vector dose level and any device-related vector loss will be provided in the study report. Baseline neurologic examinations, complete physical exam, body weight, and daily observations, including assessment of appetite, clinical pathology (cell counts with differentials, clinical chemistries, and a coagulation panel), CSF chemistry, and CSF cytology will be performed. After rAAV test vector or vehicle administration, the animals are monitored daily for signs of distress and abnormal behavior. Blood and CSF clinical pathology assessments and neurologic examinations are performed on a weekly basis for 30 days following rAAV test vector or vehicle administration, followed by every 30 days thereafter. At baseline and at each 30 day time point thereafter, anti-AAV NAbs and cytotoxic T lymphocyte (CTL) responses to the rAAV are assessed by an interferon gamma (IFN-y) enzyme-linked immunospot (ELISpot) assay.
Ninety days after rAAV or vehicle administration, animals will be euthanized. A comprehensive list of tissues (brain, spinal cord, DRG, peripheral nerves, heart, lung, liver, spleen, kidneys, esophagus, stomach, large and small intestines, mesenteric and cervical lymph nodes, adrenal glands, and gonads) are harvested, weighed as appropriate, and analyzed for histopathology. In addition, lymphocytes are harvested from the liver, spleen, and bone marrow to evaluate the presence of T cells reactive to the vector capsid in these organs at the time of necropsy. Vector biodistribution is evaluated by qPCR in tissue samples. Vector genomes are also be quantified in serum and CSF samples. Vector excretion is be evaluated by analysis of vector genomes detected in urine and feces.
Table. Rhesus Macaque GLP-Compliant Toxicology Study
Figure imgf000053_0001
5
Figure imgf000054_0001
Abbreviations'. CSF, cerebrospinal fluid; F, female; GLP, good laboratory practice; GC, genome copies; ICM, intra-cistema magna; ITFFB, intrathecal final formulation buffer; M, male; N, number of animals; N/A, not applicable; ROA, route of administration.
EXAMPLE 6: First-in-Human Clinical Trial Protocol Synopsis
Figure imgf000054_0002
Figure imgf000055_0001
Figure imgf000056_0001
Figure imgf000057_0001
Figure imgf000058_0001
Figure imgf000059_0001
Figure imgf000060_0001
Figure imgf000061_0001
All patents, patent publications, and other publications listed in this specification, as US Provisional Patent Application No. 63/298,046, filed January 10, 2022, well as the sequence listing file thereof, is incorporated herein by reference. While the invention has been described with reference to a particularly preferred embodiment, it will be appreciated that modifications can be made without departing from the spirit of the invention. Such modifications are intended to fall within the scope of the appended claims.

Claims

CLAIMS:
1. A recombinant adeno-associated virus (rAAV) comprising an AAV capsid and packaged therein a vector genome, wherein the vector genome comprises:
(a) an engineered human C9orf72 coding sequence encoding functional human C9 protein;
(b) a spacer sequence located between (a) and (c);
(c) at least one miRNA coding sequence which is specific for a target site in an endogenous human c9orf72 nucleic acid sequence in a C9orf72 patient; wherein the engineered nucleic acid sequence of (a) lacks the target site for the at least one miRNA of (c), thereby preventing the at least one miRNA from targeting the engineered c9orf72 coding sequence; and
(d) regulatory sequences operably linked to (a) and (c) which direct expression thereof in a cell.
2. The rAAV according to claim 1, wherein the AAV capsid is selected from AAVhu68, AAVrh91, AAV9, AAVhu95, AAVhu96, or AAV1 capsid.
3. The rAAV according to claim 1 or 2, wherein the engineered C9ORF72 coding sequence has a nucleic acid sequence of SEQ ID NO: 13 or a sequence at least 80% identical thereto.
4. The rAAV according to claim 1 to 3, wherein the engineered C9orf72 coding sequence has the nucleic acid sequence of SEQ ID NO: 13 or a sequence at least about 90% identical thereto.
5. The rAAV according to any one of claims 1 to 4, wherein the at least one miRNA comprises a sequence of one or more of an miRNA targeting sequence comprising a 5’ flanking region, at least SEQ ID NO: 15 (miR487) or a sequence at least 99% identical to SEQ ID NO: 15, and a 3’ flanking region, wherein the at least one miRNA does not bind to the engineered C9orf72 coding sequence of (a) or its encoded messenger RNA (mRNA).
6. The rAAV according to claim 5, wherein the 5’ flank is selected from a sequence of SEQ ID NO: 5 or SEQ ID NO: 22.
7. The rAAV according to any one of claims 1 to 6, wherein the spacer is 75 nucleotides to about 250 nucleotides in length.
8. The rAAV according to any one of claims 1 to 7, wherein the at least one miRNA coding sequence is 3’ to the engineered C9orf72 coding sequence.
9. The rAAV according to any one of claims 1 to 7, wherein the at least one miRNA coding sequence is located within an intron sequence.
10. The rAAV according to any one of claims 1 to 9, wherein the at least one miRNA coding sequence further comprising one or more than one miRNA coding sequence.
11. The rAAV according to any one of claims 1 to 10, wherein the regulatory sequences in the vector genome further comprise a constitutive promoter.
12. The rAAV according to claim 11, wherein the promoter is a CB7 promoter comprising a cytomegalovirus immediate early enhancer and a chicken beta actin promoter.
13. The rAAV according to any one of claims 1 to 10, wherein the regulatory sequences comprise a neuron specific promoter.
14. A pharmaceutical composition comprising the rAAV according to any one of claims 1 to 13 and a pharmaceutically acceptable aqueous suspending liquid, excipient, and/or diluent.
15. A recombinant AAV according to any one of claims 1 to 13 or a composition according to claim 14 suitable for treatment of a patient having C9orf72-associated disorder.
16. A recombinant AAV according to claim 1 to 12 for use in preparing a medicament for treatment of a patient having a C9orf72-associated disorder.
17. A method for treating a patient having a C9orf72-associated disorder comprising delivering an effective amount of the recombinant AAV according to any one of claims 1 to 13 or the composition according to claim 14 to the patient in need thereof.
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