Modulators of adeno-associated virus transduction and uses thereof - Patents.com

Abstract

The present disclosure provides compositions and methods for modulating the transduction efficiency of AAV particles. Specifically, the present disclosure provides AAV transduction regulators that modulate genes or gene products associated with the transduction efficiency of AAV in gene therapy.

Description

[Technical Field]

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS This application claims the benefit of U.S. Provisional Patent Application No. 63 / 283,072, filed November 24, 2021. The entire contents of the aforementioned application are incorporated herein by reference.

[0002] The present disclosure relates to the use of adeno-associated virus (AAV) transduction regulators to alter AAV transduction efficiency in gene therapy. [Background technology]

[0003] AAV is a non-enveloped virus that can be engineered to deliver therapeutic payloads to target cells. The ability to generate recombinant AAV particles that are free of specific viral genes and contain therapeutic genes of interest provides a safe platform for delivering gene therapy across a variety of therapeutic areas. AAV vectors have been used in clinical trials for various diseases and have achieved promising results. Despite recent progress, there is a need for novel compositions and methods for modulating the transduction efficiency of AAV in gene therapy. Summary of the Invention

[0004] In one aspect, the disclosure features a method of modulating the transduction efficiency of an AAV particle, the method including contacting a cell with an AAV transduction modulator, thereby modulating the transduction efficiency of the AAV particle.

[0005] In some embodiments, the modulator modulates (e.g., increases or decreases) a gene or gene product associated with AAV transduction efficiency, hi some embodiments, the gene or gene product is a mammalian (e.g., human) gene or gene product.

[0006] In some embodiments, the modulator inhibits a gene or gene product, e.g., a gene or gene product associated with decreased transduction efficiency of AAV particles, hi some embodiments, the modulator activates a gene or gene product, e.g., a gene or gene product associated with increased transduction efficiency of AAV particles.

[0007] In some embodiments, the gene or gene product is associated with increased transduction efficiency of AAV particles (e.g., AAV-R or GPR108). In some embodiments, the gene or gene product is associated with increased transduction efficiency of AAV particles of a first serotype (e.g., AAV2), increased transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both.

[0008] In some embodiments, the gene or gene product is associated with decreased transduction efficiency of AAV particles (e.g., WDR11 or MRE11). In some embodiments, the gene or gene product is associated with decreased transduction efficiency of AAV particles of a first serotype (e.g., AAV2), decreased transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both.

[0009] In some embodiments, the gene or gene product, when modulated, increases the transduction efficiency of AAV particles (e.g., AAV-R or GPR108). In some embodiments, the gene or gene product, when modulated, increases the transduction efficiency of AAV particles of a first serotype (e.g., AAV2), the transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both.

[0010] In some embodiments, the gene or gene product, when modulated, decreases the transduction efficiency of AAV particles (e.g., WDR11 or MRE11). In some embodiments, the gene or gene product, when modulated, decreases the transduction efficiency of AAV particles of a first serotype (e.g., AAV2), the transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both.

[0011] In some embodiments, the gene product is RNA (e.g., mRNA). In some embodiments, the gene product is a protein. In some embodiments, the gene or gene product is selectively expressed in a target tissue (e.g., brain or liver). The following dependent claims describe AAV transduction regulators based on their mechanism. In some embodiments, the regulator alters (e.g., increases or decreases) the expression of a gene. In some embodiments, the regulator alters the structure of a gene. In some embodiments, the regulator alters (e.g., increases or decreases) the activity (e.g., enzymatic activity) of a gene product. In some embodiments, the regulator alters (e.g., increases or decreases) the level (e.g., abundance) of a gene product. In some embodiments, the regulator alters (e.g., increases or decreases) the stability of a gene product. In some embodiments, the regulator alters (e.g., increases or decreases) the transduction efficiency of AAV particles, e.g., as determined by an assay described herein (e.g., FACS analysis, e.g., as described in Example 1 or 2).

[0012] In some embodiments, the modulator increases the transduction efficiency of AAV particles. In some embodiments, the transduction efficiency is increased by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90%, or at least 1-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 60-fold, 70-fold, 80-fold, 90-fold, 100-fold, 200-fold, 300-fold, 400-fold, 500-fold, 600-fold, 700-fold, 800-fold, 900-fold, or 1000-fold compared to a baseline level of transduction efficiency. In some embodiments, the modulator increases transduction by at least 10, 20, 30, 40, 50, or 60 viral copies per genome. In some embodiments, the regulatory factor induces transduction at a rate of at least 10 per μg of DNA. 3 , 10 4 , 10 5 , 10 6 , or 10 7 The viral copy number increases to .

[0013] In some embodiments, the modulator reduces the transduction efficiency of AAV particles. In some embodiments, the transduction efficiency is reduced by at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% compared to a baseline level of transduction efficiency. In some embodiments, the modulator reduces transduction to 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 viral copies per genome or less. In some embodiments, the modulator reduces transduction to 10 copies per μg of DNA or less. 2 , 10 3 , or 10 4 Reduce the viral copy number to:

[0014] In some embodiments, the baseline level of transduction efficiency is the level of transduction efficiency in cells that have not been contacted with an AAV transduction regulatory agent, hi some embodiments, the baseline level of transduction efficiency is the level of transduction efficiency before the cells are contacted with an AAV transduction regulatory agent.

[0015] In some embodiments, the gene or gene product increases the transduction efficiency of AAV2 particles, and optionally, the gene or gene product does not increase or does not substantially increase the transduction efficiency of AAV9 particles. In some embodiments, the gene or gene product is essential for transduction of AAV2 particles, and optionally, the gene or gene product is not essential for transduction of AAV9 particles. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GRP108.

[0016] In some embodiments, the gene or gene product is selected from EXT1, EXT2, NDST1, BCL10, OAF, PDCD10, LMO4, MALT1, ZNF644, CHUK, GLCE, EP300, ARID4B, RAB21, MED13, DHX15, WASHC5, IKBKB, USP24, HSPA14, CXXC1, UBE2A, INTS8, CDC42, NFKB1, SIN3A, USP7, ARF5, CARD10, JAK1, SLC35C2, PAXK1, ZC3H11A, FAM20B, FAM72A, DHX36, INTS12, RPRD1B, or a combination thereof.

[0017] In some embodiments, the gene or gene product is associated with endosomal sorting (e.g., RAB21, WASHC5, or USP7). In some embodiments, the gene or gene product is associated with vesicle-mediated transport (e.g., CDC42 or ARF5). In some embodiments, the gene or gene product is associated with NFKB signaling (e.g., BCL10, MALT1, NFKB1, IKBKB, CHUK, or CARD10). In some embodiments, the gene or gene product is associated with heparan sulfate biosynthesis (e.g., EXT1, EXT2, NDST1, GLCE, or FAM20B). In some embodiments, the gene or gene product is associated with H3K9 methylation (e.g., ZNF644). In some embodiments, the gene or gene product is associated with pre-mRNA processing (e.g., DHX15). In some embodiments, the gene or gene product is associated with transcription (e.g., LMO4, EP300, MED13, SIN3, ARID4B, ZC3H11A, CXXC1, RPRD1B, or UBE2A). In some embodiments, the gene or gene product is associated with the Integrator complex and / or RNA polymerase II function (e.g., INTS8 or INST12). In some embodiments, the gene or gene product is associated with DNA repair and / or AAV genome degradation (e.g., DHX36, ARID4B, UBE2A, or USP24). In some embodiments, the gene or gene product is associated with cell proliferation and / or apoptosis (e.g., PDCD10). In some embodiments, the gene or gene product is associated with spinocarpal tarsal synostosis (e.g., OAF). In some embodiments, the gene or gene product is associated with protein folding (e.g., HSPA14). In some embodiments, the gene or gene product is associated with helicase activity (e.g., DHX36). In some embodiments, the gene or gene product is associated with fucosylation of Notch and / or transport of GCP-fucose (eg, SLC35C2).

[0018] In some embodiments, the gene or gene product increases the transduction efficiency of AAV9 particles, and optionally, the gene or gene product does not increase or does not substantially increase the transduction efficiency of AAV2 particles. In some embodiments, the gene or gene product is essential for transduction of AAV9 particles, and optionally, the gene or gene product is not essential for transduction of AAV2 particles. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GRP108.

[0019] In some embodiments, the gene or gene product is selected from TMPRSS11B, HTT, SNRNP70, BRD7, DMXL1, RAB10, CNGA1, KLHDC3, CHP1, CYP3A5, ELOVL4, PNISR, ZCCHC14, AZGP1, TPST1, SC5D, ELP2, ELP3, IPO9, RAB14, WDR7, XRCC4, GDI2, or a combination thereof.

[0020] In some embodiments, the gene or gene product is associated with microtubule-mediated transport or vesicle function (e.g., HTT). In some embodiments, the gene or gene product is an ion channel (e.g., CNGA1). In some embodiments, the gene or gene product is associated with nuclear protein import (e.g., IPO9). In some embodiments, the gene or gene product is associated with O-sulfation of tyrosine residues within acidic motifs of polypeptides (e.g., TPST1). In some embodiments, the gene or gene product is associated with protection of viral RNA (e.g., ZCCHC14). In some embodiments, the gene or gene product is associated with RNA binding by AAV proteins (e.g., PNISR). In some embodiments, the gene or gene product is associated with calcium ion-regulated exocytosis (e.g., CHP1). In some embodiments, the gene or gene product is associated with intracellular transport (e.g., RAB10, RAB14, GDI2, WDR7, or DMXL1). In some embodiments, the gene or gene product is a subunit (e.g., a catalytic tRNA acetyltransferase subunit) of an elongator complex, e.g., an RNA polymerase (e.g., RNA polymerase II) (e.g., ELP2 or ELP3). In some embodiments, the gene or gene product is chromatin-associated (e.g., KLHDC3). In some embodiments, the gene or gene product is associated with cholesterol biosynthesis (e.g., SC5D).

[0021] In some embodiments, the gene or gene product increases the transduction efficiency of AAV2 and AAV9 particles. In some embodiments, the gene or gene product is essential for transduction of AAV2 and AAV9 particles. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GRP108.

[0022] In some embodiments, the gene or gene product is selected from KIAA0319L, BAMBI, TM9SF2, PHIP, DCLRE1C, VPS35, GPR108, CYREN, ACP2, F8A2, F8A1, F8A3, RBPJ, ATP2C1, ICMT, RABIF, IER3IP1, RBM10, SMG7, GTF2I, ELAVL1, MEPCE, RAB4A, IER3IP1, SAMD1, or a combination thereof.

[0023] In some embodiments, the gene or gene product is associated with influenza infection (e.g., ACP2). In some embodiments, the gene or gene product binds to an unmethylated CGI (e.g., SAMD1). In some embodiments, the gene or gene product is associated with intracellular vesicle trafficking (e.g., RABIF). In some embodiments, the gene or gene product is associated with post-translational modification of a cysteine ​​residue (e.g., a C-terminal cysteine ​​residue) in, for example, a target protein (e.g., ICMT). In some embodiments, the gene or gene product binds to an AAV capsid protein (e.g., KIAA0319L). In some embodiments, the gene or gene product is associated with inhibition of a TLR (e.g., TLR9) (e.g., GPR108). In some embodiments, the gene or gene product is associated with endosomal trafficking of, for example, AAV-R (e.g., VPS35). In some embodiments, the gene or gene product is a calcium ATPase pump (e.g., ATP2C1). In some embodiments, the gene or gene product is associated with Notch signaling (e.g., RBPJ). In some embodiments, the gene or gene product is associated with HSPG metabolism (e.g., TM9SF2). In some embodiments, the gene or gene product is associated with inhibition of NHEJ (e.g., CYREN). In some embodiments, the gene or gene product is associated with viral hairpin degradation (e.g., DCLRE1C). In some embodiments, the gene or gene product is associated with Glc transporter translocation, and optionally, the gene or gene product binds to insulin receptor substrate 1 protein (e.g., PHIP).

[0024] In some embodiments, the gene or gene product reduces the transduction efficiency of AAV2 particles, and optionally, the gene or gene product, when regulated, does not reduce or does not substantially reduce the transduction efficiency of AAV9 particles. In some embodiments, the gene or gene product inhibits or prevents transduction of AAV2 particles, and optionally, the gene or gene product does not inhibit or prevent transduction of AAV9 particles. In some embodiments, the gene or gene product is WRD11. In some embodiments, the gene or gene product is MRE11.

[0025] In some embodiments, the gene or gene product is GREB1L, BIRC2, TYMSOS, MSL3, SIK3, GTF2H5, PIGW, ATRAID, PPP4R1, ZFC3H1, SETDB1, SMCHD1, TMEM123, UHRF1, CLUL1, SMAD5, SETX, STEEP1, DENND6A, RTN4RL2, MTMR9, STRADA, PSIP1, BMPR1A, HIKESHI, AP3M1, MEN1, MYL12B, CREB1, RAB12, SMTNL1, MRGBP, WTAP, SUMO2, TCN 1, ALDH3B1, ARL14EP, MYL12A, RHOD, PGAP2, EIF4A1, PIGN, DAXX, HDLBP, GOLGA1, SARNP, UBE2L6, TRIM49, SIK2, SOX4, OR6Q1, OR4D6, UNC93B1, CATSPERZ, PIGT, PYM1, MICOS13, RIN1, DOT1L, TRIM49C, MAPK20, COL8A1, FASN, KDM3B, PIGF, PIGA, PIGY, GPC3, TRAPPC2L, RAB31, ELP3, or a combination thereof.

[0026] In some embodiments, the gene or gene product is associated with retinoic acid receptor activity (e.g., GREB1L). In some embodiments, the gene or gene product is thymidylate synthetase (e.g., TYMSOS). In some embodiments, the gene or gene product is associated with chromatin remodeling (e.g., SMCHD1). In some embodiments, the gene or gene product is associated with histone H4 acetylation (e.g., MSL3). In some embodiments, the gene or gene product is associated with transcription and / or DNA repair (e.g., GTF2H5). In some embodiments, the gene or gene product is a histone methyltransferase (e.g., SETDB1). In some embodiments, the gene or gene product is associated with exosomal degradation of polyadenylated RNA (e.g., ZFC3H1). In some embodiments, the gene or gene product is associated with recruitment of histone deacetylase to DNA (e.g., UHRF1). In some embodiments, the gene or gene product is associated with oxidative stress-induced DNA double-strand break response (e.g., SETX). In some embodiments, the gene or gene product is associated with histone modification (e.g., MEN1). In some embodiments, the gene or gene product is associated with nucleosome / DNA interactions (e.g., MRGBP). In some embodiments, the gene or gene product is associated with GPI biosynthesis (e.g., PIGW, PIGN, PIGT, PIGF, PIGA, or PIGY). In some embodiments, the gene or gene product is associated with GPI anchor maturation (e.g., PGAP2). In some embodiments, the gene or gene product is associated with vesicle-mediated endocytosis (e.g., DENND6A, GOLGA1, MTMR9, GPC3, PPP4R1, RAB12, RAB31, RHOD, RIN1, TMEM123, or TRAPPC2L). In some embodiments, the gene or gene product is associated with clathrin-coated vesicle-mediated endocytosis (e.g., AP3M1). In some embodiments, the gene or gene product is related to a BMP receptor kinase (eg, SMAD5, BMPR1A, or CREB1).In some embodiments, the gene or gene product is associated with transcription (e.g., PSIP1). In some embodiments, the gene or gene product is associated with nuclear import of HSP70 proteins (e.g., HIKESHI). In some embodiments, the gene or gene product is associated with Ser / Thr kinases (e.g., SIK2 or SIK3). In some embodiments, the gene or gene product is associated with protein sumoylation (e.g., SUMO2, UBE2L6).

[0027] In some embodiments, the gene or gene product reduces the transduction efficiency of AAV9 particles, and optionally, the gene or gene product does not reduce or substantially reduce the transduction efficiency of AAV2 particles. In some embodiments, the gene or gene product inhibits or prevents transduction of AAV9 particles, and optionally, the gene or gene product does not inhibit or prevent transduction of AAV2 particles. In some embodiments, the gene or gene product is WRD11. In some embodiments, the gene or gene product is MRE11.

[0028] In some embodiments, the gene or gene product is selected from AP2A1, AP2B1, TM9SF4, ACTR5, PTMA, PAPOLA, PDHA1, PDHB, SLC25A19, GAK, AUNIP, FCHO2, ACTB, LIPT1, UCHL5, INO80E, ECHS1, NELFB, EDC4, PRMT1, PDS5B, PELI3, FBXL20, SLC35A1, or a combination thereof.

[0029] In some embodiments, the gene or gene product binds to ATP, chaperone proteins, and / or clathrin (e.g., GAK). In some embodiments, the gene or gene product is associated with the trafficking of clathrin-coated vesicles (e.g., AP2B1 or AP2A1). In some embodiments, the gene or gene product is associated with clathrin-mediated endocytosis (e.g., FCHO2). In some embodiments, the gene or gene product is associated with vesicle trafficking (e.g., ACTB). In some embodiments, the gene or gene product is associated with the innate immune response (e.g., PELI3 or FBXL20). In some embodiments, the gene or gene product is associated with glucose metabolism (e.g., PDHB or PDHA1). In some embodiments, the gene or gene product is associated with DNA resection and / or homologous recombination, e.g., after DNA damage (e.g., AUNIP). In some embodiments, the gene or gene product is associated with DNA repair, e.g., after DNA damage (e.g., UCHL5, INO80E, PDS5B, ACTR5, or PRMT1). In some embodiments, the gene or gene product is associated with transport of CMP sialic acid from the cytosol to Golgi vesicles (e.g., SLC35A1). In some embodiments, the gene or gene product is associated with localization of polypeptides containing a glycine-rich transmembrane domain, e.g., to the cell surface (e.g., TM9SF4). In some embodiments, the gene or gene product is associated with synthesis of poly(A) tails (e.g., PAPOLA). In some embodiments, the gene or gene product is PTMA. In some embodiments, the gene or gene product is associated with elongation of mRNA by RNA polymerase II (e.g., NELFB). In some embodiments, the gene or gene product is associated with mRNA degradation (e.g., EDC4). In some embodiments, the gene or gene product encodes a mitochondrial lipoyltransferase (e.g., LIPT1). In some embodiments, the gene or gene product is associated with mitochondrial fatty acid β-oxidation (e.g., ECHS1). In some embodiments, the gene or gene product encodes the mitochondrial thiamine pyrophosphate carrier (e.g., SLC25A19).

[0030] In some embodiments, the gene or gene product reduces the transduction efficiency of AAV2 and AAV9 particles. In some embodiments, the gene or gene product inhibits or prevents transduction of AAV2 and AAV9 particles. In some embodiments, the gene or gene product is WRD11. In some embodiments, the gene or gene product is MRE11.

[0031] In some embodiments, the gene or gene product is selected from the group consisting of PITPNB, PITP, FAM91A1, WDR11, AP1G1, AP1M1, AP1S1, AP1S3, HEATR5B, STX16, AP1B1, PIAS1, DENR, ARL1, ZFAT, TBC1D23, LIN37, RALGAPB, B3GNT2, ELOVL1, AP2B1, KIAA2013, PTEN, MCTS1, NBN, HELZ, SLC38A10, FBXL20, TGIF1, KDSR, CPD, CHD7, USP9X, SIMC1, TAF11, VAPA, MTMR6, RAB1B, SLF2, MRE11, VTI1A, MBOAT7, PPP6R3, or a combination thereof.

[0032] In some embodiments, the gene or gene product is associated with the long-chain FA elongation cycle (e.g., ELOVL1). In some embodiments, the gene or gene product is associated with lipoic acid biosynthesis (e.g., PIAS1). In some embodiments, the gene or gene product is associated with a protein phosphatase catalytic subunit (e.g., PPP6R3). In some embodiments, the gene or gene product is associated with the WDR11 pathway (e.g., WDR11, FAM91A1, AP1G1, AP1S1, AP1M1, AP1S3, or TBC1D23). In some embodiments, the gene or gene product is associated with retrograde transport of, for example, PI and / or PC from the Golgi apparatus to the endoplasmic reticulum (e.g., PITP). In some embodiments, the gene or gene product is associated with vesicle transport from late endosomes to the trans-Golgi network (e.g., STX16). In some embodiments, the gene or gene product is associated with the activity or recruitment of golgin, arfaptin, and / or Arf-GEF to the trans-Golgi network (e.g., ARL1). In some embodiments, the gene or gene product encodes a component of clathrin-dependent vesicles and / or is associated with AP1G1 / AP-1-mediated protein transport (e.g., HEATR5B).

[0033] In some embodiments, the gene or gene product is AAV-R, GPR108, WDR11, or MRE11. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GPR108. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0034] In some embodiments, the regulatory element is (a) a gene editing system that targets one or more sites within a gene or its regulatory elements, (b) a nucleic acid encoding one or more components of the gene editing system, or (c) a combination thereof. In some embodiments, the gene editing system is a CRISPR / Cas system, a zinc finger nuclease system, a TALEN system, or a meganuclease system.

[0035] In some embodiments, the gene editing system binds to a target sequence in an early (e.g., first, second, or third) exon or intron of a gene. In some embodiments, the gene editing system binds to a target sequence of a gene, and the target sequence is upstream of exon 4, e.g., in exon 1, exon 2, or exon 3. In some embodiments, the gene editing system binds to a target sequence in a later exon or intron of a gene. In some embodiments, the gene editing system binds to a target sequence of a gene, and the target sequence is downstream of the penultimate exon, e.g., the third to last exon, the penultimate exon, or the last exon. In some embodiments, the gene editing system is a CRISPR / Cas system comprising a guide RNA (gRNA) molecule comprising a targeting sequence that hybridizes to the target sequence of the gene. In some embodiments, the CRISPR / Cas system is a CRISPR / Cas9 system. In some embodiments, the CRISPR / Cas system is a CRISPR / Cas12a system.

[0036] In some embodiments, the regulatory element is a small interfering RNA (siRNA) or small hairpin (shRNA) specific to the gene, or a nucleic acid encoding the siRNA or shRNA. In some embodiments, the siRNA or shRNA comprises a nucleotide sequence complementary to the nucleotide sequence of an mRNA encoded by the gene. In some embodiments, the regulatory element is a guide RNA (gRNA) specific to the gene, or a nucleic acid encoding the gRNA. In some embodiments, the gRNA comprises a nucleotide sequence complementary to the nucleotide sequence of the gene.

[0037] In some embodiments, the modulator is a gene-specific antisense oligonucleotide (ASO) or a nucleic acid encoding the ASO. In some embodiments, the ASO comprises a nucleotide sequence complementary to the nucleotide sequence of an mRNA encoded by the gene.

[0038] In some embodiments, the modulator is a small molecule (e.g., a compound described herein, e.g., in Figure 7). In some embodiments, the small molecule is a protein degradation inducer.

[0039] In some embodiments, the modulator is a protein or peptide, or a nucleic acid encoding the protein or peptide. In some embodiments, the modulator is an antibody molecule (e.g., an scFv or sdAb). In some embodiments, the modulator is a dominant-negative binding partner of the protein encoded by the gene, or a nucleic acid encoding the dominant-negative binding partner. In some embodiments, the modulator is a dominant-negative variant (e.g., catalytically inactive) of the protein encoded by the gene, or a nucleic acid encoding the dominant-negative variant.

[0040] In some embodiments, the AAV particles comprise an AAV genome. In some embodiments, the AAV particles comprise AAV-like particles. In some embodiments, the AAV particles comprise a capsid. In some embodiments, the AAV particles have a serotype of AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, or a combination thereof. In some embodiments, the AAV particles are AAV2 particles. In some embodiments, the AAV particles are AAV9 particles.

[0041] In some embodiments, the AAV particles have a tropism for the CNS (e.g., AAV1, AAV2, AAV4, AAV5, AAV8, or AAV9). In some embodiments, the AAV particles have a tropism for the heart (e.g., AAV1, AAV8, or AAV9). In some embodiments, the AAV particles have a tropism for the kidney (e.g., AAV2). In some embodiments, the AAV particles have a tropism for the liver (e.g., AAV7, AAV8, or AAV9). In some embodiments, the AAV particles have a tropism for the lung (e.g., AAV4, AAV5, AAV6, or AAV9). In some embodiments, the AAV particles have a tropism for the pancreas (e.g., AAV8). In some embodiments, the AAV particles have a tropism for photoreceptor cells (e.g., AAV2, AAV5, or AAV8). In some embodiments, the AAV particle has tropism for the retinal pigment epithelium (RPE) (e.g., AAV1, AAV2, AAV4, AAV5, or AAV8). In some embodiments, the AAV particle has tropism for skeletal muscle (e.g., AAV1, AAV6, AAV7, AAV8, or AAV9).

[0042] In some embodiments, the method results in high gene regulation (e.g., gene editing) efficiency in a first tissue (e.g., at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 98%) and limited effect in a second tissue (e.g., 20%, 15%, 10%, 5%, 2%, or less gene regulation (e.g., gene editing) efficiency). In some embodiments, the method results in high regulation (e.g., gene editing) efficiency in the liver (e.g., at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 98%) and limited effect in skeletal muscle, bone marrow, or both (e.g., 20%, 15%, 10%, 5%, 2%, or less gene regulation (e.g., gene editing) efficiency).

[0043] In some embodiments, the AAV particles comprise a nucleotide sequence encoding a therapeutic protein, e.g., a protein associated with a disorder described herein. In some embodiments, the AAV particles comprise a nucleotide sequence encoding NGF, APOE2 (e.g., hAPOE2), TERT (e.g., hTERT), MAPT, GAD, AADC, NTN, GDNF, GCase, HTT, SMN, SMN2, SOD1, or C9orf72. In some embodiments, the AAV particles comprise a nucleotide sequence encoding a therapeutic nucleic acid, e.g., a nucleic acid targeting a nucleotide sequence encoding a protein associated with a disorder described herein.

[0044] In some embodiments, the cell is a brain cell, liver cell, spinal cord cell, dorsal root ganglion (DRG) cell, spleen cell, lymph node cell, kidney cell, lung cell, heart cell, muscle cell (e.g., skeletal muscle cell, thigh muscle cell), septum cell, bone marrow cell, or gonad cell. In some embodiments, the cell is a central nervous system (CNS) cell. In some embodiments, the CNS cell is an astrocyte, oligodendrocyte, microglia, or ependymal cell. In some embodiments, the cell is a brain cell. In some embodiments, the brain cell is a neuron or glial cell. In some embodiments, the cell is a DRG cell. In some embodiments, the cell is a hepatocyte. In some embodiments, the hepatocyte is a hepatic parenchymal cell, hepatic stellate cell, Kupffer cell, or hepatic sinusoidal endothelial cell.

[0045] In some embodiments, the cells are contacted with the AAV transduction regulator in vitro. In some embodiments, the cells are contacted with the AAV transduction regulator ex vivo. In some embodiments, the cells are contacted with the AAV transduction regulator in vivo.

[0046] In some embodiments, the methods include contacting the cells with a plurality of AAV transduction regulators or AAV regulatory factors that regulate a plurality of genes or gene products associated with AAV transduction efficiency.

[0047] In another aspect, the present disclosure provides a method for modulating the transduction efficiency of an AAV particle, the method comprising administering an effective amount of an AAV transduction modulator to a subject in need thereof, thereby modulating the transduction efficiency of the AAV particle.

[0048] In some embodiments, the modulator modulates (e.g., increases or decreases) a gene or gene product associated with AAV transduction efficiency, hi some embodiments, the gene or gene product is a mammalian (e.g., human) gene or gene product.

[0049] In some embodiments, the modulator inhibits a gene or gene product, e.g., a gene or gene product associated with decreased transduction efficiency of AAV particles, hi some embodiments, the modulator activates a gene or gene product, e.g., a gene or gene product associated with increased transduction efficiency of AAV particles.

[0050] In some embodiments, the gene or gene product is associated with increased transduction efficiency of AAV particles. In some embodiments, the gene or gene product is associated with increased transduction efficiency of AAV particles of a first serotype (e.g., AAV2), increased transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GRP108.

[0051] In some embodiments, the gene or gene product is associated with decreased transduction efficiency of AAV particles. In some embodiments, the gene or gene product is associated with decreased transduction efficiency of AAV particles of a first serotype (e.g., AAV2), decreased transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both. In some embodiments, the gene or gene product is WRD11. In some embodiments, the gene or gene product is MRE11.

[0052] In some embodiments, the gene or gene product, when modulated, increases the transduction efficiency of AAV particles, ie, the gene or gene product, when modulated, increases the transduction efficiency of AAV particles of a first serotype (e.g., AAV2), the transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both.

[0053] In some embodiments, the gene or gene product, when modulated, decreases the transduction efficiency of AAV particles, ie, the gene or gene product, when modulated, decreases the transduction efficiency of AAV particles of a first serotype (e.g., AAV2), the transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both.

[0054] In some embodiments, the gene product is RNA (e.g., mRNA). In some embodiments, the gene product is a protein. In some embodiments, the gene or gene product is selectively expressed in a target tissue (e.g., brain or liver). The following dependent claims describe AAV transduction regulators based on their mechanism. In some embodiments, the regulator alters (e.g., increases or decreases) the expression of a gene. In some embodiments, the regulator alters the structure of a gene. In some embodiments, the regulator alters (e.g., increases or decreases) the activity (e.g., enzymatic activity) of a gene product. In some embodiments, the regulator alters (e.g., increases or decreases) the level (e.g., abundance) of a gene product. In some embodiments, the regulator alters (e.g., increases or decreases) the stability of a gene product. In some embodiments, the regulator alters (e.g., increases or decreases) the transduction efficiency of AAV particles, e.g., as determined by an assay described herein (e.g., FACS analysis, e.g., as described in Example 1 or 2).

[0055] In some embodiments, the gene or gene product is AAV-R, GPR108, WDR11, or MRE11. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GPR108. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0056] In some embodiments, the method results in high gene regulation (e.g., gene editing) efficiency in a first tissue (e.g., at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 98%) and limited effect in a second tissue (e.g., 20%, 15%, 10%, 5%, 2%, or less gene regulation (e.g., gene editing) efficiency). In some embodiments, the method results in high regulation (e.g., gene editing) efficiency in the liver (e.g., at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 98%) and limited effect in skeletal muscle, bone marrow, or both (e.g., 20%, 15%, 10%, 5%, 2%, or less gene regulation (e.g., gene editing) efficiency).

[0057] In some embodiments, the modulator increases the transduction efficiency of AAV particles. In some embodiments, the transduction efficiency is increased by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90%, or at least 1-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 60-fold, 70-fold, 80-fold, 90-fold, 100-fold, 200-fold, 300-fold, 400-fold, 500-fold, 600-fold, 700-fold, 800-fold, 900-fold, or 1000-fold compared to a baseline level of transduction efficiency. In some embodiments, the modulator increases transduction by at least 10, 20, 30, 40, 50, or 60 viral copies per genome. In some embodiments, the regulatory factor induces transduction at a rate of at least 10 per μg of DNA. 3 , 10 4 , 105 , 10 6 , or 10 7 The viral copy number increases to .

[0058] In some embodiments, the modulator reduces the transduction efficiency of AAV particles. In some embodiments, the transduction efficiency is reduced by at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% compared to a baseline level of transduction efficiency. In some embodiments, the modulator reduces transduction to 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 viral copies per genome or less. In some embodiments, the modulator reduces transduction to 10 copies per μg of DNA or less. 2 , 10 3 , or 10 4 Reduce the viral copy number to:

[0059] In some embodiments, the baseline level of transduction efficiency is the level of transduction efficiency in cells that have not been contacted with an AAV transduction regulatory agent, hi some embodiments, the baseline level of transduction efficiency is the level of transduction efficiency before the cells are contacted with an AAV transduction regulatory agent.

[0060] In some embodiments, the gene or gene product increases the transduction efficiency of AAV2 particles, and optionally, the gene or gene product does not increase or does not substantially increase the transduction efficiency of AAV9 particles. In some embodiments, the gene or gene product is essential for transduction of AAV2 particles, and optionally, the gene or gene product is not essential for transduction of AAV9 particles. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GRP108.

[0061] In some embodiments, the gene or gene product is selected from EXT1, EXT2, NDST1, BCL10, OAF, PDCD10, LMO4, MALT1, ZNF644, CHUK, GLCE, EP300, ARID4B, RAB21, MED13, DHX15, WASHC5, IKBKB, USP24, HSPA14, CXXC1, UBE2A, INTS8, CDC42, NFKB1, SIN3A, USP7, ARF5, CARD10, JAK1, SLC35C2, PAXK1, ZC3H11A, FAM20B, FAM72A, DHX36, INTS12, RPRD1B, or a combination thereof.

[0062] In some embodiments, the gene or gene product is associated with endosomal sorting (e.g., RAB21, WASHC5, or USP7). In some embodiments, the gene or gene product is associated with vesicle-mediated transport (e.g., CDC42 or ARF5). In some embodiments, the gene or gene product is associated with NFKB signaling (e.g., BCL10, MALT1, NFKB1, IKBKB, CHUK, or CARD10). In some embodiments, the gene or gene product is associated with heparan sulfate biosynthesis (e.g., EXT1, EXT2, NDST1, GLCE, or FAM20B). In some embodiments, the gene or gene product is associated with H3K9 methylation (e.g., ZNF644). In some embodiments, the gene or gene product is associated with pre-mRNA processing (e.g., DHX15). In some embodiments, the gene or gene product is associated with transcription (e.g., LMO4, EP300, MED13, SIN3, ARID4B, ZC3H11A, CXXC1, RPRD1B, or UBE2A). In some embodiments, the gene or gene product is associated with the Integrator complex and / or RNA polymerase II function (e.g., INTS8 or INST12). In some embodiments, the gene or gene product is associated with DNA repair and / or AAV genome degradation (e.g., DHX36, ARID4B, UBE2A, or USP24). In some embodiments, the gene or gene product is associated with cell proliferation and / or apoptosis (e.g., PDCD10). In some embodiments, the gene or gene product is associated with spinocarpal tarsal synostosis (e.g., OAF). In some embodiments, the gene or gene product is associated with protein folding (e.g., HSPA14). In some embodiments, the gene or gene product is associated with helicase activity (e.g., DHX36). In some embodiments, the gene or gene product is associated with fucosylation of Notch and / or transport of GCP-fucose (eg, SLC35C2).

[0063] In some embodiments, the gene or gene product increases the transduction efficiency of AAV9 particles, and optionally, the gene or gene product does not increase or does not substantially increase the transduction efficiency of AAV2 particles. In some embodiments, the gene or gene product is essential for transduction of AAV9 particles, and optionally, the gene or gene product is not essential for transduction of AAV2 particles. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GRP108.

[0064] In some embodiments, the gene or gene product is selected from TMPRSS11B, HTT, SNRNP70, BRD7, DMXL1, RAB10, CNGA1, KLHDC3, CHP1, CYP3A5, ELOVL4, PNISR, ZCCHC14, AZGP1, TPST1, SC5D, ELP2, ELP3, IPO9, RAB14, WDR7, XRCC4, GDI2, or a combination thereof.

[0065] In some embodiments, the gene or gene product is associated with microtubule-mediated transport or vesicle function (e.g., HTT). In some embodiments, the gene or gene product is an ion channel (e.g., CNGA1). In some embodiments, the gene or gene product is associated with nuclear protein import (e.g., IPO9). In some embodiments, the gene or gene product is associated with O-sulfation of tyrosine residues within acidic motifs of polypeptides (e.g., TPST1). In some embodiments, the gene or gene product is associated with protection of viral RNA (e.g., ZCCHC14). In some embodiments, the gene or gene product is associated with RNA binding by AAV proteins (e.g., PNISR). In some embodiments, the gene or gene product is associated with calcium ion-regulated exocytosis (e.g., CHP1). In some embodiments, the gene or gene product is associated with intracellular transport (e.g., RAB10, RAB14, GDI2, WDR7, or DMXL1). In some embodiments, the gene or gene product is a subunit (e.g., a catalytic tRNA acetyltransferase subunit) of an elongator complex, e.g., an RNA polymerase (e.g., RNA polymerase II) (e.g., ELP2 or ELP3). In some embodiments, the gene or gene product is chromatin-associated (e.g., KLHDC3). In some embodiments, the gene or gene product is associated with cholesterol biosynthesis (e.g., SC5D).

[0066] In some embodiments, the gene or gene product increases the transduction efficiency of AAV2 and AAV9 particles. In some embodiments, the gene or gene product is essential for transduction of AAV2 and AAV9 particles. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GRP108.

[0067] In some embodiments, the gene or gene product is selected from KIAA0319L, BAMBI, TM9SF2, PHIP, DCLRE1C, VPS35, GPR108, CYREN, ACP2, F8A2, F8A1, F8A3, RBPJ, ATP2C1, ICMT, RABIF, IER3IP1, RBM10, SMG7, GTF2I, ELAVL1, MEPCE, RAB4A, IER3IP1, SAMD1, or a combination thereof.

[0068] In some embodiments, the gene or gene product is associated with influenza infection (e.g., ACP2). In some embodiments, the gene or gene product binds to an unmethylated CGI (e.g., SAMD1). In some embodiments, the gene or gene product is associated with intracellular vesicle trafficking (e.g., RABIF). In some embodiments, the gene or gene product is associated with post-translational modification of a cysteine ​​residue (e.g., a C-terminal cysteine ​​residue) in, for example, a target protein (e.g., ICMT). In some embodiments, the gene or gene product binds to an AAV capsid protein (e.g., KIAA0319L). In some embodiments, the gene or gene product is associated with inhibition of a TLR (e.g., TLR9) (e.g., GPR108). In some embodiments, the gene or gene product is associated with endosomal trafficking of, for example, AAV-R (e.g., VPS35). In some embodiments, the gene or gene product is a calcium ATPase pump (e.g., ATP2C1). In some embodiments, the gene or gene product is associated with Notch signaling (e.g., RBPJ). In some embodiments, the gene or gene product is associated with HSPG metabolism (e.g., TM9SF2). In some embodiments, the gene or gene product is associated with inhibition of NHEJ (e.g., CYREN). In some embodiments, the gene or gene product is associated with viral hairpin degradation (e.g., DCLRE1C). In some embodiments, the gene or gene product is associated with Glc transporter translocation, and optionally, the gene or gene product binds to insulin receptor substrate 1 protein (e.g., PHIP).

[0069] In some embodiments, the gene or gene product reduces the transduction efficiency of AAV2 particles, and optionally, the gene or gene product, when regulated, does not reduce or does not substantially reduce the transduction efficiency of AAV9 particles. In some embodiments, the gene or gene product inhibits or prevents transduction of AAV2 particles, and optionally, the gene or gene product does not inhibit or prevent transduction of AAV9 particles. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0070] In some embodiments, the gene or gene product is GREB1L, BIRC2, TYMSOS, MSL3, SIK3, GTF2H5, PIGW, ATRAID, PPP4R1, ZFC3H1, SETDB1, SMCHD1, TMEM123, UHRF1, CLUL1, SMAD5, SETX, STEEP1, DENND6A, RTN4RL2, MTMR9, STRADA, PSIP1, BMPR1A, HIKESHI, AP3M1, MEN1, MYL12B, CREB1, RAB12, SMTNL1, MRGBP, WTAP, SUMO2, TCN 1, ALDH3B1, ARL14EP, MYL12A, RHOD, PGAP2, EIF4A1, PIGN, DAXX, HDLBP, GOLGA1, SARNP, UBE2L6, TRIM49, SIK2, SOX4, OR6Q1, OR4D6, UNC93B1, CATSPERZ, PIGT, PYM1, MICOS13, RIN1, DOT1L, TRIM49C, MAPK20, COL8A1, FASN, KDM3B, PIGF, PIGA, PIGY, GPC3, TRAPPC2L, RAB31, ELP3, or a combination thereof.

[0071] In some embodiments, the gene or gene product is associated with retinoic acid receptor activity (e.g., GREB1L). In some embodiments, the gene or gene product is thymidylate synthetase (e.g., TYMSOS). In some embodiments, the gene or gene product is associated with chromatin remodeling (e.g., SMCHD1). In some embodiments, the gene or gene product is associated with histone H4 acetylation (e.g., MSL3). In some embodiments, the gene or gene product is associated with transcription and / or DNA repair (e.g., GTF2H5). In some embodiments, the gene or gene product is a histone methyltransferase (e.g., SETDB1). In some embodiments, the gene or gene product is associated with exosomal degradation of polyadenylated RNA (e.g., ZFC3H1). In some embodiments, the gene or gene product is associated with recruitment of histone deacetylase to DNA (e.g., UHRF1). In some embodiments, the gene or gene product is associated with oxidative stress-induced DNA double-strand break response (e.g., SETX). In some embodiments, the gene or gene product is associated with histone modification (e.g., MEN1). In some embodiments, the gene or gene product is associated with nucleosome / DNA interactions (e.g., MRGBP). In some embodiments, the gene or gene product is associated with GPI biosynthesis (e.g., PIGW, PIGN, PIGT, PIGF, PIGA, or PIGY). In some embodiments, the gene or gene product is associated with GPI anchor maturation (e.g., PGAP2). In some embodiments, the gene or gene product is associated with vesicle-mediated endocytosis (e.g., DENND6A, GOLGA1, MTMR9, GPC3, PPP4R1, RAB12, RAB31, RHOD, RIN1, TMEM123, or TRAPPC2L). In some embodiments, the gene or gene product is associated with clathrin-coated vesicle-mediated endocytosis (e.g., AP3M1). In some embodiments, the gene or gene product is related to a BMP receptor kinase (eg, SMAD5, BMPR1A, or CREB1).In some embodiments, the gene or gene product is associated with transcription (e.g., PSIP1). In some embodiments, the gene or gene product is associated with nuclear import of HSP70 proteins (e.g., HIKESHI). In some embodiments, the gene or gene product is associated with Ser / Thr kinases (e.g., SIK2 or SIK3). In some embodiments, the gene or gene product is associated with protein sumoylation (e.g., SUMO2, UBE2L6).

[0072] In some embodiments, the gene or gene product reduces the transduction efficiency of AAV9 particles, and optionally, the gene or gene product does not reduce or substantially reduce the transduction efficiency of AAV2 particles. In some embodiments, the gene or gene product inhibits or prevents transduction of AAV9 particles, and optionally, the gene or gene product does not inhibit or prevent transduction of AAV2 particles. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0073] In some embodiments, the gene or gene product is selected from AP2A1, AP2B1, TM9SF4, ACTR5, PTMA, PAPOLA, PDHA1, PDHB, SLC25A19, GAK, AUNIP, FCHO2, ACTB, LIPT1, UCHL5, INO80E, ECHS1, NELFB, EDC4, PRMT1, PDS5B, PELI3, FBXL20, SLC35A1, or a combination thereof.

[0074] In some embodiments, the gene or gene product binds to ATP, chaperone proteins, and / or clathrin (e.g., GAK). In some embodiments, the gene or gene product is associated with the trafficking of clathrin-coated vesicles (e.g., AP2B1 or AP2A1). In some embodiments, the gene or gene product is associated with clathrin-mediated endocytosis (e.g., FCHO2). In some embodiments, the gene or gene product is associated with vesicle trafficking (e.g., ACTB). In some embodiments, the gene or gene product is associated with the innate immune response (e.g., PELI3 or FBXL20). In some embodiments, the gene or gene product is associated with glucose metabolism (e.g., PDHB or PDHA1). In some embodiments, the gene or gene product is associated with DNA resection and / or homologous recombination, e.g., after DNA damage (e.g., AUNIP). In some embodiments, the gene or gene product is associated with DNA repair, e.g., after DNA damage (e.g., UCHL5, INO80E, PDS5B, ACTR5, or PRMT1). In some embodiments, the gene or gene product is associated with transport of CMP sialic acid from the cytosol to Golgi vesicles (e.g., SLC35A1). In some embodiments, the gene or gene product is associated with localization of polypeptides containing a glycine-rich transmembrane domain, e.g., to the cell surface (e.g., TM9SF4). In some embodiments, the gene or gene product is associated with synthesis of poly(A) tails (e.g., PAPOLA). In some embodiments, the gene or gene product is PTMA. In some embodiments, the gene or gene product is associated with elongation of mRNA by RNA polymerase II (e.g., NELFB). In some embodiments, the gene or gene product is associated with mRNA degradation (e.g., EDC4). In some embodiments, the gene or gene product encodes a mitochondrial lipoyltransferase (e.g., LIPT1). In some embodiments, the gene or gene product is associated with mitochondrial fatty acid β-oxidation (e.g., ECHS1). In some embodiments, the gene or gene product encodes the mitochondrial thiamine pyrophosphate carrier (e.g., SLC25A19).

[0075] In some embodiments, the gene or gene product reduces the transduction efficiency of AAV2 and AAV9 particles, hi some embodiments, the gene or gene product inhibits or prevents transduction of AAV2 and AAV9 particles.

[0076] In some embodiments, the gene or gene product is selected from the group consisting of PITPNB, PITP, FAM91A1, WDR11, AP1G1, AP1M1, AP1S1, AP1S3, HEATR5B, STX16, AP1B1, PIAS1, DENR, ARL1, ZFAT, TBC1D23, LIN37, RALGAPB, B3GNT2, ELOVL1, AP2B1, KIAA2013, PTEN, MCTS1, NBN, HELZ, SLC38A10, FBXL20, TGIF1, KDSR, CPD, CHD7, USP9X, SIMC1, TAF11, VAPA, MTMR6, RAB1B, SLF2, MRE11, VTI1A, MBOAT7, PPP6R3, or a combination thereof.

[0077] In some embodiments, the gene or gene product is associated with the long-chain FA elongation cycle (e.g., ELOVL1). In some embodiments, the gene or gene product is associated with lipoic acid biosynthesis (e.g., PIAS1). In some embodiments, the gene or gene product is associated with a protein phosphatase catalytic subunit (e.g., PPP6R3). In some embodiments, the gene or gene product is associated with the WDR11 pathway (e.g., WDR11, FAM91A1, AP1G1, AP1S1, AP1M1, AP1S3, or TBC1D23). In some embodiments, the gene or gene product is associated with retrograde transport of, for example, PI and / or PC from the Golgi apparatus to the endoplasmic reticulum (e.g., PITP). In some embodiments, the gene or gene product is associated with vesicle transport from late endosomes to the trans-Golgi network (e.g., STX16). In some embodiments, the gene or gene product is associated with the activity or recruitment of golgin, arfaptin, and / or Arf-GEF to the trans-Golgi network (e.g., ARL1). In some embodiments, the gene or gene product encodes a component of clathrin-dependent vesicles and / or is involved in AP1G1 / AP-1 mediated protein transport (eg, HEATR5B).

[0078] In some embodiments, the regulatory element is (a) a gene editing system that targets one or more sites within a gene or its regulatory elements, (b) a nucleic acid encoding one or more components of the gene editing system, or (c) a combination thereof. In some embodiments, the gene editing system is a CRISPR / Cas system, a zinc finger nuclease system, a TALEN system, or a meganuclease system.

[0079] In some embodiments, the gene editing system binds to a target sequence in an early (e.g., first, second, or third) exon or intron of a gene. In some embodiments, the gene editing system binds to a target sequence of a gene, and the target sequence is upstream of exon 4, e.g., in exon 1, exon 2, or exon 3. In some embodiments, the gene editing system binds to a target sequence in a later exon or intron of a gene. In some embodiments, the gene editing system binds to a target sequence of a gene, and the target sequence is downstream of the penultimate exon, e.g., the third to last exon, the penultimate exon, or the last exon. In some embodiments, the gene editing system is a CRISPR / Cas system comprising a guide RNA (gRNA) molecule comprising a targeting sequence that hybridizes to the target sequence of the gene. In some embodiments, the CRISPR / Cas system is a CRISPR / Cas9 system. In some embodiments, the CRISPR / Cas system is a CRISPR / Cas12a system.

[0080] In some embodiments, the regulatory element is a small interfering RNA (siRNA) or small hairpin (shRNA) specific to the gene, or a nucleic acid encoding the siRNA or shRNA. In some embodiments, the siRNA or shRNA comprises a nucleotide sequence complementary to the nucleotide sequence of an mRNA encoded by the gene. In some embodiments, the regulatory element is a guide RNA (gRNA) specific to the gene, or a nucleic acid encoding the gRNA. In some embodiments, the gRNA comprises a nucleotide sequence complementary to the nucleotide sequence of the gene.

[0081] In some embodiments, the modulator is a gene-specific antisense oligonucleotide (ASO) or a nucleic acid encoding the ASO. In some embodiments, the ASO comprises a nucleotide sequence complementary to the nucleotide sequence of an mRNA encoded by the gene.

[0082] In some embodiments, the modulator is a small molecule (e.g., a compound described herein, e.g., in Figure 7). In some embodiments, the small molecule is a protein degradation inducer.

[0083] In some embodiments, the modulator is a protein or peptide, or a nucleic acid encoding the protein or peptide. In some embodiments, the modulator is an antibody molecule (e.g., an scFv or sdAb). In some embodiments, the modulator is a dominant-negative binding partner of the protein encoded by the gene, or a nucleic acid encoding the dominant-negative binding partner. In some embodiments, the modulator is a dominant-negative variant (e.g., catalytically inactive) of the protein encoded by the gene, or a nucleic acid encoding the dominant-negative variant.

[0084] In some embodiments, the AAV particles comprise an AAV genome. In some embodiments, the AAV particles comprise AAV-like particles. In some embodiments, the AAV particles comprise a capsid. In some embodiments, the AAV particles have a serotype of AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, or a combination thereof. In some embodiments, the AAV particles are AAV2 particles. In some embodiments, the AAV particles are AAV9 particles.

[0085] In some embodiments, the AAV particles have a tropism for the CNS (e.g., AAV1, AAV2, AAV4, AAV5, AAV8, or AAV9). In some embodiments, the AAV particles have a tropism for the heart (e.g., AAV1, AAV8, or AAV9). In some embodiments, the AAV particles have a tropism for the kidney (e.g., AAV2). In some embodiments, the AAV particles have a tropism for the liver (e.g., AAV7, AAV8, or AAV9). In some embodiments, the AAV particles have a tropism for the lung (e.g., AAV4, AAV5, AAV6, or AAV9). In some embodiments, the AAV particles have a tropism for the pancreas (e.g., AAV8). In some embodiments, the AAV particles have a tropism for photoreceptor cells (e.g., AAV2, AAV5, or AAV8). In some embodiments, the AAV particle has tropism for the retinal pigment epithelium (RPE) (e.g., AAV1, AAV2, AAV4, AAV5, or AAV8). In some embodiments, the AAV particle has tropism for skeletal muscle (e.g., AAV1, AAV6, AAV7, AAV8, or AAV9).

[0086] In some embodiments, the AAV particles comprise a nucleotide sequence encoding a therapeutic protein, e.g., a protein associated with a disorder described herein. In some embodiments, the AAV particles comprise a nucleotide sequence encoding NGF, APOE2 (e.g., hAPOE2), TERT (e.g., hTERT), MAPT, GAD, AADC, NTN, GDNF, GCase, HTT, SMN, SMN2, SOD1, or C9orf72. In some embodiments, the AAV particles comprise a nucleotide sequence encoding a therapeutic nucleic acid, e.g., a nucleic acid targeting a nucleotide sequence encoding a protein associated with a disorder described herein.

[0087] In some embodiments, the modulator is administered intravenously.

[0088] In some embodiments, the subject has never been administered or is not currently being administered a therapy comprising an AAV genome or AAV particles when the AAV transduction modulator is administered, hi some embodiments, the subject has been administered an AAV transduction modulator for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, or 1, 2, 3, 4, 5, or 6 months before the subject was administered the therapy. In some embodiments, the subject was administered an AAV transduction modulator within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, 1, 2, 3, 4, 5, or 6 months or less before being administered the therapy.

[0089] In some embodiments, the subject has been administered or is currently administered a therapy comprising an AAV genome or AAV particles when the AAV transduction modulator is administered, hi some embodiments, the subject has been administered the therapy for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, or 1, 2, 3, 4, 5, or 6 months prior to administration of the AAV transduction modulator. In some embodiments, the subject has been administered therapy for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, 1, 2, 3, 4, 5, or 6 months or less before the AAV transduction modulator was administered.

[0090] In some embodiments, the subject has a disorder or a symptom thereof, or is at risk of having a disorder or a symptom thereof. In some embodiments, the disorder is a neurodegenerative disorder. In some embodiments, the neurodegenerative disorder is Alzheimer's disease, Parkinson's disease, Huntington's disease, multiple sclerosis (MS), amyotrophic lateral sclerosis (ALS), or Batten disease. In some embodiments, the disorder is mild Alzheimer's disease, mild to moderate Alzheimer's disease, mild to severe Alzheimer's disease, early dementia, Parkinson's disease (e.g., idiopathic Parkinson's disease, bilateral idiopathic Parkinson's disease, intermediate to late stage Parkinson's disease), Huntington's disease (e.g., manifest Huntington's disease), SMA type 1, presymptomatic SMA, or amyotrophic lateral sclerosis (ALS) (e.g., familial ALS, SOD1-mutant ALS, or C9orf72-mutant ALS). In some embodiments, the disorder is an ocular disorder. In some embodiments, the ocular disorder is blindness, e.g., hereditary blindness or non-hereditary blindness, hi some embodiments, the ocular disorder is Leber's congenital amaurosis, age-related macular degeneration, congenital choroideremia, or color vision deficiency.

[0091] In some embodiments, the method reduces the toxicity of the therapy, enhances the efficacy of the therapy, or both.

[0092] In some embodiments, the methods involve administering to the subject multiple AAV transduction regulators or AAV regulators that regulate multiple genes or gene products associated with AAV transduction efficiency.

[0093] In another aspect, the disclosure provides a method of treating a disorder, comprising administering to a subject in need thereof an effective amount of a therapy comprising an AAV genome or AAV particles, wherein a gene or gene product associated with AAV transduction efficiency is modulated in the subject, thereby treating the disorder.

[0094] In some embodiments, the subject has not been administered or is not currently being administered a therapy when the AAV transduction modulator is administered, hi some embodiments, the subject has been administered an AAV transduction modulator for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, or 1, 2, 3, 4, 5, or 6 months before the subject was administered the therapy. In some embodiments, the subject was administered an AAV transduction modulator within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, 1, 2, 3, 4, 5, or 6 months or less before being administered the therapy.

[0095] In some embodiments, the disorder is a neurodegenerative disorder. In some embodiments, the neurodegenerative disorder is Alzheimer's disease, Parkinson's disease, Huntington's disease, multiple sclerosis (MS), amyotrophic lateral sclerosis (ALS), or Batten disease. In some embodiments, the disorder is mild Alzheimer's disease, mild to moderate Alzheimer's disease, mild to severe Alzheimer's disease, early dementia, Parkinson's disease (e.g., idiopathic Parkinson's disease, bilateral idiopathic Parkinson's disease, intermediate to late stage Parkinson's disease), Huntington's disease (e.g., manifest Huntington's disease), SMA type 1, presymptomatic SMA, or amyotrophic lateral sclerosis (ALS) (e.g., familial ALS, SOD1-mutated ALS, or C9orf72-mutated ALS). In some embodiments, the disorder is an ocular disorder. In some embodiments, the ocular disorder is blindness, e.g., hereditary or non-hereditary blindness. In some embodiments, the ocular disorder is Leber's congenital amaurosis, age-related macular degeneration, congenital choroideremia, or color blindness. In some embodiments, the method reduces the toxicity of the therapy, enhances the efficacy of the therapy, or both.

[0096] In some embodiments, the modulator modulates (e.g., increases or decreases) a gene or gene product associated with AAV transduction efficiency, hi some embodiments, the gene or gene product is a mammalian (e.g., human) gene or gene product.

[0097] In some embodiments, the modulator inhibits a gene or gene product, e.g., a gene or gene product associated with decreased transduction efficiency of AAV particles, hi some embodiments, the modulator activates a gene or gene product, e.g., a gene or gene product associated with increased transduction efficiency of AAV particles.

[0098] In some embodiments, the gene or gene product is associated with increased transduction efficiency of AAV particles. In some embodiments, the gene or gene product is associated with increased transduction efficiency of AAV particles of a first serotype (e.g., AAV2), increased transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GRP108.

[0099] In some embodiments, the gene or gene product is associated with decreased transduction efficiency of AAV particles. In some embodiments, the gene or gene product is associated with decreased transduction efficiency of AAV particles of a first serotype (e.g., AAV2), decreased transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0100] In some embodiments, the gene or gene product, when modulated, increases the transduction efficiency of AAV particles, ie, the gene or gene product, when modulated, increases the transduction efficiency of AAV particles of a first serotype (e.g., AAV2), the transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both.

[0101] In some embodiments, the gene or gene product, when modulated, decreases the transduction efficiency of AAV particles, ie, the gene or gene product, when modulated, decreases the transduction efficiency of AAV particles of a first serotype (e.g., AAV2), the transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both.

[0102] In some embodiments, the gene product is RNA (e.g., mRNA). In some embodiments, the gene product is a protein. In some embodiments, the gene or gene product is selectively expressed in a target tissue (e.g., brain or liver). The following dependent claims describe AAV transduction regulators based on their mechanism. In some embodiments, the regulator alters (e.g., increases or decreases) the expression of a gene. In some embodiments, the regulator alters the structure of a gene. In some embodiments, the regulator alters (e.g., increases or decreases) the activity (e.g., enzymatic activity) of a gene product. In some embodiments, the regulator alters (e.g., increases or decreases) the level (e.g., abundance) of a gene product. In some embodiments, the regulator alters (e.g., increases or decreases) the stability of a gene product. In some embodiments, the regulator alters (e.g., increases or decreases) the transduction efficiency of AAV particles, e.g., as determined by an assay described herein (e.g., FACS analysis, e.g., as described in Example 1 or 2).

[0103] In some embodiments, the gene or gene product is AAV-R, GPR108, WDR11, or MRE11. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GPR108. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0104] In some embodiments, the method results in high gene regulation (e.g., gene editing) efficiency in a first tissue (e.g., at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 98%) and limited effect in a second tissue (e.g., 20%, 15%, 10%, 5%, 2%, or less gene regulation (e.g., gene editing) efficiency). In some embodiments, the method results in high regulation (e.g., gene editing) efficiency in the liver (e.g., at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 98%) and limited effect in skeletal muscle, bone marrow, or both (e.g., 20%, 15%, 10%, 5%, 2%, or less gene regulation (e.g., gene editing) efficiency).

[0105] In some embodiments, the modulator is administered intravenously.

[0106] In some embodiments, the modulator increases the transduction efficiency of AAV particles. In some embodiments, the transduction efficiency is increased by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90%, or at least 1-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 60-fold, 70-fold, 80-fold, 90-fold, 100-fold, 200-fold, 300-fold, 400-fold, 500-fold, 600-fold, 700-fold, 800-fold, 900-fold, or 1000-fold compared to a baseline level of transduction efficiency. In some embodiments, the modulator increases transduction by at least 10, 20, 30, 40, 50, or 60 viral copies per genome. In some embodiments, the regulatory factor induces transduction at a rate of at least 10 per μg of DNA. 3 , 10 4 , 10 5 , 10 6 , or 10 7 The viral copy number increases to .

[0107] In some embodiments, the modulator reduces the transduction efficiency of AAV particles. In some embodiments, the transduction efficiency is reduced by at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% compared to a baseline level of transduction efficiency. In some embodiments, the modulator reduces transduction to 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 viral copies per genome or less. In some embodiments, the modulator reduces transduction to 10 copies per μg of DNA or less. 2 , 10 3 , or 10 4 Reduce the viral copy number to:

[0108] In some embodiments, the baseline level of transduction efficiency is the level of transduction efficiency in cells that have not been contacted with an AAV transduction regulatory agent, hi some embodiments, the baseline level of transduction efficiency is the level of transduction efficiency before the cells are contacted with an AAV transduction regulatory agent.

[0109] In some embodiments, the gene or gene product increases the transduction efficiency of AAV2 particles, and optionally, the gene or gene product does not increase or does not substantially increase the transduction efficiency of AAV9 particles. In some embodiments, the gene or gene product is essential for transduction of AAV2 particles, and optionally, the gene or gene product is not essential for transduction of AAV9 particles. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GRP108.

[0110] In some embodiments, the gene or gene product is selected from EXT1, EXT2, NDST1, BCL10, OAF, PDCD10, LMO4, MALT1, ZNF644, CHUK, GLCE, EP300, ARID4B, RAB21, MED13, DHX15, WASHC5, IKBKB, USP24, HSPA14, CXXC1, UBE2A, INTS8, CDC42, NFKB1, SIN3A, USP7, ARF5, CARD10, JAK1, SLC35C2, PAXK1, ZC3H11A, FAM20B, FAM72A, DHX36, INTS12, RPRD1B, or a combination thereof.

[0111] In some embodiments, the gene or gene product is associated with endosomal sorting (e.g., RAB21, WASHC5, or USP7). In some embodiments, the gene or gene product is associated with vesicle-mediated transport (e.g., CDC42 or ARF5). In some embodiments, the gene or gene product is associated with NFKB signaling (e.g., BCL10, MALT1, NFKB1, IKBKB, CHUK, or CARD10). In some embodiments, the gene or gene product is associated with heparan sulfate biosynthesis (e.g., EXT1, EXT2, NDST1, GLCE, or FAM20B). In some embodiments, the gene or gene product is associated with H3K9 methylation (e.g., ZNF644). In some embodiments, the gene or gene product is associated with pre-mRNA processing (e.g., DHX15). In some embodiments, the gene or gene product is associated with transcription (e.g., LMO4, EP300, MED13, SIN3, ARID4B, ZC3H11A, CXXC1, RPRD1B, or UBE2A). In some embodiments, the gene or gene product is associated with the Integrator complex and / or RNA polymerase II function (e.g., INTS8 or INST12). In some embodiments, the gene or gene product is associated with DNA repair and / or AAV genome degradation (e.g., DHX36, ARID4B, UBE2A, or USP24). In some embodiments, the gene or gene product is associated with cell proliferation and / or apoptosis (e.g., PDCD10). In some embodiments, the gene or gene product is associated with spinocarpal tarsal synostosis (e.g., OAF). In some embodiments, the gene or gene product is associated with protein folding (e.g., HSPA14). In some embodiments, the gene or gene product is associated with helicase activity (e.g., DHX36). In some embodiments, the gene or gene product is associated with fucosylation of Notch and / or transport of GCP-fucose (eg, SLC35C2).

[0112] In some embodiments, the gene or gene product increases the transduction efficiency of AAV9 particles, and optionally, the gene or gene product does not increase or does not substantially increase the transduction efficiency of AAV2 particles. In some embodiments, the gene or gene product is essential for transduction of AAV9 particles, and optionally, the gene or gene product is not essential for transduction of AAV2 particles. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GRP108.

[0113] In some embodiments, the gene or gene product is selected from TMPRSS11B, HTT, SNRNP70, BRD7, DMXL1, RAB10, CNGA1, KLHDC3, CHP1, CYP3A5, ELOVL4, PNISR, ZCCHC14, AZGP1, TPST1, SC5D, ELP2, ELP3, IPO9, RAB14, WDR7, XRCC4, GDI2, or a combination thereof.

[0114] In some embodiments, the gene or gene product is associated with microtubule-mediated transport or vesicle function (e.g., HTT). In some embodiments, the gene or gene product is an ion channel (e.g., CNGA1). In some embodiments, the gene or gene product is associated with nuclear protein import (e.g., IPO9). In some embodiments, the gene or gene product is associated with O-sulfation of tyrosine residues within acidic motifs of polypeptides (e.g., TPST1). In some embodiments, the gene or gene product is associated with protection of viral RNA (e.g., ZCCHC14). In some embodiments, the gene or gene product is associated with RNA binding by AAV proteins (e.g., PNISR). In some embodiments, the gene or gene product is associated with calcium ion-regulated exocytosis (e.g., CHP1). In some embodiments, the gene or gene product is associated with intracellular transport (e.g., RAB10, RAB14, GDI2, WDR7, or DMXL1). In some embodiments, the gene or gene product is a subunit (e.g., a catalytic tRNA acetyltransferase subunit) of an elongator complex, e.g., an RNA polymerase (e.g., RNA polymerase II) (e.g., ELP2 or ELP3). In some embodiments, the gene or gene product is chromatin-associated (e.g., KLHDC3). In some embodiments, the gene or gene product is associated with cholesterol biosynthesis (e.g., SC5D).

[0115] In some embodiments, the gene or gene product increases the transduction efficiency of AAV2 and AAV9 particles. In some embodiments, the gene or gene product is essential for transduction of AAV2 and AAV9 particles.

[0116] In some embodiments, the gene or gene product is selected from KIAA0319L, BAMBI, TM9SF2, PHIP, DCLRE1C, VPS35, GPR108, CYREN, ACP2, F8A2, F8A1, F8A3, RBPJ, ATP2C1, ICMT, RABIF, IER3IP1, RBM10, SMG7, GTF2I, ELAVL1, MEPCE, RAB4A, IER3IP1, SAMD1, or a combination thereof.

[0117] In some embodiments, the gene or gene product is associated with influenza infection (e.g., ACP2). In some embodiments, the gene or gene product binds to an unmethylated CGI (e.g., SAMD1). In some embodiments, the gene or gene product is associated with intracellular vesicle trafficking (e.g., RABIF). In some embodiments, the gene or gene product is associated with post-translational modification of a cysteine ​​residue (e.g., a C-terminal cysteine ​​residue) in, for example, a target protein (e.g., ICMT). In some embodiments, the gene or gene product binds to an AAV capsid protein (e.g., KIAA0319L). In some embodiments, the gene or gene product is associated with inhibition of a TLR (e.g., TLR9) (e.g., GPR108). In some embodiments, the gene or gene product is associated with endosomal trafficking of, for example, AAV-R (e.g., VPS35). In some embodiments, the gene or gene product is a calcium ATPase pump (e.g., ATP2C1). In some embodiments, the gene or gene product is associated with Notch signaling (e.g., RBPJ). In some embodiments, the gene or gene product is associated with HSPG metabolism (e.g., TM9SF2). In some embodiments, the gene or gene product is associated with inhibition of NHEJ (e.g., CYREN). In some embodiments, the gene or gene product is associated with viral hairpin degradation (e.g., DCLRE1C). In some embodiments, the gene or gene product is associated with Glc transporter translocation, and optionally, the gene or gene product binds to insulin receptor substrate 1 protein (e.g., PHIP).

[0118] In some embodiments, the gene or gene product reduces the transduction efficiency of AAV2 particles, and optionally, the gene or gene product, when regulated, does not reduce or does not substantially reduce the transduction efficiency of AAV9 particles. In some embodiments, the gene or gene product inhibits or prevents transduction of AAV2 particles, and optionally, the gene or gene product does not inhibit or prevent transduction of AAV9 particles. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0119] In some embodiments, the gene or gene product is GREB1L, BIRC2, TYMSOS, MSL3, SIK3, GTF2H5, PIGW, ATRAID, PPP4R1, ZFC3H1, SETDB1, SMCHD1, TMEM123, UHRF1, CLUL1, SMAD5, SETX, STEEP1, DENND6A, RTN4RL2, MTMR9, STRADA, PSIP1, BMPR1A, HIKESHI, AP3M1, MEN1, MYL12B, CREB1, RAB12, SMTNL1, MRGBP, WTAP, SUMO2, TCN 1, ALDH3B1, ARL14EP, MYL12A, RHOD, PGAP2, EIF4A1, PIGN, DAXX, HDLBP, GOLGA1, SARNP, UBE2L6, TRIM49, SIK2, SOX4, OR6Q1, OR4D6, UNC93B1, CATSPERZ, PIGT, PYM1, MICOS13, RIN1, DOT1L, TRIM49C, MAPK20, COL8A1, FASN, KDM3B, PIGF, PIGA, PIGY, GPC3, TRAPPC2L, RAB31, ELP3, or a combination thereof.

[0120] In some embodiments, the gene or gene product is associated with retinoic acid receptor activity (e.g., GREB1L). In some embodiments, the gene or gene product is thymidylate synthetase (e.g., TYMSOS). In some embodiments, the gene or gene product is associated with chromatin remodeling (e.g., SMCHD1). In some embodiments, the gene or gene product is associated with histone H4 acetylation (e.g., MSL3). In some embodiments, the gene or gene product is associated with transcription and / or DNA repair (e.g., GTF2H5). In some embodiments, the gene or gene product is a histone methyltransferase (e.g., SETDB1). In some embodiments, the gene or gene product is associated with exosomal degradation of polyadenylated RNA (e.g., ZFC3H1). In some embodiments, the gene or gene product is associated with recruitment of histone deacetylase to DNA (e.g., UHRF1). In some embodiments, the gene or gene product is associated with oxidative stress-induced DNA double-strand break response (e.g., SETX). In some embodiments, the gene or gene product is associated with histone modification (e.g., MEN1). In some embodiments, the gene or gene product is associated with nucleosome / DNA interactions (e.g., MRGBP). In some embodiments, the gene or gene product is associated with GPI biosynthesis (e.g., PIGW, PIGN, PIGT, PIGF, PIGA, or PIGY). In some embodiments, the gene or gene product is associated with GPI anchor maturation (e.g., PGAP2). In some embodiments, the gene or gene product is associated with vesicle-mediated endocytosis (e.g., DENND6A, GOLGA1, MTMR9, GPC3, PPP4R1, RAB12, RAB31, RHOD, RIN1, TMEM123, or TRAPPC2L). In some embodiments, the gene or gene product is associated with clathrin-coated vesicle-mediated endocytosis (e.g., AP3M1). In some embodiments, the gene or gene product is related to a BMP receptor kinase (eg, SMAD5, BMPR1A, or CREB1).In some embodiments, the gene or gene product is associated with transcription (e.g., PSIP1). In some embodiments, the gene or gene product is associated with nuclear import of HSP70 proteins (e.g., HIKESHI). In some embodiments, the gene or gene product is associated with Ser / Thr kinases (e.g., SIK2 or SIK3). In some embodiments, the gene or gene product is associated with protein sumoylation (e.g., SUMO2, UBE2L6).

[0121] In some embodiments, the gene or gene product reduces the transduction efficiency of AAV9 particles, and optionally, the gene or gene product does not reduce or substantially reduce the transduction efficiency of AAV2 particles. In some embodiments, the gene or gene product inhibits or prevents transduction of AAV9 particles, and optionally, the gene or gene product does not inhibit or prevent transduction of AAV2 particles. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0122] In some embodiments, the gene or gene product is selected from AP2A1, AP2B1, TM9SF4, ACTR5, PTMA, PAPOLA, PDHA1, PDHB, SLC25A19, GAK, AUNIP, FCHO2, ACTB, LIPT1, UCHL5, INO80E, ECHS1, NELFB, EDC4, PRMT1, PDS5B, PELI3, FBXL20, SLC35A1, or a combination thereof.

[0123] In some embodiments, the gene or gene product binds to ATP, chaperone proteins, and / or clathrin (e.g., GAK). In some embodiments, the gene or gene product is associated with the trafficking of clathrin-coated vesicles (e.g., AP2B1 or AP2A1). In some embodiments, the gene or gene product is associated with clathrin-mediated endocytosis (e.g., FCHO2). In some embodiments, the gene or gene product is associated with vesicle trafficking (e.g., ACTB). In some embodiments, the gene or gene product is associated with the innate immune response (e.g., PELI3 or FBXL20). In some embodiments, the gene or gene product is associated with glucose metabolism (e.g., PDHB or PDHA1). In some embodiments, the gene or gene product is associated with DNA resection and / or homologous recombination, e.g., after DNA damage (e.g., AUNIP). In some embodiments, the gene or gene product is associated with DNA repair, e.g., after DNA damage (e.g., UCHL5, INO80E, PDS5B, ACTR5, or PRMT1). In some embodiments, the gene or gene product is associated with transport of CMP sialic acid from the cytosol to Golgi vesicles (e.g., SLC35A1). In some embodiments, the gene or gene product is associated with localization of polypeptides containing a glycine-rich transmembrane domain, e.g., to the cell surface (e.g., TM9SF4). In some embodiments, the gene or gene product is associated with synthesis of poly(A) tails (e.g., PAPOLA). In some embodiments, the gene or gene product is PTMA. In some embodiments, the gene or gene product is associated with elongation of mRNA by RNA polymerase II (e.g., NELFB). In some embodiments, the gene or gene product is associated with mRNA degradation (e.g., EDC4). In some embodiments, the gene or gene product encodes a mitochondrial lipoyltransferase (e.g., LIPT1). In some embodiments, the gene or gene product is associated with mitochondrial fatty acid β-oxidation (e.g., ECHS1). In some embodiments, the gene or gene product encodes the mitochondrial thiamine pyrophosphate carrier (e.g., SLC25A19).

[0124] In some embodiments, the gene or gene product reduces the transduction efficiency of AAV2 and AAV9 particles. In some embodiments, the gene or gene product inhibits or prevents transduction of AAV2 and AAV9 particles. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0125] In some embodiments, the gene or gene product is selected from the group consisting of PITPNB, PITP, FAM91A1, WDR11, AP1G1, AP1M1, AP1S1, AP1S3, HEATR5B, STX16, AP1B1, PIAS1, DENR, ARL1, ZFAT, TBC1D23, LIN37, RALGAPB, B3GNT2, ELOVL1, AP2B1, KIAA2013, PTEN, MCTS1, NBN, HELZ, SLC38A10, FBXL20, TGIF1, KDSR, CPD, CHD7, USP9X, SIMC1, TAF11, VAPA, MTMR6, RAB1B, SLF2, MRE11, VTI1A, MBOAT7, PPP6R3, or a combination thereof.

[0126] In some embodiments, the gene or gene product is associated with the long-chain FA elongation cycle (e.g., ELOVL1). In some embodiments, the gene or gene product is associated with lipoic acid biosynthesis (e.g., PIAS1). In some embodiments, the gene or gene product is associated with a protein phosphatase catalytic subunit (e.g., PPP6R3). In some embodiments, the gene or gene product is associated with the WDR11 pathway (e.g., WDR11, FAM91A1, AP1G1, AP1S1, AP1M1, AP1S3, or TBC1D23). In some embodiments, the gene or gene product is associated with retrograde transport of, for example, PI and / or PC from the Golgi apparatus to the endoplasmic reticulum (e.g., PITP). In some embodiments, the gene or gene product is associated with vesicle transport from late endosomes to the trans-Golgi network (e.g., STX16). In some embodiments, the gene or gene product is associated with the activity or recruitment of golgin, arfaptin, and / or Arf-GEF to the trans-Golgi network (e.g., ARL1). In some embodiments, the gene or gene product encodes a component of clathrin-dependent vesicles and / or is involved in AP1G1 / AP-1 mediated protein transport (eg, HEATR5B).

[0127] In some embodiments, the regulatory element is (a) a gene editing system that targets one or more sites within a gene or its regulatory elements, (b) a nucleic acid encoding one or more components of the gene editing system, or (c) a combination thereof. In some embodiments, the gene editing system is a CRISPR / Cas system, a zinc finger nuclease system, a TALEN system, or a meganuclease system.

[0128] In some embodiments, the gene editing system binds to a target sequence in an early (e.g., first, second, or third) exon or intron of a gene. In some embodiments, the gene editing system binds to a target sequence of a gene, and the target sequence is upstream of exon 4, e.g., in exon 1, exon 2, or exon 3. In some embodiments, the gene editing system binds to a target sequence in a later exon or intron of a gene. In some embodiments, the gene editing system binds to a target sequence of a gene, and the target sequence is downstream of the penultimate exon, e.g., the third to last exon, the penultimate exon, or the last exon. In some embodiments, the gene editing system is a CRISPR / Cas system comprising a guide RNA (gRNA) molecule comprising a targeting sequence that hybridizes to the target sequence of the gene. In some embodiments, the CRISPR / Cas system is a CRISPR / Cas9 system. In some embodiments, the CRISPR / Cas system is a CRISPR / Cas12a system.

[0129] In some embodiments, the regulatory element is a small interfering RNA (siRNA) or small hairpin (shRNA) specific to the gene, or a nucleic acid encoding the siRNA or shRNA. In some embodiments, the siRNA or shRNA comprises a nucleotide sequence complementary to the nucleotide sequence of an mRNA encoded by the gene. In some embodiments, the regulatory element is a guide RNA (gRNA) specific to the gene, or a nucleic acid encoding the gRNA. In some embodiments, the gRNA comprises a nucleotide sequence complementary to the nucleotide sequence of the gene.

[0130] In some embodiments, the modulator is a gene-specific antisense oligonucleotide (ASO) or a nucleic acid encoding the ASO. In some embodiments, the ASO comprises a nucleotide sequence complementary to the nucleotide sequence of an mRNA encoded by the gene.

[0131] In some embodiments, the modulator is a small molecule (e.g., a compound described herein, e.g., in Figure 7). In some embodiments, the small molecule is a protein degradation inducer.

[0132] In some embodiments, the modulator is a protein or peptide, or a nucleic acid encoding the protein or peptide. In some embodiments, the modulator is an antibody molecule (e.g., an scFv or sdAb). In some embodiments, the modulator is a dominant-negative binding partner of the protein encoded by the gene, or a nucleic acid encoding the dominant-negative binding partner. In some embodiments, the modulator is a dominant-negative variant (e.g., catalytically inactive) of the protein encoded by the gene, or a nucleic acid encoding the dominant-negative variant.

[0133] In some embodiments, the AAV particles comprise an AAV genome. In some embodiments, the AAV particles comprise AAV-like particles. In some embodiments, the AAV particles comprise a capsid. In some embodiments, the AAV particles have a serotype of AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, or a combination thereof. In some embodiments, the AAV particles are AAV2 particles. In some embodiments, the AAV particles are AAV9 particles.

[0134] In some embodiments, the AAV particles have a tropism for the CNS (e.g., AAV1, AAV2, AAV4, AAV5, AAV8, or AAV9). In some embodiments, the AAV particles have a tropism for the heart (e.g., AAV1, AAV8, or AAV9). In some embodiments, the AAV particles have a tropism for the kidney (e.g., AAV2). In some embodiments, the AAV particles have a tropism for the liver (e.g., AAV7, AAV8, or AAV9). In some embodiments, the AAV particles have a tropism for the lung (e.g., AAV4, AAV5, AAV6, or AAV9). In some embodiments, the AAV particles have a tropism for the pancreas (e.g., AAV8). In some embodiments, the AAV particles have a tropism for photoreceptor cells (e.g., AAV2, AAV5, or AAV8). In some embodiments, the AAV particle has tropism for the retinal pigment epithelium (RPE) (e.g., AAV1, AAV2, AAV4, AAV5, or AAV8). In some embodiments, the AAV particle has tropism for skeletal muscle (e.g., AAV1, AAV6, AAV7, AAV8, or AAV9).

[0135] In some embodiments, the AAV particles comprise a nucleotide sequence encoding a therapeutic protein, e.g., a protein associated with a disorder described herein. In some embodiments, the AAV particles comprise a nucleotide sequence encoding NGF, APOE2 (e.g., hAPOE2), TERT (e.g., hTERT), MAPT, GAD, AADC, NTN, GDNF, GCase, HTT, SMN, SMN2, SOD1, or C9orf72. In some embodiments, the AAV particles comprise a nucleotide sequence encoding a therapeutic nucleic acid, e.g., a nucleic acid targeting a nucleotide sequence encoding a protein associated with a disorder described herein.

[0136] In some embodiments, the methods involve administering to the subject multiple AAV transduction regulators or AAV regulators that regulate multiple genes or gene products associated with AAV transduction efficiency.

[0137] In another aspect, the disclosure provides a method of treating a disorder, comprising administering to a subject in need thereof an effective amount of a therapy comprising (a) an AAV transduction modulator and (b) an AAV genome or AAV particle, thereby treating the disorder.

[0138] In some embodiments, the subject has not been administered or is not currently being administered a therapy when the AAV transduction modulator is administered, hi some embodiments, the subject has been administered an AAV transduction modulator for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, or 1, 2, 3, 4, 5, or 6 months before the subject was administered the therapy. In some embodiments, the subject was administered an AAV transduction modulator within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, 1, 2, 3, 4, 5, or 6 months or less before being administered the therapy.

[0139] In some embodiments, the subject has been administered or is currently being administered a therapy when the AAV transduction modulator is administered, hi some embodiments, the subject has been administered a therapy for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, or 1, 2, 3, 4, 5, or 6 months prior to administration of the AAV transduction modulator. In some embodiments, the subject has been administered therapy for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, 1, 2, 3, 4, 5, or 6 months or less before the AAV transduction modulator was administered.

[0140] In some embodiments, the disorder is a neurodegenerative disorder. In some embodiments, the neurodegenerative disorder is Alzheimer's disease, Parkinson's disease, Huntington's disease, multiple sclerosis (MS), amyotrophic lateral sclerosis (ALS), or Batten disease. In some embodiments, the disorder is mild Alzheimer's disease, mild to moderate Alzheimer's disease, mild to severe Alzheimer's disease, early dementia, Parkinson's disease (e.g., idiopathic Parkinson's disease, bilateral idiopathic Parkinson's disease, intermediate to late stage Parkinson's disease), Huntington's disease (e.g., manifest Huntington's disease), SMA type 1, presymptomatic SMA, or amyotrophic lateral sclerosis (ALS) (e.g., familial ALS, SOD1-mutated ALS, or C9orf72-mutated ALS). In some embodiments, the disorder is an ocular disorder. In some embodiments, the ocular disorder is blindness, e.g., hereditary or non-hereditary blindness. In some embodiments, the ocular disorder is Leber's congenital amaurosis, age-related macular degeneration, congenital choroideremia, or color blindness. In some embodiments, the method reduces the toxicity of the therapy, enhances the efficacy of the therapy, or both.

[0141] In some embodiments, the modulator modulates (e.g., increases or decreases) a gene or gene product associated with AAV transduction efficiency, hi some embodiments, the gene or gene product is a mammalian (e.g., human) gene or gene product.

[0142] In some embodiments, the modulator inhibits a gene or gene product, e.g., a gene or gene product associated with decreased transduction efficiency of AAV particles, hi some embodiments, the modulator activates a gene or gene product, e.g., a gene or gene product associated with increased transduction efficiency of AAV particles.

[0143] In some embodiments, the gene or gene product is associated with increased transduction efficiency of AAV particles. In some embodiments, the gene or gene product is associated with increased transduction efficiency of AAV particles of a first serotype (e.g., AAV2), increased transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GPR108.

[0144] In some embodiments, the gene or gene product is associated with decreased transduction efficiency of AAV particles. In some embodiments, the gene or gene product is associated with decreased transduction efficiency of AAV particles of a first serotype (e.g., AAV2), decreased transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0145] In some embodiments, the gene or gene product, when modulated, increases the transduction efficiency of AAV particles, ie, the gene or gene product, when modulated, increases the transduction efficiency of AAV particles of a first serotype (e.g., AAV2), the transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both.

[0146] In some embodiments, the gene or gene product, when modulated, decreases the transduction efficiency of AAV particles, ie, the gene or gene product, when modulated, decreases the transduction efficiency of AAV particles of a first serotype (e.g., AAV2), the transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both.

[0147] In some embodiments, the gene product is RNA (e.g., mRNA). In some embodiments, the gene product is a protein. In some embodiments, the gene or gene product is selectively expressed in a target tissue (e.g., brain or liver). The following dependent claims describe AAV transduction regulators based on their mechanism. In some embodiments, the regulator alters (e.g., increases or decreases) the expression of a gene. In some embodiments, the regulator alters the structure of a gene. In some embodiments, the regulator alters (e.g., increases or decreases) the activity (e.g., enzymatic activity) of a gene product. In some embodiments, the regulator alters (e.g., increases or decreases) the level (e.g., abundance) of a gene product. In some embodiments, the regulator alters (e.g., increases or decreases) the stability of a gene product. In some embodiments, the regulator alters (e.g., increases or decreases) the transduction efficiency of AAV particles, e.g., as determined by an assay described herein (e.g., FACS analysis, e.g., as described in Example 1 or 2).

[0148] In some embodiments, the gene or gene product is AAV-R, GPR108, WDR11, or MRE11. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GPR108. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0149] In some embodiments, the method results in high gene regulation (e.g., gene editing) efficiency in a first tissue (e.g., at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 98%) and limited effect in a second tissue (e.g., 20%, 15%, 10%, 5%, 2%, or less gene regulation (e.g., gene editing) efficiency). In some embodiments, the method results in high regulation (e.g., gene editing) efficiency in the liver (e.g., at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 98%) and limited effect in skeletal muscle, bone marrow, or both (e.g., 20%, 15%, 10%, 5%, 2%, or less gene regulation (e.g., gene editing) efficiency).

[0150] In some embodiments, the modulator is administered intravenously.

[0151] In some embodiments, the modulator increases the transduction efficiency of AAV particles. In some embodiments, the transduction efficiency is increased by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90%, or at least 1-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 60-fold, 70-fold, 80-fold, 90-fold, 100-fold, 200-fold, 300-fold, 400-fold, 500-fold, 600-fold, 700-fold, 800-fold, 900-fold, or 1000-fold compared to a baseline level of transduction efficiency. In some embodiments, the modulator increases transduction by at least 10, 20, 30, 40, 50, or 60 viral copies per genome. In some embodiments, the regulatory factor induces transduction at a rate of at least 10 per μg of DNA. 3 , 10 4 , 10 5 , 10 6 , or 10 7 The viral copy number increases to .

[0152] In some embodiments, the modulator reduces the transduction efficiency of AAV particles. In some embodiments, the transduction efficiency is reduced by at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% compared to a baseline level of transduction efficiency. In some embodiments, the modulator reduces transduction to 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 viral copies per genome or less. In some embodiments, the modulator reduces transduction to 10 copies per μg of DNA or less. 2 , 10 3 , or 10 4 Reduce the viral copy number to:

[0153] In some embodiments, the baseline level of transduction efficiency is the level of transduction efficiency in cells that have not been contacted with an AAV transduction regulatory agent, hi some embodiments, the baseline level of transduction efficiency is the level of transduction efficiency before the cells are contacted with an AAV transduction regulatory agent.

[0154] In some embodiments, the gene or gene product increases the transduction efficiency of AAV2 particles, and optionally, the gene or gene product does not increase or does not substantially increase the transduction efficiency of AAV9 particles. In some embodiments, the gene or gene product is essential for transduction of AAV2 particles, and optionally, the gene or gene product is not essential for transduction of AAV9 particles. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GRP108.

[0155] In some embodiments, the gene or gene product is selected from EXT1, EXT2, NDST1, BCL10, OAF, PDCD10, LMO4, MALT1, ZNF644, CHUK, GLCE, EP300, ARID4B, RAB21, MED13, DHX15, WASHC5, IKBKB, USP24, HSPA14, CXXC1, UBE2A, INTS8, CDC42, NFKB1, SIN3A, USP7, ARF5, CARD10, JAK1, SLC35C2, PAXK1, ZC3H11A, FAM20B, FAM72A, DHX36, INTS12, RPRD1B, or a combination thereof.

[0156] In some embodiments, the gene or gene product is associated with endosomal sorting (e.g., RAB21, WASHC5, or USP7). In some embodiments, the gene or gene product is associated with vesicle-mediated transport (e.g., CDC42 or ARF5). In some embodiments, the gene or gene product is associated with NFKB signaling (e.g., BCL10, MALT1, NFKB1, IKBKB, CHUK, or CARD10). In some embodiments, the gene or gene product is associated with heparan sulfate biosynthesis (e.g., EXT1, EXT2, NDST1, GLCE, or FAM20B). In some embodiments, the gene or gene product is associated with H3K9 methylation (e.g., ZNF644). In some embodiments, the gene or gene product is associated with pre-mRNA processing (e.g., DHX15). In some embodiments, the gene or gene product is associated with transcription (e.g., LMO4, EP300, MED13, SIN3, ARID4B, ZC3H11A, CXXC1, RPRD1B, or UBE2A). In some embodiments, the gene or gene product is associated with the Integrator complex and / or RNA polymerase II function (e.g., INTS8 or INST12). In some embodiments, the gene or gene product is associated with DNA repair and / or AAV genome degradation (e.g., DHX36, ARID4B, UBE2A, or USP24). In some embodiments, the gene or gene product is associated with cell proliferation and / or apoptosis (e.g., PDCD10). In some embodiments, the gene or gene product is associated with spinocarpal tarsal synostosis (e.g., OAF). In some embodiments, the gene or gene product is associated with protein folding (e.g., HSPA14). In some embodiments, the gene or gene product is associated with helicase activity (e.g., DHX36). In some embodiments, the gene or gene product is associated with fucosylation of Notch and / or transport of GCP-fucose (eg, SLC35C2).

[0157] In some embodiments, the gene or gene product increases the transduction efficiency of AAV9 particles, and optionally, the gene or gene product does not increase or does not substantially increase the transduction efficiency of AAV2 particles. In some embodiments, the gene or gene product is essential for transduction of AAV9 particles, and optionally, the gene or gene product is not essential for transduction of AAV2 particles. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GRP108.

[0158] In some embodiments, the gene or gene product is selected from TMPRSS11B, HTT, SNRNP70, BRD7, DMXL1, RAB10, CNGA1, KLHDC3, CHP1, CYP3A5, ELOVL4, PNISR, ZCCHC14, AZGP1, TPST1, SC5D, ELP2, ELP3, IPO9, RAB14, WDR7, XRCC4, GDI2, or a combination thereof.

[0159] In some embodiments, the gene or gene product is associated with microtubule-mediated transport or vesicle function (e.g., HTT). In some embodiments, the gene or gene product is an ion channel (e.g., CNGA1). In some embodiments, the gene or gene product is associated with nuclear protein import (e.g., IPO9). In some embodiments, the gene or gene product is associated with O-sulfation of tyrosine residues within acidic motifs of polypeptides (e.g., TPST1). In some embodiments, the gene or gene product is associated with protection of viral RNA (e.g., ZCCHC14). In some embodiments, the gene or gene product is associated with RNA binding by AAV proteins (e.g., PNISR). In some embodiments, the gene or gene product is associated with calcium ion-regulated exocytosis (e.g., CHP1). In some embodiments, the gene or gene product is associated with intracellular transport (e.g., RAB10, RAB14, GDI2, WDR7, or DMXL1). In some embodiments, the gene or gene product is a subunit (e.g., a catalytic tRNA acetyltransferase subunit) of an elongator complex, e.g., an RNA polymerase (e.g., RNA polymerase II) (e.g., ELP2 or ELP3). In some embodiments, the gene or gene product is chromatin-associated (e.g., KLHDC3). In some embodiments, the gene or gene product is associated with cholesterol biosynthesis (e.g., SC5D).

[0160] In some embodiments, the gene or gene product increases the transduction efficiency of AAV2 and AAV9 particles. In some embodiments, the gene or gene product is essential for transduction of AAV2 and AAV9 particles. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GRP108.

[0161] In some embodiments, the gene or gene product is selected from KIAA0319L, BAMBI, TM9SF2, PHIP, DCLRE1C, VPS35, GPR108, CYREN, ACP2, F8A2, F8A1, F8A3, RBPJ, ATP2C1, ICMT, RABIF, IER3IP1, RBM10, SMG7, GTF2I, ELAVL1, MEPCE, RAB4A, IER3IP1, SAMD1, or a combination thereof.

[0162] In some embodiments, the gene or gene product is associated with influenza infection (e.g., ACP2). In some embodiments, the gene or gene product binds to an unmethylated CGI (e.g., SAMD1). In some embodiments, the gene or gene product is associated with intracellular vesicle trafficking (e.g., RABIF). In some embodiments, the gene or gene product is associated with post-translational modification of a cysteine ​​residue (e.g., a C-terminal cysteine ​​residue) in, for example, a target protein (e.g., ICMT). In some embodiments, the gene or gene product binds to an AAV capsid protein (e.g., KIAA0319L). In some embodiments, the gene or gene product is associated with inhibition of a TLR (e.g., TLR9) (e.g., GPR108). In some embodiments, the gene or gene product is associated with endosomal trafficking of, for example, AAV-R (e.g., VPS35). In some embodiments, the gene or gene product is a calcium ATPase pump (e.g., ATP2C1). In some embodiments, the gene or gene product is associated with Notch signaling (e.g., RBPJ). In some embodiments, the gene or gene product is associated with HSPG metabolism (e.g., TM9SF2). In some embodiments, the gene or gene product is associated with inhibition of NHEJ (e.g., CYREN). In some embodiments, the gene or gene product is associated with viral hairpin degradation (e.g., DCLRE1C). In some embodiments, the gene or gene product is associated with Glc transporter translocation, and optionally, the gene or gene product binds to insulin receptor substrate 1 protein (e.g., PHIP).

[0163] In some embodiments, the gene or gene product reduces the transduction efficiency of AAV2 particles, and optionally, the gene or gene product, when regulated, does not reduce or does not substantially reduce the transduction efficiency of AAV9 particles. In some embodiments, the gene or gene product inhibits or prevents transduction of AAV2 particles, and optionally, the gene or gene product does not inhibit or prevent transduction of AAV9 particles. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0164] In some embodiments, the gene or gene product is GREB1L, BIRC2, TYMSOS, MSL3, SIK3, GTF2H5, PIGW, ATRAID, PPP4R1, ZFC3H1, SETDB1, SMCHD1, TMEM123, UHRF1, CLUL1, SMAD5, SETX, STEEP1, DENND6A, RTN4RL2, MTMR9, STRADA, PSIP1, BMPR1A, HIKESHI, AP3M1, MEN1, MYL12B, CREB1, RAB12, SMTNL1, MRGBP, WTAP, SUMO2, TCN 1, ALDH3B1, ARL14EP, MYL12A, RHOD, PGAP2, EIF4A1, PIGN, DAXX, HDLBP, GOLGA1, SARNP, UBE2L6, TRIM49, SIK2, SOX4, OR6Q1, OR4D6, UNC93B1, CATSPERZ, PIGT, PYM1, MICOS13, RIN1, DOT1L, TRIM49C, MAPK20, COL8A1, FASN, KDM3B, PIGF, PIGA, PIGY, GPC3, TRAPPC2L, RAB31, ELP3, or a combination thereof.

[0165] In some embodiments, the gene or gene product is associated with retinoic acid receptor activity (e.g., GREB1L). In some embodiments, the gene or gene product is thymidylate synthetase (e.g., TYMSOS). In some embodiments, the gene or gene product is associated with chromatin remodeling (e.g., SMCHD1). In some embodiments, the gene or gene product is associated with histone H4 acetylation (e.g., MSL3). In some embodiments, the gene or gene product is associated with transcription and / or DNA repair (e.g., GTF2H5). In some embodiments, the gene or gene product is a histone methyltransferase (e.g., SETDB1). In some embodiments, the gene or gene product is associated with exosomal degradation of polyadenylated RNA (e.g., ZFC3H1). In some embodiments, the gene or gene product is associated with recruitment of histone deacetylase to DNA (e.g., UHRF1). In some embodiments, the gene or gene product is associated with oxidative stress-induced DNA double-strand break response (e.g., SETX). In some embodiments, the gene or gene product is associated with histone modification (e.g., MEN1). In some embodiments, the gene or gene product is associated with nucleosome / DNA interactions (e.g., MRGBP). In some embodiments, the gene or gene product is associated with GPI biosynthesis (e.g., PIGW, PIGN, PIGT, PIGF, PIGA, or PIGY). In some embodiments, the gene or gene product is associated with GPI anchor maturation (e.g., PGAP2). In some embodiments, the gene or gene product is associated with vesicle-mediated endocytosis (e.g., DENND6A, GOLGA1, MTMR9, GPC3, PPP4R1, RAB12, RAB31, RHOD, RIN1, TMEM123, or TRAPPC2L). In some embodiments, the gene or gene product is associated with clathrin-coated vesicle-mediated endocytosis (e.g., AP3M1). In some embodiments, the gene or gene product is related to a BMP receptor kinase (eg, SMAD5, BMPR1A, or CREB1).In some embodiments, the gene or gene product is associated with transcription (e.g., PSIP1). In some embodiments, the gene or gene product is associated with nuclear import of HSP70 proteins (e.g., HIKESHI). In some embodiments, the gene or gene product is associated with Ser / Thr kinases (e.g., SIK2 or SIK3). In some embodiments, the gene or gene product is associated with protein sumoylation (e.g., SUMO2, UBE2L6).

[0166] In some embodiments, the gene or gene product reduces the transduction efficiency of AAV9 particles, and optionally, the gene or gene product does not reduce or substantially reduce the transduction efficiency of AAV2 particles. In some embodiments, the gene or gene product inhibits or prevents transduction of AAV9 particles, and optionally, the gene or gene product does not inhibit or prevent transduction of AAV2 particles. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0167] In some embodiments, the gene or gene product is selected from AP2A1, AP2B1, TM9SF4, ACTR5, PTMA, PAPOLA, PDHA1, PDHB, SLC25A19, GAK, AUNIP, FCHO2, ACTB, LIPT1, UCHL5, INO80E, ECHS1, NELFB, EDC4, PRMT1, PDS5B, PELI3, FBXL20, SLC35A1, or a combination thereof.

[0168] In some embodiments, the gene or gene product binds to ATP, chaperone proteins, and / or clathrin (e.g., GAK). In some embodiments, the gene or gene product is associated with the trafficking of clathrin-coated vesicles (e.g., AP2B1 or AP2A1). In some embodiments, the gene or gene product is associated with clathrin-mediated endocytosis (e.g., FCHO2). In some embodiments, the gene or gene product is associated with vesicle trafficking (e.g., ACTB). In some embodiments, the gene or gene product is associated with the innate immune response (e.g., PELI3 or FBXL20). In some embodiments, the gene or gene product is associated with glucose metabolism (e.g., PDHB or PDHA1). In some embodiments, the gene or gene product is associated with DNA resection and / or homologous recombination, e.g., after DNA damage (e.g., AUNIP). In some embodiments, the gene or gene product is associated with DNA repair, e.g., after DNA damage (e.g., UCHL5, INO80E, PDS5B, ACTR5, or PRMT1). In some embodiments, the gene or gene product is associated with transport of CMP sialic acid from the cytosol to Golgi vesicles (e.g., SLC35A1). In some embodiments, the gene or gene product is associated with localization of polypeptides containing a glycine-rich transmembrane domain, e.g., to the cell surface (e.g., TM9SF4). In some embodiments, the gene or gene product is associated with synthesis of poly(A) tails (e.g., PAPOLA). In some embodiments, the gene or gene product is PTMA. In some embodiments, the gene or gene product is associated with elongation of mRNA by RNA polymerase II (e.g., NELFB). In some embodiments, the gene or gene product is associated with mRNA degradation (e.g., EDC4). In some embodiments, the gene or gene product encodes a mitochondrial lipoyltransferase (e.g., LIPT1). In some embodiments, the gene or gene product is associated with mitochondrial fatty acid β-oxidation (e.g., ECHS1). In some embodiments, the gene or gene product encodes the mitochondrial thiamine pyrophosphate carrier (e.g., SLC25A19).

[0169] In some embodiments, the gene or gene product reduces the transduction efficiency of AAV2 and AAV9 particles. In some embodiments, the gene or gene product inhibits or prevents transduction of AAV2 and AAV9 particles. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0170] In some embodiments, the gene or gene product is selected from the group consisting of PITPNB, PITP, FAM91A1, WDR11, AP1G1, AP1M1, AP1S1, AP1S3, HEATR5B, STX16, AP1B1, PIAS1, DENR, ARL1, ZFAT, TBC1D23, LIN37, RALGAPB, B3GNT2, ELOVL1, AP2B1, KIAA2013, PTEN, MCTS1, NBN, HELZ, SLC38A10, FBXL20, TGIF1, KDSR, CPD, CHD7, USP9X, SIMC1, TAF11, VAPA, MTMR6, RAB1B, SLF2, MRE11, VTI1A, MBOAT7, PPP6R3, or a combination thereof.

[0171] In some embodiments, the gene or gene product is associated with the long-chain FA elongation cycle (e.g., ELOVL1). In some embodiments, the gene or gene product is associated with lipoic acid biosynthesis (e.g., PIAS1). In some embodiments, the gene or gene product is associated with a protein phosphatase catalytic subunit (e.g., PPP6R3). In some embodiments, the gene or gene product is associated with the WDR11 pathway (e.g., WDR11, FAM91A1, AP1G1, AP1S1, AP1M1, AP1S3, or TBC1D23). In some embodiments, the gene or gene product is associated with retrograde transport of, for example, PI and / or PC from the Golgi apparatus to the endoplasmic reticulum (e.g., PITP). In some embodiments, the gene or gene product is associated with vesicle transport from late endosomes to the trans-Golgi network (e.g., STX16). In some embodiments, the gene or gene product is associated with the activity or recruitment of golgin, arfaptin, and / or Arf-GEF to the trans-Golgi network (e.g., ARL1). In some embodiments, the gene or gene product encodes a component of clathrin-dependent vesicles and / or is involved in AP1G1 / AP-1 mediated protein transport (eg, HEATR5B).

[0172] In some embodiments, the regulatory element is (a) a gene editing system that targets one or more sites within a gene or its regulatory elements, (b) a nucleic acid encoding one or more components of the gene editing system, or (c) a combination thereof. In some embodiments, the gene editing system is a CRISPR / Cas system, a zinc finger nuclease system, a TALEN system, or a meganuclease system.

[0173] In some embodiments, the gene editing system binds to a target sequence in an early (e.g., first, second, or third) exon or intron of a gene. In some embodiments, the gene editing system binds to a target sequence of a gene, and the target sequence is upstream of exon 4, e.g., in exon 1, exon 2, or exon 3. In some embodiments, the gene editing system binds to a target sequence in a later exon or intron of a gene. In some embodiments, the gene editing system binds to a target sequence of a gene, and the target sequence is downstream of the penultimate exon, e.g., the third to last exon, the penultimate exon, or the last exon. In some embodiments, the gene editing system is a CRISPR / Cas system comprising a guide RNA (gRNA) molecule comprising a targeting sequence that hybridizes to the target sequence of the gene. In some embodiments, the CRISPR / Cas system is a CRISPR / Cas9 system. In some embodiments, the CRISPR / Cas system is a CRISPR / Cas12a system.

[0174] In some embodiments, the regulatory element is a small interfering RNA (siRNA) or small hairpin (shRNA) specific to the gene, or a nucleic acid encoding the siRNA or shRNA. In some embodiments, the siRNA or shRNA comprises a nucleotide sequence complementary to the nucleotide sequence of an mRNA encoded by the gene. In some embodiments, the regulatory element is a guide RNA (gRNA) specific to the gene, or a nucleic acid encoding the gRNA. In some embodiments, the gRNA comprises a nucleotide sequence complementary to the nucleotide sequence of the gene.

[0175] In some embodiments, the modulator is a gene-specific antisense oligonucleotide (ASO) or a nucleic acid encoding the ASO. In some embodiments, the ASO comprises a nucleotide sequence complementary to the nucleotide sequence of an mRNA encoded by the gene.

[0176] In some embodiments, the modulator is a small molecule (e.g., a compound described herein, e.g., in Figure 7). In some embodiments, the small molecule is a protein degradation inducer.

[0177] In some embodiments, the modulator is a protein or peptide, or a nucleic acid encoding the protein or peptide. In some embodiments, the modulator is an antibody molecule (e.g., an scFv or sdAb). In some embodiments, the modulator is a dominant-negative binding partner of the protein encoded by the gene, or a nucleic acid encoding the dominant-negative binding partner. In some embodiments, the modulator is a dominant-negative variant (e.g., catalytically inactive) of the protein encoded by the gene, or a nucleic acid encoding the dominant-negative variant.

[0178] In some embodiments, the AAV particles comprise an AAV genome. In some embodiments, the AAV particles comprise AAV-like particles. In some embodiments, the AAV particles comprise a capsid. In some embodiments, the AAV particles have a serotype of AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, or a combination thereof. In some embodiments, the AAV particles are AAV2 particles. In some embodiments, the AAV particles are AAV9 particles.

[0179] In some embodiments, the AAV particles have a tropism for the CNS (e.g., AAV1, AAV2, AAV4, AAV5, AAV8, or AAV9). In some embodiments, the AAV particles have a tropism for the heart (e.g., AAV1, AAV8, or AAV9). In some embodiments, the AAV particles have a tropism for the kidney (e.g., AAV2). In some embodiments, the AAV particles have a tropism for the liver (e.g., AAV7, AAV8, or AAV9). In some embodiments, the AAV particles have a tropism for the lung (e.g., AAV4, AAV5, AAV6, or AAV9). In some embodiments, the AAV particles have a tropism for the pancreas (e.g., AAV8). In some embodiments, the AAV particles have a tropism for photoreceptor cells (e.g., AAV2, AAV5, or AAV8). In some embodiments, the AAV particle has tropism for the retinal pigment epithelium (RPE) (e.g., AAV1, AAV2, AAV4, AAV5, or AAV8). In some embodiments, the AAV particle has tropism for skeletal muscle (e.g., AAV1, AAV6, AAV7, AAV8, or AAV9).

[0180] In some embodiments, the AAV particles comprise a nucleotide sequence encoding a therapeutic protein, e.g., a protein associated with a disorder described herein. In some embodiments, the AAV particles comprise a nucleotide sequence encoding NGF, APOE2 (e.g., hAPOE2), TERT (e.g., hTERT), MAPT, GAD, AADC, NTN, GDNF, GCase, HTT, SMN, SMN2, SOD1, or C9orf72. In some embodiments, the AAV particles comprise a nucleotide sequence encoding a therapeutic nucleic acid, e.g., a nucleic acid targeting a nucleotide sequence encoding a protein associated with a disorder described herein.

[0181] In some embodiments, the methods involve administering to the subject multiple AAV transduction regulators or AAV regulators that regulate multiple genes or gene products associated with AAV transduction efficiency.

[0182] In another aspect, the disclosure provides a method of preparing a subject for a therapy comprising an AAV genome or AAV particle, the method comprising administering to the subject an effective amount of an AAV transduction modulator, thereby preparing the subject for the therapy.

[0183] In some embodiments, the subject has not been administered or is not currently being administered a therapy when the AAV transduction modulator is administered, hi some embodiments, the subject has been administered an AAV transduction modulator for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, or 1, 2, 3, 4, 5, or 6 months before the subject was administered the therapy. In some embodiments, the subject was administered an AAV transduction modulator within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, 1, 2, 3, 4, 5, or 6 months or less before being administered the therapy.

[0184] In some embodiments, the subject has a disorder or a symptom thereof, or is at risk of having a disorder or a symptom thereof. In some embodiments, the disorder is a neurodegenerative disorder. In some embodiments, the neurodegenerative disorder is Alzheimer's disease, Parkinson's disease, Huntington's disease, multiple sclerosis (MS), amyotrophic lateral sclerosis (ALS), or Batten disease. In some embodiments, the disorder is mild Alzheimer's disease, mild to moderate Alzheimer's disease, mild to severe Alzheimer's disease, early dementia, Parkinson's disease (e.g., idiopathic Parkinson's disease, bilateral idiopathic Parkinson's disease, intermediate to late stage Parkinson's disease), Huntington's disease (e.g., manifest Huntington's disease), SMA type 1, presymptomatic SMA, or amyotrophic lateral sclerosis (ALS) (e.g., familial ALS, SOD1-mutant ALS, or C9orf72-mutant ALS). In some embodiments, the disorder is an ocular disorder. In some embodiments, the ocular disorder is blindness, e.g., hereditary blindness or non-hereditary blindness. In some embodiments, the ocular disorder is Leber's congenital amaurosis, age-related macular degeneration, congenital choroideremia, or color vision deficiency. In some embodiments, the method reduces toxicity of a therapy, enhances efficacy of a therapy, or both.

[0185] In some embodiments, the modulator modulates (e.g., increases or decreases) a gene or gene product associated with AAV transduction efficiency, hi some embodiments, the gene or gene product is a mammalian (e.g., human) gene or gene product.

[0186] In some embodiments, the modulator inhibits a gene or gene product, e.g., a gene or gene product associated with decreased transduction efficiency of AAV particles, hi some embodiments, the modulator activates a gene or gene product, e.g., a gene or gene product associated with increased transduction efficiency of AAV particles.

[0187] In some embodiments, the gene or gene product is associated with increased transduction efficiency of AAV particles. In some embodiments, the gene or gene product is associated with increased transduction efficiency of AAV particles of a first serotype (e.g., AAV2), increased transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GPR108.

[0188] In some embodiments, the gene or gene product is associated with decreased transduction efficiency of AAV particles. In some embodiments, the gene or gene product is associated with decreased transduction efficiency of AAV particles of a first serotype (e.g., AAV2), decreased transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0189] In some embodiments, the gene or gene product, when modulated, increases the transduction efficiency of AAV particles, ie, the gene or gene product, when modulated, increases the transduction efficiency of AAV particles of a first serotype (e.g., AAV2), the transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both.

[0190] In some embodiments, the gene or gene product, when modulated, decreases the transduction efficiency of AAV particles, ie, the gene or gene product, when modulated, decreases the transduction efficiency of AAV particles of a first serotype (e.g., AAV2), the transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both.

[0191] In some embodiments, the gene product is RNA (e.g., mRNA). In some embodiments, the gene product is a protein. In some embodiments, the gene or gene product is selectively expressed in a target tissue (e.g., brain or liver). The following dependent claims describe AAV transduction regulators based on their mechanism. In some embodiments, the regulator alters (e.g., increases or decreases) the expression of a gene. In some embodiments, the regulator alters the structure of a gene. In some embodiments, the regulator alters (e.g., increases or decreases) the activity (e.g., enzymatic activity) of a gene product. In some embodiments, the regulator alters (e.g., increases or decreases) the level (e.g., abundance) of a gene product. In some embodiments, the regulator alters (e.g., increases or decreases) the stability of a gene product. In some embodiments, the regulator alters (e.g., increases or decreases) the transduction efficiency of AAV particles, e.g., as determined by an assay described herein (e.g., FACS analysis, e.g., as described in Example 1 or 2).

[0192] In some embodiments, the modulator increases the transduction efficiency of AAV particles. In some embodiments, the transduction efficiency is increased by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90%, or at least 1-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 60-fold, 70-fold, 80-fold, 90-fold, 100-fold, 200-fold, 300-fold, 400-fold, 500-fold, 600-fold, 700-fold, 800-fold, 900-fold, or 1000-fold compared to a baseline level of transduction efficiency. In some embodiments, the modulator increases transduction by at least 10, 20, 30, 40, 50, or 60 viral copies per genome. In some embodiments, the regulatory factor induces transduction at a rate of at least 10 per μg of DNA. 3 , 10 4 , 10 5 , 10 6 , or 10 7 The viral copy number increases to .

[0193] In some embodiments, the modulator reduces the transduction efficiency of AAV particles. In some embodiments, the transduction efficiency is reduced by at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% compared to a baseline level of transduction efficiency. In some embodiments, the modulator reduces transduction to 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 viral copies per genome or less. In some embodiments, the modulator reduces transduction to 10 copies per μg of DNA or less. 2 , 10 3 , or 10 4 Reduce the viral copy number to:

[0194] In some embodiments, the baseline level of transduction efficiency is the level of transduction efficiency in cells that have not been contacted with an AAV transduction regulatory agent, hi some embodiments, the baseline level of transduction efficiency is the level of transduction efficiency before the cells are contacted with an AAV transduction regulatory agent.

[0195] In some embodiments, the gene or gene product increases the transduction efficiency of AAV2 particles, and optionally, the gene or gene product does not increase or does not substantially increase the transduction efficiency of AAV9 particles. In some embodiments, the gene or gene product is essential for transduction of AAV2 particles, and optionally, the gene or gene product is not essential for transduction of AAV9 particles. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GRP108.

[0196] In some embodiments, the gene or gene product is selected from EXT1, EXT2, NDST1, BCL10, OAF, PDCD10, LMO4, MALT1, ZNF644, CHUK, GLCE, EP300, ARID4B, RAB21, MED13, DHX15, WASHC5, IKBKB, USP24, HSPA14, CXXC1, UBE2A, INTS8, CDC42, NFKB1, SIN3A, USP7, ARF5, CARD10, JAK1, SLC35C2, PAXK1, ZC3H11A, FAM20B, FAM72A, DHX36, INTS12, RPRD1B, or a combination thereof.

[0197] In some embodiments, the gene or gene product is associated with endosomal sorting (e.g., RAB21, WASHC5, or USP7). In some embodiments, the gene or gene product is associated with vesicle-mediated transport (e.g., CDC42 or ARF5). In some embodiments, the gene or gene product is associated with NFKB signaling (e.g., BCL10, MALT1, NFKB1, IKBKB, CHUK, or CARD10). In some embodiments, the gene or gene product is associated with heparan sulfate biosynthesis (e.g., EXT1, EXT2, NDST1, GLCE, or FAM20B). In some embodiments, the gene or gene product is associated with H3K9 methylation (e.g., ZNF644). In some embodiments, the gene or gene product is associated with pre-mRNA processing (e.g., DHX15). In some embodiments, the gene or gene product is associated with transcription (e.g., LMO4, EP300, MED13, SIN3, ARID4B, ZC3H11A, CXXC1, RPRD1B, or UBE2A). In some embodiments, the gene or gene product is associated with the Integrator complex and / or RNA polymerase II function (e.g., INTS8 or INST12). In some embodiments, the gene or gene product is associated with DNA repair and / or AAV genome degradation (e.g., DHX36, ARID4B, UBE2A, or USP24). In some embodiments, the gene or gene product is associated with cell proliferation and / or apoptosis (e.g., PDCD10). In some embodiments, the gene or gene product is associated with spinocarpal tarsal synostosis (e.g., OAF). In some embodiments, the gene or gene product is associated with protein folding (e.g., HSPA14). In some embodiments, the gene or gene product is associated with helicase activity (e.g., DHX36). In some embodiments, the gene or gene product is associated with fucosylation of Notch and / or transport of GCP-fucose (eg, SLC35C2).

[0198] In some embodiments, the gene or gene product increases the transduction efficiency of AAV9 particles, and optionally, the gene or gene product does not increase or does not substantially increase the transduction efficiency of AAV2 particles. In some embodiments, the gene or gene product is essential for transduction of AAV9 particles, and optionally, the gene or gene product is not essential for transduction of AAV2 particles. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GRP108.

[0199] In some embodiments, the gene or gene product is selected from TMPRSS11B, HTT, SNRNP70, BRD7, DMXL1, RAB10, CNGA1, KLHDC3, CHP1, CYP3A5, ELOVL4, PNISR, ZCCHC14, AZGP1, TPST1, SC5D, ELP2, ELP3, IPO9, RAB14, WDR7, XRCC4, GDI2, or a combination thereof.

[0200] In some embodiments, the gene or gene product is associated with microtubule-mediated transport or vesicle function (e.g., HTT). In some embodiments, the gene or gene product is an ion channel (e.g., CNGA1). In some embodiments, the gene or gene product is associated with nuclear protein import (e.g., IPO9). In some embodiments, the gene or gene product is associated with O-sulfation of tyrosine residues within acidic motifs of polypeptides (e.g., TPST1). In some embodiments, the gene or gene product is associated with protection of viral RNA (e.g., ZCCHC14). In some embodiments, the gene or gene product is associated with RNA binding by AAV proteins (e.g., PNISR). In some embodiments, the gene or gene product is associated with calcium ion-regulated exocytosis (e.g., CHP1). In some embodiments, the gene or gene product is associated with intracellular transport (e.g., RAB10, RAB14, GDI2, WDR7, or DMXL1). In some embodiments, the gene or gene product is a subunit (e.g., a catalytic tRNA acetyltransferase subunit) of an elongator complex, e.g., an RNA polymerase (e.g., RNA polymerase II) (e.g., ELP2 or ELP3). In some embodiments, the gene or gene product is chromatin-associated (e.g., KLHDC3). In some embodiments, the gene or gene product is associated with cholesterol biosynthesis (e.g., SC5D).

[0201] In some embodiments, the gene or gene product increases the transduction efficiency of AAV2 and AAV9 particles. In some embodiments, the gene or gene product is essential for transduction of AAV2 and AAV9 particles. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GRP108.

[0202] In some embodiments, the gene or gene product is selected from KIAA0319L, BAMBI, TM9SF2, PHIP, DCLRE1C, VPS35, GPR108, CYREN, ACP2, F8A2, F8A1, F8A3, RBPJ, ATP2C1, ICMT, RABIF, IER3IP1, RBM10, SMG7, GTF2I, ELAVL1, MEPCE, RAB4A, IER3IP1, SAMD1, or a combination thereof.

[0203] In some embodiments, the gene or gene product is associated with influenza infection (e.g., ACP2). In some embodiments, the gene or gene product binds to an unmethylated CGI (e.g., SAMD1). In some embodiments, the gene or gene product is associated with intracellular vesicle trafficking (e.g., RABIF). In some embodiments, the gene or gene product is associated with post-translational modification of a cysteine ​​residue (e.g., a C-terminal cysteine ​​residue) in, for example, a target protein (e.g., ICMT). In some embodiments, the gene or gene product binds to an AAV capsid protein (e.g., KIAA0319L). In some embodiments, the gene or gene product is associated with inhibition of a TLR (e.g., TLR9) (e.g., GPR108). In some embodiments, the gene or gene product is associated with endosomal trafficking of, for example, AAV-R (e.g., VPS35). In some embodiments, the gene or gene product is a calcium ATPase pump (e.g., ATP2C1). In some embodiments, the gene or gene product is associated with Notch signaling (e.g., RBPJ). In some embodiments, the gene or gene product is associated with HSPG metabolism (e.g., TM9SF2). In some embodiments, the gene or gene product is associated with inhibition of NHEJ (e.g., CYREN). In some embodiments, the gene or gene product is associated with viral hairpin degradation (e.g., DCLRE1C). In some embodiments, the gene or gene product is associated with Glc transporter translocation, and optionally, the gene or gene product binds to insulin receptor substrate 1 protein (e.g., PHIP).

[0204] In some embodiments, the gene or gene product reduces the transduction efficiency of AAV2 particles, and optionally, the gene or gene product, when regulated, does not reduce or does not substantially reduce the transduction efficiency of AAV9 particles. In some embodiments, the gene or gene product inhibits or prevents transduction of AAV2 particles, and optionally, the gene or gene product does not inhibit or prevent transduction of AAV9 particles. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0205] In some embodiments, the gene or gene product is GREB1L, BIRC2, TYMSOS, MSL3, SIK3, GTF2H5, PIGW, ATRAID, PPP4R1, ZFC3H1, SETDB1, SMCHD1, TMEM123, UHRF1, CLUL1, SMAD5, SETX, STEEP1, DENND6A, RTN4RL2, MTMR9, STRADA, PSIP1, BMPR1A, HIKESHI, AP3M1, MEN1, MYL12B, CREB1, RAB12, SMTNL1, MRGBP, WTAP, SUMO2, TCN 1, ALDH3B1, ARL14EP, MYL12A, RHOD, PGAP2, EIF4A1, PIGN, DAXX, HDLBP, GOLGA1, SARNP, UBE2L6, TRIM49, SIK2, SOX4, OR6Q1, OR4D6, UNC93B1, CATSPERZ, PIGT, PYM1, MICOS13, RIN1, DOT1L, TRIM49C, MAPK20, COL8A1, FASN, KDM3B, PIGF, PIGA, PIGY, GPC3, TRAPPC2L, RAB31, ELP3, or a combination thereof.

[0206] In some embodiments, the gene or gene product is associated with retinoic acid receptor activity (e.g., GREB1L). In some embodiments, the gene or gene product is thymidylate synthetase (e.g., TYMSOS). In some embodiments, the gene or gene product is associated with chromatin remodeling (e.g., SMCHD1). In some embodiments, the gene or gene product is associated with histone H4 acetylation (e.g., MSL3). In some embodiments, the gene or gene product is associated with transcription and / or DNA repair (e.g., GTF2H5). In some embodiments, the gene or gene product is a histone methyltransferase (e.g., SETDB1). In some embodiments, the gene or gene product is associated with exosomal degradation of polyadenylated RNA (e.g., ZFC3H1). In some embodiments, the gene or gene product is associated with recruitment of histone deacetylase to DNA (e.g., UHRF1). In some embodiments, the gene or gene product is associated with oxidative stress-induced DNA double-strand break response (e.g., SETX). In some embodiments, the gene or gene product is associated with histone modification (e.g., MEN1). In some embodiments, the gene or gene product is associated with nucleosome / DNA interactions (e.g., MRGBP). In some embodiments, the gene or gene product is associated with GPI biosynthesis (e.g., PIGW, PIGN, PIGT, PIGF, PIGA, or PIGY). In some embodiments, the gene or gene product is associated with GPI anchor maturation (e.g., PGAP2). In some embodiments, the gene or gene product is associated with vesicle-mediated endocytosis (e.g., DENND6A, GOLGA1, MTMR9, GPC3, PPP4R1, RAB12, RAB31, RHOD, RIN1, TMEM123, or TRAPPC2L). In some embodiments, the gene or gene product is associated with clathrin-coated vesicle-mediated endocytosis (e.g., AP3M1). In some embodiments, the gene or gene product is related to a BMP receptor kinase (eg, SMAD5, BMPR1A, or CREB1).In some embodiments, the gene or gene product is associated with transcription (e.g., PSIP1). In some embodiments, the gene or gene product is associated with nuclear import of HSP70 proteins (e.g., HIKESHI). In some embodiments, the gene or gene product is associated with Ser / Thr kinases (e.g., SIK2 or SIK3). In some embodiments, the gene or gene product is associated with protein sumoylation (e.g., SUMO2, UBE2L6).

[0207] In some embodiments, the gene or gene product reduces the transduction efficiency of AAV9 particles, and optionally, the gene or gene product does not reduce or substantially reduce the transduction efficiency of AAV2 particles. In some embodiments, the gene or gene product inhibits or prevents transduction of AAV9 particles, and optionally, the gene or gene product does not inhibit or prevent transduction of AAV2 particles. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0208] In some embodiments, the gene or gene product is selected from AP2A1, AP2B1, TM9SF4, ACTR5, PTMA, PAPOLA, PDHA1, PDHB, SLC25A19, GAK, AUNIP, FCHO2, ACTB, LIPT1, UCHL5, INO80E, ECHS1, NELFB, EDC4, PRMT1, PDS5B, PELI3, FBXL20, SLC35A1, or a combination thereof.

[0209] In some embodiments, the gene or gene product binds to ATP, chaperone proteins, and / or clathrin (e.g., GAK). In some embodiments, the gene or gene product is associated with the trafficking of clathrin-coated vesicles (e.g., AP2B1 or AP2A1). In some embodiments, the gene or gene product is associated with clathrin-mediated endocytosis (e.g., FCHO2). In some embodiments, the gene or gene product is associated with vesicle trafficking (e.g., ACTB). In some embodiments, the gene or gene product is associated with the innate immune response (e.g., PELI3 or FBXL20). In some embodiments, the gene or gene product is associated with glucose metabolism (e.g., PDHB or PDHA1). In some embodiments, the gene or gene product is associated with DNA resection and / or homologous recombination, e.g., after DNA damage (e.g., AUNIP). In some embodiments, the gene or gene product is associated with DNA repair, e.g., after DNA damage (e.g., UCHL5, INO80E, PDS5B, ACTR5, or PRMT1). In some embodiments, the gene or gene product is associated with transport of CMP sialic acid from the cytosol to Golgi vesicles (e.g., SLC35A1). In some embodiments, the gene or gene product is associated with localization of polypeptides containing a glycine-rich transmembrane domain, e.g., to the cell surface (e.g., TM9SF4). In some embodiments, the gene or gene product is associated with synthesis of poly(A) tails (e.g., PAPOLA). In some embodiments, the gene or gene product is PTMA. In some embodiments, the gene or gene product is associated with elongation of mRNA by RNA polymerase II (e.g., NELFB). In some embodiments, the gene or gene product is associated with mRNA degradation (e.g., EDC4). In some embodiments, the gene or gene product encodes a mitochondrial lipoyltransferase (e.g., LIPT1). In some embodiments, the gene or gene product is associated with mitochondrial fatty acid β-oxidation (e.g., ECHS1). In some embodiments, the gene or gene product encodes the mitochondrial thiamine pyrophosphate carrier (e.g., SLC25A19).

[0210] In some embodiments, the gene or gene product reduces the transduction efficiency of AAV2 and AAV9 particles. In some embodiments, the gene or gene product inhibits or prevents transduction of AAV2 and AAV9 particles. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0211] In some embodiments, the gene or gene product is selected from the group consisting of PITPNB, PITP, FAM91A1, WDR11, AP1G1, AP1M1, AP1S1, AP1S3, HEATR5B, STX16, AP1B1, PIAS1, DENR, ARL1, ZFAT, TBC1D23, LIN37, RALGAPB, B3GNT2, ELOVL1, AP2B1, KIAA2013, PTEN, MCTS1, NBN, HELZ, SLC38A10, FBXL20, TGIF1, KDSR, CPD, CHD7, USP9X, SIMC1, TAF11, VAPA, MTMR6, RAB1B, SLF2, MRE11, VTI1A, MBOAT7, PPP6R3, or a combination thereof.

[0212] In some embodiments, the gene or gene product is associated with the long-chain FA elongation cycle (e.g., ELOVL1). In some embodiments, the gene or gene product is associated with lipoic acid biosynthesis (e.g., PIAS1). In some embodiments, the gene or gene product is associated with a protein phosphatase catalytic subunit (e.g., PPP6R3). In some embodiments, the gene or gene product is associated with the WDR11 pathway (e.g., WDR11, FAM91A1, AP1G1, AP1S1, AP1M1, AP1S3, or TBC1D23). In some embodiments, the gene or gene product is associated with retrograde transport of, for example, PI and / or PC from the Golgi apparatus to the endoplasmic reticulum (e.g., PITP). In some embodiments, the gene or gene product is associated with vesicle transport from late endosomes to the trans-Golgi network (e.g., STX16). In some embodiments, the gene or gene product is associated with the activity or recruitment of golgin, arfaptin, and / or Arf-GEF to the trans-Golgi network (e.g., ARL1). In some embodiments, the gene or gene product encodes a component of clathrin-dependent vesicles and / or is involved in AP1G1 / AP-1 mediated protein transport (eg, HEATR5B).

[0213] In some embodiments, the gene or gene product is AAV-R, GPR108, WDR11, or MRE11. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GPR108. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0214] In some embodiments, the method results in high gene regulation (e.g., gene editing) efficiency in a first tissue (e.g., at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 98%) and limited effect in a second tissue (e.g., 20%, 15%, 10%, 5%, 2%, or less gene regulation (e.g., gene editing) efficiency). In some embodiments, the method results in high regulation (e.g., gene editing) efficiency in the liver (e.g., at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 98%) and limited effect in skeletal muscle, bone marrow, or both (e.g., 20%, 15%, 10%, 5%, 2%, or less gene regulation (e.g., gene editing) efficiency).

[0215] In some embodiments, the modulator is administered intravenously.

[0216] In some embodiments, the regulatory element is (a) a gene editing system that targets one or more sites within a gene or its regulatory elements, (b) a nucleic acid encoding one or more components of the gene editing system, or (c) a combination thereof. In some embodiments, the gene editing system is a CRISPR / Cas system, a zinc finger nuclease system, a TALEN system, or a meganuclease system.

[0217] In some embodiments, the gene editing system binds to a target sequence in an early (e.g., first, second, or third) exon or intron of a gene. In some embodiments, the gene editing system binds to a target sequence of a gene, and the target sequence is upstream of exon 4, e.g., in exon 1, exon 2, or exon 3. In some embodiments, the gene editing system binds to a target sequence in a later exon or intron of a gene. In some embodiments, the gene editing system binds to a target sequence of a gene, and the target sequence is downstream of the penultimate exon, e.g., the third to last exon, the penultimate exon, or the last exon. In some embodiments, the gene editing system is a CRISPR / Cas system comprising a guide RNA (gRNA) molecule comprising a targeting sequence that hybridizes to the target sequence of the gene. In some embodiments, the CRISPR / Cas system is a CRISPR / Cas9 system. In some embodiments, the CRISPR / Cas system is a CRISPR / Cas12a system.

[0218] In some embodiments, the regulatory element is a small interfering RNA (siRNA) or small hairpin (shRNA) specific to the gene, or a nucleic acid encoding the siRNA or shRNA. In some embodiments, the siRNA or shRNA comprises a nucleotide sequence complementary to the nucleotide sequence of an mRNA encoded by the gene. In some embodiments, the regulatory element is a guide RNA (gRNA) specific to the gene, or a nucleic acid encoding the gRNA. In some embodiments, the gRNA comprises a nucleotide sequence complementary to the nucleotide sequence of the gene.

[0219] In some embodiments, the modulator is a gene-specific antisense oligonucleotide (ASO) or a nucleic acid encoding the ASO. In some embodiments, the ASO comprises a nucleotide sequence complementary to the nucleotide sequence of an mRNA encoded by the gene.

[0220] In some embodiments, the modulator is a small molecule (e.g., a compound described herein, e.g., in Figure 7). In some embodiments, the small molecule is a protein degradation inducer.

[0221] In some embodiments, the modulator is a protein or peptide, or a nucleic acid encoding the protein or peptide. In some embodiments, the modulator is an antibody molecule (e.g., an scFv or sdAb). In some embodiments, the modulator is a dominant-negative binding partner of the protein encoded by the gene, or a nucleic acid encoding the dominant-negative binding partner. In some embodiments, the modulator is a dominant-negative variant (e.g., catalytically inactive) of the protein encoded by the gene, or a nucleic acid encoding the dominant-negative variant.

[0222] In some embodiments, the AAV particles comprise an AAV genome. In some embodiments, the AAV particles comprise AAV-like particles. In some embodiments, the AAV particles comprise a capsid. In some embodiments, the AAV particles have a serotype of AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, or a combination thereof. In some embodiments, the AAV particles are AAV2 particles. In some embodiments, the AAV particles are AAV9 particles.

[0223] In some embodiments, the AAV particles have a tropism for the CNS (e.g., AAV1, AAV2, AAV4, AAV5, AAV8, or AAV9). In some embodiments, the AAV particles have a tropism for the heart (e.g., AAV1, AAV8, or AAV9). In some embodiments, the AAV particles have a tropism for the kidney (e.g., AAV2). In some embodiments, the AAV particles have a tropism for the liver (e.g., AAV7, AAV8, or AAV9). In some embodiments, the AAV particles have a tropism for the lung (e.g., AAV4, AAV5, AAV6, or AAV9). In some embodiments, the AAV particles have a tropism for the pancreas (e.g., AAV8). In some embodiments, the AAV particles have a tropism for photoreceptor cells (e.g., AAV2, AAV5, or AAV8). In some embodiments, the AAV particle has tropism for the retinal pigment epithelium (RPE) (e.g., AAV1, AAV2, AAV4, AAV5, or AAV8). In some embodiments, the AAV particle has tropism for skeletal muscle (e.g., AAV1, AAV6, AAV7, AAV8, or AAV9).

[0224] In some embodiments, the AAV particles comprise a nucleotide sequence encoding a therapeutic protein, e.g., a protein associated with a disorder described herein. In some embodiments, the AAV particles comprise a nucleotide sequence encoding NGF, APOE2 (e.g., hAPOE2), TERT (e.g., hTERT), MAPT, GAD, AADC, NTN, GDNF, GCase, HTT, SMN, SMN2, SOD1, or C9orf72. In some embodiments, the AAV particles comprise a nucleotide sequence encoding a therapeutic nucleic acid, e.g., a nucleic acid targeting a nucleotide sequence encoding a protein associated with a disorder described herein.

[0225] In some embodiments, the methods involve administering to the subject multiple AAV transduction regulators or AAV regulators that regulate multiple genes or gene products associated with AAV transduction efficiency.

[0226] In another aspect, the disclosure provides a method for reducing toxicity of a therapy comprising an AAV genome or AAV particle, the method comprising administering an effective amount of an AAV transduction modulator to a subject in need thereof, thereby reducing the toxicity of the therapy.

[0227] In some embodiments, the subject has not been administered or is not currently being administered a therapy when the AAV transduction modulator is administered, hi some embodiments, the subject has been administered an AAV transduction modulator for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, or 1, 2, 3, 4, 5, or 6 months before the subject was administered the therapy. In some embodiments, the subject was administered an AAV transduction modulator within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, 1, 2, 3, 4, 5, or 6 months or less before being administered the therapy.

[0228] In some embodiments, the subject has been administered or is currently being administered a therapy when the AAV transduction modulator is administered, hi some embodiments, the subject has been administered a therapy for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, or 1, 2, 3, 4, 5, or 6 months prior to administration of the AAV transduction modulator. In some embodiments, the subject has been administered therapy for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, 1, 2, 3, 4, 5, or 6 months or less before the AAV transduction modulator was administered.

[0229] In some embodiments, toxicity is reduced by at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% compared to a baseline toxicity level. In some embodiments, the baseline toxicity level is the toxicity level in a subject who has not previously been administered an AAV transduction modulator. In some embodiments, the baseline toxicity level is the toxicity level before the subject was administered an AAV transduction modulator. In some embodiments, the method reduces dorsal root ganglion (DRG) toxicity. In some embodiments, the method reduces liver toxicity. In some embodiments, the method reduces cardiomyocyte toxicity. In some embodiments, the method reduces retinal pigment epithelium (RPE) toxicity.

[0230] In some embodiments, the subject has a disorder or a symptom thereof, or is at risk of having a disorder or a symptom thereof. In some embodiments, the disorder is a neurodegenerative disorder. In some embodiments, the neurodegenerative disorder is Alzheimer's disease, Parkinson's disease, Huntington's disease, multiple sclerosis (MS), amyotrophic lateral sclerosis (ALS), or Batten disease. In some embodiments, the disorder is mild Alzheimer's disease, mild to moderate Alzheimer's disease, mild to severe Alzheimer's disease, early dementia, Parkinson's disease (e.g., idiopathic Parkinson's disease, bilateral idiopathic Parkinson's disease, intermediate to late stage Parkinson's disease), Huntington's disease (e.g., manifest Huntington's disease), SMA type 1, presymptomatic SMA, or amyotrophic lateral sclerosis (ALS) (e.g., familial ALS, SOD1-mutant ALS, or C9orf72-mutant ALS). In some embodiments, the disorder is an ocular disorder. In some embodiments, the ocular disorder is blindness, e.g., hereditary blindness or non-hereditary blindness. In some embodiments, the ocular disorder is Leber's congenital amaurosis, age-related macular degeneration, congenital choroideremia, or color vision deficiency. In some embodiments, the method reduces toxicity of a therapy, enhances efficacy of a therapy, or both.

[0231] In some embodiments, the modulator modulates (e.g., increases or decreases) a gene or gene product associated with AAV transduction efficiency, hi some embodiments, the gene or gene product is a mammalian (e.g., human) gene or gene product.

[0232] In some embodiments, the modulator inhibits a gene or gene product, e.g., a gene or gene product associated with decreased transduction efficiency of AAV particles, hi some embodiments, the modulator activates a gene or gene product, e.g., a gene or gene product associated with increased transduction efficiency of AAV particles.

[0233] In some embodiments, the gene or gene product is associated with increased transduction efficiency of AAV particles. In some embodiments, the gene or gene product is associated with increased transduction efficiency of AAV particles of a first serotype (e.g., AAV2), increased transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GPR108.

[0234] In some embodiments, the gene or gene product is associated with decreased transduction efficiency of AAV particles. In some embodiments, the gene or gene product is associated with decreased transduction efficiency of AAV particles of a first serotype (e.g., AAV2), decreased transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0235] In some embodiments, the gene or gene product, when modulated, increases the transduction efficiency of AAV particles, ie, the gene or gene product, when modulated, increases the transduction efficiency of AAV particles of a first serotype (e.g., AAV2), the transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both.

[0236] In some embodiments, the gene or gene product, when modulated, decreases the transduction efficiency of AAV particles, ie, the gene or gene product, when modulated, decreases the transduction efficiency of AAV particles of a first serotype (e.g., AAV2), the transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both.

[0237] In some embodiments, the gene product is RNA (e.g., mRNA). In some embodiments, the gene product is a protein. In some embodiments, the gene or gene product is selectively expressed in a target tissue (e.g., brain or liver). The following dependent claims describe AAV transduction regulators based on their mechanism. In some embodiments, the regulator alters (e.g., increases or decreases) the expression of a gene. In some embodiments, the regulator alters the structure of a gene. In some embodiments, the regulator alters (e.g., increases or decreases) the activity (e.g., enzymatic activity) of a gene product. In some embodiments, the regulator alters (e.g., increases or decreases) the level (e.g., abundance) of a gene product. In some embodiments, the regulator alters (e.g., increases or decreases) the stability of a gene product. In some embodiments, the regulator alters (e.g., increases or decreases) the transduction efficiency of AAV particles, e.g., as determined by an assay described herein (e.g., FACS analysis, e.g., as described in Example 1 or 2).

[0238] In some embodiments, the gene or gene product is AAV-R, GPR108, WDR11, or MRE11. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GPR108. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0239] In some embodiments, the method results in high gene regulation (e.g., gene editing) efficiency in a first tissue (e.g., at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 98%) and limited effect in a second tissue (e.g., 20%, 15%, 10%, 5%, 2%, or less gene regulation (e.g., gene editing) efficiency). In some embodiments, the method results in high regulation (e.g., gene editing) efficiency in the liver (e.g., at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 98%) and limited effect in skeletal muscle, bone marrow, or both (e.g., 20%, 15%, 10%, 5%, 2%, or less gene regulation (e.g., gene editing) efficiency).

[0240] In some embodiments, the modulator is administered intravenously.

[0241] In some embodiments, the modulator increases the transduction efficiency of AAV particles. In some embodiments, the transduction efficiency is increased by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90%, or at least 1-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 60-fold, 70-fold, 80-fold, 90-fold, 100-fold, 200-fold, 300-fold, 400-fold, 500-fold, 600-fold, 700-fold, 800-fold, 900-fold, or 1000-fold compared to a baseline level of transduction efficiency. In some embodiments, the modulator increases transduction by at least 10, 20, 30, 40, 50, or 60 viral copies per genome. In some embodiments, the regulatory factor induces transduction at a rate of at least 10 per μg of DNA. 3 , 10 4 , 10 5 , 10 6 , or 10 7 The viral copy number increases to .

[0242] In some embodiments, the modulator reduces the transduction efficiency of AAV particles. In some embodiments, the transduction efficiency is reduced by at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% compared to a baseline level of transduction efficiency. In some embodiments, the modulator reduces transduction to 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 viral copies per genome or less. In some embodiments, the modulator reduces transduction to 10 copies per μg of DNA or less. 2 , 10 3 , or 10 4 Reduce the viral copy number to:

[0243] In some embodiments, the baseline level of transduction efficiency is the level of transduction efficiency in cells that have not been contacted with an AAV transduction regulatory agent, hi some embodiments, the baseline level of transduction efficiency is the level of transduction efficiency before the cells are contacted with an AAV transduction regulatory agent.

[0244] In some embodiments, the gene or gene product increases the transduction efficiency of AAV2 particles, and optionally, the gene or gene product does not increase or does not substantially increase the transduction efficiency of AAV9 particles. In some embodiments, the gene or gene product is essential for transduction of AAV2 particles, and optionally, the gene or gene product is not essential for transduction of AAV9 particles. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GRP108.

[0245] In some embodiments, the gene or gene product is selected from EXT1, EXT2, NDST1, BCL10, OAF, PDCD10, LMO4, MALT1, ZNF644, CHUK, GLCE, EP300, ARID4B, RAB21, MED13, DHX15, WASHC5, IKBKB, USP24, HSPA14, CXXC1, UBE2A, INTS8, CDC42, NFKB1, SIN3A, USP7, ARF5, CARD10, JAK1, SLC35C2, PAXK1, ZC3H11A, FAM20B, FAM72A, DHX36, INTS12, RPRD1B, or a combination thereof.

[0246] In some embodiments, the gene or gene product is associated with endosomal sorting (e.g., RAB21, WASHC5, or USP7). In some embodiments, the gene or gene product is associated with vesicle-mediated transport (e.g., CDC42 or ARF5). In some embodiments, the gene or gene product is associated with NFKB signaling (e.g., BCL10, MALT1, NFKB1, IKBKB, CHUK, or CARD10). In some embodiments, the gene or gene product is associated with heparan sulfate biosynthesis (e.g., EXT1, EXT2, NDST1, GLCE, or FAM20B). In some embodiments, the gene or gene product is associated with H3K9 methylation (e.g., ZNF644). In some embodiments, the gene or gene product is associated with pre-mRNA processing (e.g., DHX15). In some embodiments, the gene or gene product is associated with transcription (e.g., LMO4, EP300, MED13, SIN3, ARID4B, ZC3H11A, CXXC1, RPRD1B, or UBE2A). In some embodiments, the gene or gene product is associated with the Integrator complex and / or RNA polymerase II function (e.g., INTS8 or INST12). In some embodiments, the gene or gene product is associated with DNA repair and / or AAV genome degradation (e.g., DHX36, ARID4B, UBE2A, or USP24). In some embodiments, the gene or gene product is associated with cell proliferation and / or apoptosis (e.g., PDCD10). In some embodiments, the gene or gene product is associated with spinocarpal tarsal synostosis (e.g., OAF). In some embodiments, the gene or gene product is associated with protein folding (e.g., HSPA14). In some embodiments, the gene or gene product is associated with helicase activity (e.g., DHX36). In some embodiments, the gene or gene product is associated with fucosylation of Notch and / or transport of GCP-fucose (eg, SLC35C2).

[0247] In some embodiments, the gene or gene product increases the transduction efficiency of AAV9 particles, and optionally, the gene or gene product does not increase or does not substantially increase the transduction efficiency of AAV2 particles. In some embodiments, the gene or gene product is essential for transduction of AAV9 particles, and optionally, the gene or gene product is not essential for transduction of AAV2 particles. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GRP108.

[0248] In some embodiments, the gene or gene product is selected from TMPRSS11B, HTT, SNRNP70, BRD7, DMXL1, RAB10, CNGA1, KLHDC3, CHP1, CYP3A5, ELOVL4, PNISR, ZCCHC14, AZGP1, TPST1, SC5D, ELP2, ELP3, IPO9, RAB14, WDR7, XRCC4, GDI2, or a combination thereof.

[0249] In some embodiments, the gene or gene product is associated with microtubule-mediated transport or vesicle function (e.g., HTT). In some embodiments, the gene or gene product is an ion channel (e.g., CNGA1). In some embodiments, the gene or gene product is associated with nuclear protein import (e.g., IPO9). In some embodiments, the gene or gene product is associated with O-sulfation of tyrosine residues within acidic motifs of polypeptides (e.g., TPST1). In some embodiments, the gene or gene product is associated with protection of viral RNA (e.g., ZCCHC14). In some embodiments, the gene or gene product is associated with RNA binding by AAV proteins (e.g., PNISR). In some embodiments, the gene or gene product is associated with calcium ion-regulated exocytosis (e.g., CHP1). In some embodiments, the gene or gene product is associated with intracellular transport (e.g., RAB10, RAB14, GDI2, WDR7, or DMXL1). In some embodiments, the gene or gene product is a subunit (e.g., a catalytic tRNA acetyltransferase subunit) of an elongator complex, e.g., an RNA polymerase (e.g., RNA polymerase II) (e.g., ELP2 or ELP3). In some embodiments, the gene or gene product is chromatin-associated (e.g., KLHDC3). In some embodiments, the gene or gene product is associated with cholesterol biosynthesis (e.g., SC5D).

[0250] In some embodiments, the gene or gene product increases the transduction efficiency of AAV2 and AAV9 particles. In some embodiments, the gene or gene product is essential for transduction of AAV2 and AAV9 particles. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GRP108.

[0251] In some embodiments, the gene or gene product is selected from KIAA0319L, BAMBI, TM9SF2, PHIP, DCLRE1C, VPS35, GPR108, CYREN, ACP2, F8A2, F8A1, F8A3, RBPJ, ATP2C1, ICMT, RABIF, IER3IP1, RBM10, SMG7, GTF2I, ELAVL1, MEPCE, RAB4A, IER3IP1, SAMD1, or a combination thereof.

[0252] In some embodiments, the gene or gene product is associated with influenza infection (e.g., ACP2). In some embodiments, the gene or gene product binds to an unmethylated CGI (e.g., SAMD1). In some embodiments, the gene or gene product is associated with intracellular vesicle trafficking (e.g., RABIF). In some embodiments, the gene or gene product is associated with post-translational modification of a cysteine ​​residue (e.g., a C-terminal cysteine ​​residue) in, for example, a target protein (e.g., ICMT). In some embodiments, the gene or gene product binds to an AAV capsid protein (e.g., KIAA0319L). In some embodiments, the gene or gene product is associated with inhibition of a TLR (e.g., TLR9) (e.g., GPR108). In some embodiments, the gene or gene product is associated with endosomal trafficking of, for example, AAV-R (e.g., VPS35). In some embodiments, the gene or gene product is a calcium ATPase pump (e.g., ATP2C1). In some embodiments, the gene or gene product is associated with Notch signaling (e.g., RBPJ). In some embodiments, the gene or gene product is associated with HSPG metabolism (e.g., TM9SF2). In some embodiments, the gene or gene product is associated with inhibition of NHEJ (e.g., CYREN). In some embodiments, the gene or gene product is associated with viral hairpin degradation (e.g., DCLRE1C). In some embodiments, the gene or gene product is associated with Glc transporter translocation, and optionally, the gene or gene product binds to insulin receptor substrate 1 protein (e.g., PHIP).

[0253] In some embodiments, the gene or gene product reduces the transduction efficiency of AAV2 particles, and optionally, the gene or gene product, when regulated, does not reduce or does not substantially reduce the transduction efficiency of AAV9 particles. In some embodiments, the gene or gene product inhibits or prevents transduction of AAV2 particles, and optionally, the gene or gene product does not inhibit or prevent transduction of AAV9 particles. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0254] In some embodiments, the gene or gene product is GREB1L, BIRC2, TYMSOS, MSL3, SIK3, GTF2H5, PIGW, ATRAID, PPP4R1, ZFC3H1, SETDB1, SMCHD1, TMEM123, UHRF1, CLUL1, SMAD5, SETX, STEEP1, DENND6A, RTN4RL2, MTMR9, STRADA, PSIP1, BMPR1A, HIKESHI, AP3M1, MEN1, MYL12B, CREB1, RAB12, SMTNL1, MRGBP, WTAP, SUMO2, TCN 1, ALDH3B1, ARL14EP, MYL12A, RHOD, PGAP2, EIF4A1, PIGN, DAXX, HDLBP, GOLGA1, SARNP, UBE2L6, TRIM49, SIK2, SOX4, OR6Q1, OR4D6, UNC93B1, CATSPERZ, PIGT, PYM1, MICOS13, RIN1, DOT1L, TRIM49C, MAPK20, COL8A1, FASN, KDM3B, PIGF, PIGA, PIGY, GPC3, TRAPPC2L, RAB31, ELP3, or a combination thereof.

[0255] In some embodiments, the gene or gene product is associated with retinoic acid receptor activity (e.g., GREB1L). In some embodiments, the gene or gene product is thymidylate synthetase (e.g., TYMSOS). In some embodiments, the gene or gene product is associated with chromatin remodeling (e.g., SMCHD1). In some embodiments, the gene or gene product is associated with histone H4 acetylation (e.g., MSL3). In some embodiments, the gene or gene product is associated with transcription and / or DNA repair (e.g., GTF2H5). In some embodiments, the gene or gene product is a histone methyltransferase (e.g., SETDB1). In some embodiments, the gene or gene product is associated with exosomal degradation of polyadenylated RNA (e.g., ZFC3H1). In some embodiments, the gene or gene product is associated with recruitment of histone deacetylase to DNA (e.g., UHRF1). In some embodiments, the gene or gene product is associated with oxidative stress-induced DNA double-strand break response (e.g., SETX). In some embodiments, the gene or gene product is associated with histone modification (e.g., MEN1). In some embodiments, the gene or gene product is associated with nucleosome / DNA interactions (e.g., MRGBP). In some embodiments, the gene or gene product is associated with GPI biosynthesis (e.g., PIGW, PIGN, PIGT, PIGF, PIGA, or PIGY). In some embodiments, the gene or gene product is associated with GPI anchor maturation (e.g., PGAP2). In some embodiments, the gene or gene product is associated with vesicle-mediated endocytosis (e.g., DENND6A, GOLGA1, MTMR9, GPC3, PPP4R1, RAB12, RAB31, RHOD, RIN1, TMEM123, or TRAPPC2L). In some embodiments, the gene or gene product is associated with clathrin-coated vesicle-mediated endocytosis (e.g., AP3M1). In some embodiments, the gene or gene product is related to a BMP receptor kinase (eg, SMAD5, BMPR1A, or CREB1).In some embodiments, the gene or gene product is associated with transcription (e.g., PSIP1). In some embodiments, the gene or gene product is associated with nuclear import of HSP70 proteins (e.g., HIKESHI). In some embodiments, the gene or gene product is associated with Ser / Thr kinases (e.g., SIK2 or SIK3). In some embodiments, the gene or gene product is associated with protein sumoylation (e.g., SUMO2, UBE2L6).

[0256] In some embodiments, the gene or gene product reduces the transduction efficiency of AAV9 particles, and optionally, the gene or gene product does not reduce or substantially reduce the transduction efficiency of AAV2 particles. In some embodiments, the gene or gene product inhibits or prevents transduction of AAV9 particles, and optionally, the gene or gene product does not inhibit or prevent transduction of AAV2 particles. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0257] In some embodiments, the gene or gene product is selected from AP2A1, AP2B1, TM9SF4, ACTR5, PTMA, PAPOLA, PDHA1, PDHB, SLC25A19, GAK, AUNIP, FCHO2, ACTB, LIPT1, UCHL5, INO80E, ECHS1, NELFB, EDC4, PRMT1, PDS5B, PELI3, FBXL20, SLC35A1, or a combination thereof.

[0258] In some embodiments, the gene or gene product binds to ATP, chaperone proteins, and / or clathrin (e.g., GAK). In some embodiments, the gene or gene product is associated with the trafficking of clathrin-coated vesicles (e.g., AP2B1 or AP2A1). In some embodiments, the gene or gene product is associated with clathrin-mediated endocytosis (e.g., FCHO2). In some embodiments, the gene or gene product is associated with vesicle trafficking (e.g., ACTB). In some embodiments, the gene or gene product is associated with the innate immune response (e.g., PELI3 or FBXL20). In some embodiments, the gene or gene product is associated with glucose metabolism (e.g., PDHB or PDHA1). In some embodiments, the gene or gene product is associated with DNA resection and / or homologous recombination, e.g., after DNA damage (e.g., AUNIP). In some embodiments, the gene or gene product is associated with DNA repair, e.g., after DNA damage (e.g., UCHL5, INO80E, PDS5B, ACTR5, or PRMT1). In some embodiments, the gene or gene product is associated with transport of CMP sialic acid from the cytosol to Golgi vesicles (e.g., SLC35A1). In some embodiments, the gene or gene product is associated with localization of polypeptides containing a glycine-rich transmembrane domain, e.g., to the cell surface (e.g., TM9SF4). In some embodiments, the gene or gene product is associated with synthesis of poly(A) tails (e.g., PAPOLA). In some embodiments, the gene or gene product is PTMA. In some embodiments, the gene or gene product is associated with elongation of mRNA by RNA polymerase II (e.g., NELFB). In some embodiments, the gene or gene product is associated with mRNA degradation (e.g., EDC4). In some embodiments, the gene or gene product encodes a mitochondrial lipoyltransferase (e.g., LIPT1). In some embodiments, the gene or gene product is associated with mitochondrial fatty acid β-oxidation (e.g., ECHS1). In some embodiments, the gene or gene product encodes the mitochondrial thiamine pyrophosphate carrier (e.g., SLC25A19).

[0259] In some embodiments, the gene or gene product reduces the transduction efficiency of AAV2 and AAV9 particles. In some embodiments, the gene or gene product inhibits or prevents transduction of AAV2 and AAV9 particles. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0260] In some embodiments, the gene or gene product is selected from the group consisting of PITPNB, PITP, FAM91A1, WDR11, AP1G1, AP1M1, AP1S1, AP1S3, HEATR5B, STX16, AP1B1, PIAS1, DENR, ARL1, ZFAT, TBC1D23, LIN37, RALGAPB, B3GNT2, ELOVL1, AP2B1, KIAA2013, PTEN, MCTS1, NBN, HELZ, SLC38A10, FBXL20, TGIF1, KDSR, CPD, CHD7, USP9X, SIMC1, TAF11, VAPA, MTMR6, RAB1B, SLF2, MRE11, VTI1A, MBOAT7, PPP6R3, or a combination thereof.

[0261] In some embodiments, the gene or gene product is associated with the long-chain FA elongation cycle (e.g., ELOVL1). In some embodiments, the gene or gene product is associated with lipoic acid biosynthesis (e.g., PIAS1). In some embodiments, the gene or gene product is associated with a protein phosphatase catalytic subunit (e.g., PPP6R3). In some embodiments, the gene or gene product is associated with the WDR11 pathway (e.g., WDR11, FAM91A1, AP1G1, AP1S1, AP1M1, AP1S3, or TBC1D23). In some embodiments, the gene or gene product is associated with retrograde transport of, for example, PI and / or PC from the Golgi apparatus to the endoplasmic reticulum (e.g., PITP). In some embodiments, the gene or gene product is associated with vesicle transport from late endosomes to the trans-Golgi network (e.g., STX16). In some embodiments, the gene or gene product is associated with the activity or recruitment of golgin, arfaptin, and / or Arf-GEF to the trans-Golgi network (e.g., ARL1). In some embodiments, the gene or gene product encodes a component of clathrin-dependent vesicles and / or is involved in AP1G1 / AP-1 mediated protein transport (eg, HEATR5B).

[0262] In some embodiments, the regulatory element is (a) a gene editing system that targets one or more sites within a gene or its regulatory elements, (b) a nucleic acid encoding one or more components of the gene editing system, or (c) a combination thereof. In some embodiments, the gene editing system is a CRISPR / Cas system, a zinc finger nuclease system, a TALEN system, or a meganuclease system.

[0263] In some embodiments, the gene editing system binds to a target sequence in an early (e.g., first, second, or third) exon or intron of a gene. In some embodiments, the gene editing system binds to a target sequence of a gene, and the target sequence is upstream of exon 4, e.g., in exon 1, exon 2, or exon 3. In some embodiments, the gene editing system binds to a target sequence in a later exon or intron of a gene. In some embodiments, the gene editing system binds to a target sequence of a gene, and the target sequence is downstream of the penultimate exon, e.g., the third to last exon, the penultimate exon, or the last exon. In some embodiments, the gene editing system is a CRISPR / Cas system comprising a guide RNA (gRNA) molecule comprising a targeting sequence that hybridizes to the target sequence of the gene. In some embodiments, the CRISPR / Cas system is a CRISPR / Cas9 system. In some embodiments, the CRISPR / Cas system is a CRISPR / Cas12a system.

[0264] In some embodiments, the regulatory element is a small interfering RNA (siRNA) or small hairpin (shRNA) specific to the gene, or a nucleic acid encoding the siRNA or shRNA. In some embodiments, the siRNA or shRNA comprises a nucleotide sequence complementary to the nucleotide sequence of an mRNA encoded by the gene. In some embodiments, the regulatory element is a guide RNA (gRNA) specific to the gene, or a nucleic acid encoding the gRNA. In some embodiments, the gRNA comprises a nucleotide sequence complementary to the nucleotide sequence of the gene.

[0265] In some embodiments, the modulator is a gene-specific antisense oligonucleotide (ASO) or a nucleic acid encoding the ASO. In some embodiments, the ASO comprises a nucleotide sequence complementary to the nucleotide sequence of an mRNA encoded by the gene.

[0266] In some embodiments, the modulator is a small molecule (e.g., a compound described herein, e.g., in Figure 7). In some embodiments, the small molecule is a protein degradation inducer.

[0267] In some embodiments, the modulator is a protein or peptide, or a nucleic acid encoding the protein or peptide. In some embodiments, the modulator is an antibody molecule (e.g., an scFv or sdAb). In some embodiments, the modulator is a dominant-negative binding partner of the protein encoded by the gene, or a nucleic acid encoding the dominant-negative binding partner. In some embodiments, the modulator is a dominant-negative variant (e.g., catalytically inactive) of the protein encoded by the gene, or a nucleic acid encoding the dominant-negative variant.

[0268] In some embodiments, the AAV particles comprise an AAV genome. In some embodiments, the AAV particles comprise AAV-like particles. In some embodiments, the AAV particles comprise a capsid. In some embodiments, the AAV particles have a serotype of AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, or a combination thereof. In some embodiments, the AAV particles are AAV2 particles. In some embodiments, the AAV particles are AAV9 particles.

[0269] In some embodiments, the AAV particles have a tropism for the CNS (e.g., AAV1, AAV2, AAV4, AAV5, AAV8, or AAV9). In some embodiments, the AAV particles have a tropism for the heart (e.g., AAV1, AAV8, or AAV9). In some embodiments, the AAV particles have a tropism for the kidney (e.g., AAV2). In some embodiments, the AAV particles have a tropism for the liver (e.g., AAV7, AAV8, or AAV9). In some embodiments, the AAV particles have a tropism for the lung (e.g., AAV4, AAV5, AAV6, or AAV9). In some embodiments, the AAV particles have a tropism for the pancreas (e.g., AAV8). In some embodiments, the AAV particles have a tropism for photoreceptor cells (e.g., AAV2, AAV5, or AAV8). In some embodiments, the AAV particle has tropism for the retinal pigment epithelium (RPE) (e.g., AAV1, AAV2, AAV4, AAV5, or AAV8). In some embodiments, the AAV particle has tropism for skeletal muscle (e.g., AAV1, AAV6, AAV7, AAV8, or AAV9).

[0270] In some embodiments, the AAV particles comprise a nucleotide sequence encoding a therapeutic protein, e.g., a protein associated with a disorder described herein. In some embodiments, the AAV particles comprise a nucleotide sequence encoding NGF, APOE2 (e.g., hAPOE2), TERT (e.g., hTERT), MAPT, GAD, AADC, NTN, GDNF, GCase, HTT, SMN, SMN2, SOD1, or C9orf72. In some embodiments, the AAV particles comprise a nucleotide sequence encoding a therapeutic nucleic acid, e.g., a nucleic acid targeting a nucleotide sequence encoding a protein associated with a disorder described herein.

[0271] In some embodiments, the methods involve administering to the subject multiple AAV transduction regulators or AAV regulators that regulate multiple genes or gene products associated with AAV transduction efficiency.

[0272] In another aspect, the disclosure provides a method for enhancing the efficacy of a therapy comprising an AAV genome or AAV particle, the method comprising administering an effective amount of an AAV transduction modulator to a subject in need thereof, thereby enhancing the efficacy of the therapy.

[0273] In some embodiments, the subject has never been administered or is not currently administered a therapy when the AAV transduction modulator is administered. In some embodiments, the subject has never been administered or is not currently administered a therapy when the AAV transduction modulator is administered. In some embodiments, the subject has been administered an AAV transduction modulator for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, or 1, 2, 3, 4, 5, or 6 months before the subject was administered the therapy. In some embodiments, the subject was administered an AAV transduction modulator within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, 1, 2, 3, 4, 5, or 6 months or less before being administered the therapy.

[0274] In some embodiments, the subject has been administered or is currently being administered a therapy when the AAV transduction modulator is administered, hi some embodiments, the subject has been administered a therapy for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, or 1, 2, 3, 4, 5, or 6 months prior to administration of the AAV transduction modulator. In some embodiments, the subject has been administered therapy for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, 1, 2, 3, 4, 5, or 6 months or less before the AAV transduction modulator was administered.

[0275] In some embodiments, the efficacy is increased by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90%, or at least 1-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 60-fold, 70-fold, 80-fold, 90-fold, 100-fold, 200-fold, 300-fold, 400-fold, 500-fold, 600-fold, 700-fold, 800-fold, 900-fold, or 1000-fold compared to the baseline. In some embodiments, the baseline level of efficacy is the level of efficacy in a subject who has not previously been administered an AAV transduction modulator. In some embodiments, the baseline level of efficacy is the level of efficacy before the subject is administered an AAV transduction modulator.

[0276] In some embodiments, the subject has a disorder or a symptom thereof, or is at risk of having a disorder or a symptom thereof. In some embodiments, the disorder is a neurodegenerative disorder. In some embodiments, the neurodegenerative disorder is Alzheimer's disease, Parkinson's disease, Huntington's disease, multiple sclerosis (MS), amyotrophic lateral sclerosis (ALS), or Batten disease. In some embodiments, the disorder is mild Alzheimer's disease, mild to moderate Alzheimer's disease, mild to severe Alzheimer's disease, early dementia, Parkinson's disease (e.g., idiopathic Parkinson's disease, bilateral idiopathic Parkinson's disease, intermediate to late stage Parkinson's disease), Huntington's disease (e.g., manifest Huntington's disease), SMA type 1, presymptomatic SMA, or amyotrophic lateral sclerosis (ALS) (e.g., familial ALS, SOD1-mutant ALS, or C9orf72-mutant ALS). In some embodiments, the disorder is an ocular disorder. In some embodiments, the ocular disorder is blindness, e.g., hereditary blindness or non-hereditary blindness. In some embodiments, the ocular disorder is Leber's congenital amaurosis, age-related macular degeneration, congenital choroideremia, or color vision deficiency. In some embodiments, the method reduces toxicity of a therapy, enhances efficacy of a therapy, or both.

[0277] In some embodiments, the modulator modulates (e.g., increases or decreases) a gene or gene product associated with AAV transduction efficiency, hi some embodiments, the gene or gene product is a mammalian (e.g., human) gene or gene product.

[0278] In some embodiments, the modulator inhibits a gene or gene product, e.g., a gene or gene product associated with decreased transduction efficiency of AAV particles, hi some embodiments, the modulator activates a gene or gene product, e.g., a gene or gene product associated with increased transduction efficiency of AAV particles.

[0279] In some embodiments, the gene or gene product is associated with increased transduction efficiency of AAV particles. In some embodiments, the gene or gene product is associated with increased transduction efficiency of AAV particles of a first serotype (e.g., AAV2), increased transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GPR108.

[0280] In some embodiments, the gene or gene product is associated with decreased transduction efficiency of AAV particles. In some embodiments, the gene or gene product is associated with decreased transduction efficiency of AAV particles of a first serotype (e.g., AAV2), decreased transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0281] In some embodiments, the gene or gene product, when modulated, increases the transduction efficiency of AAV particles, ie, the gene or gene product, when modulated, increases the transduction efficiency of AAV particles of a first serotype (e.g., AAV2), the transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both.

[0282] In some embodiments, the gene or gene product, when modulated, decreases the transduction efficiency of AAV particles, ie, the gene or gene product, when modulated, decreases the transduction efficiency of AAV particles of a first serotype (e.g., AAV2), the transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both.

[0283] In some embodiments, the gene product is RNA (e.g., mRNA). In some embodiments, the gene product is a protein. In some embodiments, the gene or gene product is selectively expressed in a target tissue (e.g., brain or liver). The following dependent claims describe AAV transduction regulators based on their mechanism. In some embodiments, the regulator alters (e.g., increases or decreases) the expression of a gene. In some embodiments, the regulator alters the structure of a gene. In some embodiments, the regulator alters (e.g., increases or decreases) the activity (e.g., enzymatic activity) of a gene product. In some embodiments, the regulator alters (e.g., increases or decreases) the level (e.g., abundance) of a gene product. In some embodiments, the regulator alters (e.g., increases or decreases) the stability of a gene product. In some embodiments, the regulator alters (e.g., increases or decreases) the transduction efficiency of AAV particles, e.g., as determined by an assay described herein (e.g., FACS analysis, e.g., as described in Example 1 or 2).

[0284] In some embodiments, the gene or gene product is AAV-R, GPR108, WDR11, or MRE11. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GPR108. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0285] In some embodiments, the method results in high gene regulation (e.g., gene editing) efficiency in a first tissue (e.g., at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 98%) and limited effect in a second tissue (e.g., 20%, 15%, 10%, 5%, 2%, or less gene regulation (e.g., gene editing) efficiency). In some embodiments, the method results in high regulation (e.g., gene editing) efficiency in the liver (e.g., at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 98%) and limited effect in skeletal muscle, bone marrow, or both (e.g., 20%, 15%, 10%, 5%, 2%, or less gene regulation (e.g., gene editing) efficiency).

[0286] In some embodiments, the modulator is administered intravenously.

[0287] In some embodiments, the modulator increases the transduction efficiency of AAV particles. In some embodiments, the transduction efficiency is increased by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90%, or at least 1-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 60-fold, 70-fold, 80-fold, 90-fold, 100-fold, 200-fold, 300-fold, 400-fold, 500-fold, 600-fold, 700-fold, 800-fold, 900-fold, or 1000-fold compared to a baseline level of transduction efficiency. In some embodiments, the modulator increases transduction by at least 10, 20, 30, 40, 50, or 60 viral copies per genome. In some embodiments, the regulatory factor induces transduction at a rate of at least 10 per μg of DNA. 3 , 10 4 , 10 5 , 10 6 , or 10 7 The viral copy number increases to .

[0288] In some embodiments, the modulator reduces the transduction efficiency of AAV particles. In some embodiments, the transduction efficiency is reduced by at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% compared to a baseline level of transduction efficiency. In some embodiments, the modulator reduces transduction to 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 viral copies per genome or less. In some embodiments, the modulator reduces transduction to 10 copies per μg of DNA or less. 2 , 10 3 , or 10 4 Reduce the viral copy number to:

[0289] In some embodiments, the baseline level of transduction efficiency is the level of transduction efficiency in cells that have not been contacted with an AAV transduction regulatory agent, hi some embodiments, the baseline level of transduction efficiency is the level of transduction efficiency before the cells are contacted with an AAV transduction regulatory agent.

[0290] In some embodiments, the gene or gene product increases the transduction efficiency of AAV2 particles, and optionally, the gene or gene product does not increase or does not substantially increase the transduction efficiency of AAV9 particles. In some embodiments, the gene or gene product is essential for transduction of AAV2 particles, and optionally, the gene or gene product is not essential for transduction of AAV9 particles. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GRP108.

[0291] In some embodiments, the gene or gene product is selected from EXT1, EXT2, NDST1, BCL10, OAF, PDCD10, LMO4, MALT1, ZNF644, CHUK, GLCE, EP300, ARID4B, RAB21, MED13, DHX15, WASHC5, IKBKB, USP24, HSPA14, CXXC1, UBE2A, INTS8, CDC42, NFKB1, SIN3A, USP7, ARF5, CARD10, JAK1, SLC35C2, PAXK1, ZC3H11A, FAM20B, FAM72A, DHX36, INTS12, RPRD1B, or a combination thereof.

[0292] In some embodiments, the gene or gene product is associated with endosomal sorting (e.g., RAB21, WASHC5, or USP7). In some embodiments, the gene or gene product is associated with vesicle-mediated transport (e.g., CDC42 or ARF5). In some embodiments, the gene or gene product is associated with NFKB signaling (e.g., BCL10, MALT1, NFKB1, IKBKB, CHUK, or CARD10). In some embodiments, the gene or gene product is associated with heparan sulfate biosynthesis (e.g., EXT1, EXT2, NDST1, GLCE, or FAM20B). In some embodiments, the gene or gene product is associated with H3K9 methylation (e.g., ZNF644). In some embodiments, the gene or gene product is associated with pre-mRNA processing (e.g., DHX15). In some embodiments, the gene or gene product is associated with transcription (e.g., LMO4, EP300, MED13, SIN3, ARID4B, ZC3H11A, CXXC1, RPRD1B, or UBE2A). In some embodiments, the gene or gene product is associated with the Integrator complex and / or RNA polymerase II function (e.g., INTS8 or INST12). In some embodiments, the gene or gene product is associated with DNA repair and / or AAV genome degradation (e.g., DHX36, ARID4B, UBE2A, or USP24). In some embodiments, the gene or gene product is associated with cell proliferation and / or apoptosis (e.g., PDCD10). In some embodiments, the gene or gene product is associated with spinocarpal tarsal synostosis (e.g., OAF). In some embodiments, the gene or gene product is associated with protein folding (e.g., HSPA14). In some embodiments, the gene or gene product is associated with helicase activity (e.g., DHX36). In some embodiments, the gene or gene product is associated with fucosylation of Notch and / or transport of GCP-fucose (eg, SLC35C2).

[0293] In some embodiments, the gene or gene product increases the transduction efficiency of AAV9 particles, and optionally, the gene or gene product does not increase or does not substantially increase the transduction efficiency of AAV2 particles. In some embodiments, the gene or gene product is essential for transduction of AAV9 particles, and optionally, the gene or gene product is not essential for transduction of AAV2 particles. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GRP108.

[0294] In some embodiments, the gene or gene product is selected from TMPRSS11B, HTT, SNRNP70, BRD7, DMXL1, RAB10, CNGA1, KLHDC3, CHP1, CYP3A5, ELOVL4, PNISR, ZCCHC14, AZGP1, TPST1, SC5D, ELP2, ELP3, IPO9, RAB14, WDR7, XRCC4, GDI2, or a combination thereof.

[0295] In some embodiments, the gene or gene product is associated with microtubule-mediated transport or vesicle function (e.g., HTT). In some embodiments, the gene or gene product is an ion channel (e.g., CNGA1). In some embodiments, the gene or gene product is associated with nuclear protein import (e.g., IPO9). In some embodiments, the gene or gene product is associated with O-sulfation of tyrosine residues within acidic motifs of polypeptides (e.g., TPST1). In some embodiments, the gene or gene product is associated with protection of viral RNA (e.g., ZCCHC14). In some embodiments, the gene or gene product is associated with RNA binding by AAV proteins (e.g., PNISR). In some embodiments, the gene or gene product is associated with calcium ion-regulated exocytosis (e.g., CHP1). In some embodiments, the gene or gene product is associated with intracellular transport (e.g., RAB10, RAB14, GDI2, WDR7, or DMXL1). In some embodiments, the gene or gene product is a subunit (e.g., a catalytic tRNA acetyltransferase subunit) of an elongator complex, e.g., an RNA polymerase (e.g., RNA polymerase II) (e.g., ELP2 or ELP3). In some embodiments, the gene or gene product is chromatin-associated (e.g., KLHDC3). In some embodiments, the gene or gene product is associated with cholesterol biosynthesis (e.g., SC5D).

[0296] In some embodiments, the gene or gene product increases the transduction efficiency of AAV2 and AAV9 particles. In some embodiments, the gene or gene product is essential for transduction of AAV2 and AAV9 particles. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GRP108.

[0297] In some embodiments, the gene or gene product is selected from KIAA0319L, BAMBI, TM9SF2, PHIP, DCLRE1C, VPS35, GPR108, CYREN, ACP2, F8A2, F8A1, F8A3, RBPJ, ATP2C1, ICMT, RABIF, IER3IP1, RBM10, SMG7, GTF2I, ELAVL1, MEPCE, RAB4A, IER3IP1, SAMD1, or a combination thereof.

[0298] In some embodiments, the gene or gene product is associated with influenza infection (e.g., ACP2). In some embodiments, the gene or gene product binds to an unmethylated CGI (e.g., SAMD1). In some embodiments, the gene or gene product is associated with intracellular vesicle trafficking (e.g., RABIF). In some embodiments, the gene or gene product is associated with post-translational modification of a cysteine ​​residue (e.g., a C-terminal cysteine ​​residue) in, for example, a target protein (e.g., ICMT). In some embodiments, the gene or gene product binds to an AAV capsid protein (e.g., KIAA0319L). In some embodiments, the gene or gene product is associated with inhibition of a TLR (e.g., TLR9) (e.g., GPR108). In some embodiments, the gene or gene product is associated with endosomal trafficking of, for example, AAV-R (e.g., VPS35). In some embodiments, the gene or gene product is a calcium ATPase pump (e.g., ATP2C1). In some embodiments, the gene or gene product is associated with Notch signaling (e.g., RBPJ). In some embodiments, the gene or gene product is associated with HSPG metabolism (e.g., TM9SF2). In some embodiments, the gene or gene product is associated with inhibition of NHEJ (e.g., CYREN). In some embodiments, the gene or gene product is associated with viral hairpin degradation (e.g., DCLRE1C). In some embodiments, the gene or gene product is associated with Glc transporter translocation, and optionally, the gene or gene product binds to insulin receptor substrate 1 protein (e.g., PHIP).

[0299] In some embodiments, the gene or gene product reduces the transduction efficiency of AAV2 particles, and optionally, the gene or gene product, when regulated, does not reduce or does not substantially reduce the transduction efficiency of AAV9 particles. In some embodiments, the gene or gene product inhibits or prevents transduction of AAV2 particles, and optionally, the gene or gene product does not inhibit or prevent transduction of AAV9 particles. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0300] In some embodiments, the gene or gene product is GREB1L, BIRC2, TYMSOS, MSL3, SIK3, GTF2H5, PIGW, ATRAID, PPP4R1, ZFC3H1, SETDB1, SMCHD1, TMEM123, UHRF1, CLUL1, SMAD5, SETX, STEEP1, DENND6A, RTN4RL2, MTMR9, STRADA, PSIP1, BMPR1A, HIKESHI, AP3M1, MEN1, MYL12B, CREB1, RAB12, SMTNL1, MRGBP, WTAP, SUMO2, TCN 1, ALDH3B1, ARL14EP, MYL12A, RHOD, PGAP2, EIF4A1, PIGN, DAXX, HDLBP, GOLGA1, SARNP, UBE2L6, TRIM49, SIK2, SOX4, OR6Q1, OR4D6, UNC93B1, CATSPERZ, PIGT, PYM1, MICOS13, RIN1, DOT1L, TRIM49C, MAPK20, COL8A1, FASN, KDM3B, PIGF, PIGA, PIGY, GPC3, TRAPPC2L, RAB31, ELP3, or a combination thereof.

[0301] In some embodiments, the gene or gene product is associated with retinoic acid receptor activity (e.g., GREB1L). In some embodiments, the gene or gene product is thymidylate synthetase (e.g., TYMSOS). In some embodiments, the gene or gene product is associated with chromatin remodeling (e.g., SMCHD1). In some embodiments, the gene or gene product is associated with histone H4 acetylation (e.g., MSL3). In some embodiments, the gene or gene product is associated with transcription and / or DNA repair (e.g., GTF2H5). In some embodiments, the gene or gene product is a histone methyltransferase (e.g., SETDB1). In some embodiments, the gene or gene product is associated with exosomal degradation of polyadenylated RNA (e.g., ZFC3H1). In some embodiments, the gene or gene product is associated with recruitment of histone deacetylase to DNA (e.g., UHRF1). In some embodiments, the gene or gene product is associated with oxidative stress-induced DNA double-strand break response (e.g., SETX). In some embodiments, the gene or gene product is associated with histone modification (e.g., MEN1). In some embodiments, the gene or gene product is associated with nucleosome / DNA interactions (e.g., MRGBP). In some embodiments, the gene or gene product is associated with GPI biosynthesis (e.g., PIGW, PIGN, PIGT, PIGF, PIGA, or PIGY). In some embodiments, the gene or gene product is associated with GPI anchor maturation (e.g., PGAP2). In some embodiments, the gene or gene product is associated with vesicle-mediated endocytosis (e.g., DENND6A, GOLGA1, MTMR9, GPC3, PPP4R1, RAB12, RAB31, RHOD, RIN1, TMEM123, or TRAPPC2L). In some embodiments, the gene or gene product is associated with clathrin-coated vesicle-mediated endocytosis (e.g., AP3M1). In some embodiments, the gene or gene product is related to a BMP receptor kinase (eg, SMAD5, BMPR1A, or CREB1).In some embodiments, the gene or gene product is associated with transcription (e.g., PSIP1). In some embodiments, the gene or gene product is associated with nuclear import of HSP70 proteins (e.g., HIKESHI). In some embodiments, the gene or gene product is associated with Ser / Thr kinases (e.g., SIK2 or SIK3). In some embodiments, the gene or gene product is associated with protein sumoylation (e.g., SUMO2, UBE2L6).

[0302] In some embodiments, the gene or gene product reduces the transduction efficiency of AAV9 particles, and optionally, the gene or gene product does not reduce or substantially reduce the transduction efficiency of AAV2 particles. In some embodiments, the gene or gene product inhibits or prevents transduction of AAV9 particles, and optionally, the gene or gene product does not inhibit or prevent transduction of AAV2 particles. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0303] In some embodiments, the gene or gene product is selected from AP2A1, AP2B1, TM9SF4, ACTR5, PTMA, PAPOLA, PDHA1, PDHB, SLC25A19, GAK, AUNIP, FCHO2, ACTB, LIPT1, UCHL5, INO80E, ECHS1, NELFB, EDC4, PRMT1, PDS5B, PELI3, FBXL20, SLC35A1, or a combination thereof.

[0304] In some embodiments, the gene or gene product binds to ATP, chaperone proteins, and / or clathrin (e.g., GAK). In some embodiments, the gene or gene product is associated with the trafficking of clathrin-coated vesicles (e.g., AP2B1 or AP2A1). In some embodiments, the gene or gene product is associated with clathrin-mediated endocytosis (e.g., FCHO2). In some embodiments, the gene or gene product is associated with vesicle trafficking (e.g., ACTB). In some embodiments, the gene or gene product is associated with the innate immune response (e.g., PELI3 or FBXL20). In some embodiments, the gene or gene product is associated with glucose metabolism (e.g., PDHB or PDHA1). In some embodiments, the gene or gene product is associated with DNA resection and / or homologous recombination, e.g., after DNA damage (e.g., AUNIP). In some embodiments, the gene or gene product is associated with DNA repair, e.g., after DNA damage (e.g., UCHL5, INO80E, PDS5B, ACTR5, or PRMT1). In some embodiments, the gene or gene product is associated with transport of CMP sialic acid from the cytosol to Golgi vesicles (e.g., SLC35A1). In some embodiments, the gene or gene product is associated with localization of polypeptides containing a glycine-rich transmembrane domain, e.g., to the cell surface (e.g., TM9SF4). In some embodiments, the gene or gene product is associated with synthesis of poly(A) tails (e.g., PAPOLA). In some embodiments, the gene or gene product is PTMA. In some embodiments, the gene or gene product is associated with elongation of mRNA by RNA polymerase II (e.g., NELFB). In some embodiments, the gene or gene product is associated with mRNA degradation (e.g., EDC4). In some embodiments, the gene or gene product encodes a mitochondrial lipoyltransferase (e.g., LIPT1). In some embodiments, the gene or gene product is associated with mitochondrial fatty acid β-oxidation (e.g., ECHS1). In some embodiments, the gene or gene product encodes the mitochondrial thiamine pyrophosphate carrier (e.g., SLC25A19).

[0305] In some embodiments, the gene or gene product reduces the transduction efficiency of AAV2 and AAV9 particles. In some embodiments, the gene or gene product inhibits or prevents transduction of AAV2 and AAV9 particles. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0306] In some embodiments, the gene or gene product is selected from the group consisting of PITPNB, PITP, FAM91A1, WDR11, AP1G1, AP1M1, AP1S1, AP1S3, HEATR5B, STX16, AP1B1, PIAS1, DENR, ARL1, ZFAT, TBC1D23, LIN37, RALGAPB, B3GNT2, ELOVL1, AP2B1, KIAA2013, PTEN, MCTS1, NBN, HELZ, SLC38A10, FBXL20, TGIF1, KDSR, CPD, CHD7, USP9X, SIMC1, TAF11, VAPA, MTMR6, RAB1B, SLF2, MRE11, VTI1A, MBOAT7, PPP6R3, or a combination thereof.

[0307] In some embodiments, the gene or gene product is associated with the long-chain FA elongation cycle (e.g., ELOVL1). In some embodiments, the gene or gene product is associated with lipoic acid biosynthesis (e.g., PIAS1). In some embodiments, the gene or gene product is associated with a protein phosphatase catalytic subunit (e.g., PPP6R3). In some embodiments, the gene or gene product is associated with the WDR11 pathway (e.g., WDR11, FAM91A1, AP1G1, AP1S1, AP1M1, AP1S3, or TBC1D23). In some embodiments, the gene or gene product is associated with retrograde transport of, for example, PI and / or PC from the Golgi apparatus to the endoplasmic reticulum (e.g., PITP). In some embodiments, the gene or gene product is associated with vesicle transport from late endosomes to the trans-Golgi network (e.g., STX16). In some embodiments, the gene or gene product is associated with the activity or recruitment of golgin, arfaptin, and / or Arf-GEF to the trans-Golgi network (e.g., ARL1). In some embodiments, the gene or gene product encodes a component of clathrin-dependent vesicles and / or is involved in AP1G1 / AP-1 mediated protein transport (eg, HEATR5B).

[0308] In some embodiments, the regulatory element is (a) a gene editing system that targets one or more sites within a gene or its regulatory elements, (b) a nucleic acid encoding one or more components of the gene editing system, or (c) a combination thereof. In some embodiments, the gene editing system is a CRISPR / Cas system, a zinc finger nuclease system, a TALEN system, or a meganuclease system.

[0309] In some embodiments, the gene editing system binds to a target sequence in an early (e.g., first, second, or third) exon or intron of a gene. In some embodiments, the gene editing system binds to a target sequence of a gene, and the target sequence is upstream of exon 4, e.g., in exon 1, exon 2, or exon 3. In some embodiments, the gene editing system binds to a target sequence in a later exon or intron of a gene. In some embodiments, the gene editing system binds to a target sequence of a gene, and the target sequence is downstream of the penultimate exon, e.g., the third to last exon, the penultimate exon, or the last exon. In some embodiments, the gene editing system is a CRISPR / Cas system comprising a guide RNA (gRNA) molecule comprising a targeting sequence that hybridizes to the target sequence of the gene. In some embodiments, the CRISPR / Cas system is a CRISPR / Cas9 system. In some embodiments, the CRISPR / Cas system is a CRISPR / Cas12a system.

[0310] In some embodiments, the regulatory element is a small interfering RNA (siRNA) or small hairpin (shRNA) specific to the gene, or a nucleic acid encoding the siRNA or shRNA. In some embodiments, the siRNA or shRNA comprises a nucleotide sequence complementary to the nucleotide sequence of an mRNA encoded by the gene. In some embodiments, the regulatory element is a guide RNA (gRNA) specific to the gene, or a nucleic acid encoding the gRNA. In some embodiments, the gRNA comprises a nucleotide sequence complementary to the nucleotide sequence of the gene.

[0311] In some embodiments, the modulator is a gene-specific antisense oligonucleotide (ASO) or a nucleic acid encoding the ASO. In some embodiments, the ASO comprises a nucleotide sequence complementary to the nucleotide sequence of an mRNA encoded by the gene.

[0312] In some embodiments, the modulator is a small molecule (e.g., a compound described herein, e.g., in Figure 7). In some embodiments, the small molecule is a protein degradation inducer.

[0313] In some embodiments, the modulator is a protein or peptide, or a nucleic acid encoding the protein or peptide. In some embodiments, the modulator is an antibody molecule (e.g., an scFv or sdAb). In some embodiments, the modulator is a dominant-negative binding partner of the protein encoded by the gene, or a nucleic acid encoding the dominant-negative binding partner. In some embodiments, the modulator is a dominant-negative variant (e.g., catalytically inactive) of the protein encoded by the gene, or a nucleic acid encoding the dominant-negative variant.

[0314] In some embodiments, the AAV particles comprise an AAV genome. In some embodiments, the AAV particles comprise AAV-like particles. In some embodiments, the AAV particles comprise a capsid. In some embodiments, the AAV particles have a serotype of AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, or a combination thereof. In some embodiments, the AAV particles are AAV2 particles. In some embodiments, the AAV particles are AAV9 particles.

[0315] In some embodiments, the AAV particles have a tropism for the CNS (e.g., AAV1, AAV2, AAV4, AAV5, AAV8, or AAV9). In some embodiments, the AAV particles have a tropism for the heart (e.g., AAV1, AAV8, or AAV9). In some embodiments, the AAV particles have a tropism for the kidney (e.g., AAV2). In some embodiments, the AAV particles have a tropism for the liver (e.g., AAV7, AAV8, or AAV9). In some embodiments, the AAV particles have a tropism for the lung (e.g., AAV4, AAV5, AAV6, or AAV9). In some embodiments, the AAV particles have a tropism for the pancreas (e.g., AAV8). In some embodiments, the AAV particles have a tropism for photoreceptor cells (e.g., AAV2, AAV5, or AAV8). In some embodiments, the AAV particle has tropism for the retinal pigment epithelium (RPE) (e.g., AAV1, AAV2, AAV4, AAV5, or AAV8). In some embodiments, the AAV particle has tropism for skeletal muscle (e.g., AAV1, AAV6, AAV7, AAV8, or AAV9).

[0316] In some embodiments, the AAV particles comprise a nucleotide sequence encoding a therapeutic protein, e.g., a protein associated with a disorder described herein. In some embodiments, the AAV particles comprise a nucleotide sequence encoding NGF, APOE2 (e.g., hAPOE2), TERT (e.g., hTERT), MAPT, GAD, AADC, NTN, GDNF, GCase, HTT, SMN, SMN2, SOD1, or C9orf72. In some embodiments, the AAV particles comprise a nucleotide sequence encoding a therapeutic nucleic acid, e.g., a nucleic acid targeting a nucleotide sequence encoding a protein associated with a disorder described herein.

[0317] In some embodiments, the methods involve administering to the subject multiple AAV transduction regulators or AAV regulators that regulate multiple genes or gene products associated with AAV transduction efficiency.

[0318] In one aspect, the disclosure features a method of producing a cell with increased AAV transduction efficiency, the method including contacting a cell with an AAV transduction modulator, thereby producing the cell.

[0319] In some embodiments, the cell is a brain cell, liver cell, spinal cord cell, dorsal root ganglion (DRG) cell, spleen cell, lymph node cell, kidney cell, lung cell, heart cell, muscle cell (e.g., skeletal muscle cell, thigh muscle cell), septum cell, bone marrow cell, or gonad cell. In some embodiments, the cell is a central nervous system (CNS) cell. In some embodiments, the CNS cell is an astrocyte, oligodendrocyte, microglia, or ependymal cell. In some embodiments, the cell is a brain cell. In some embodiments, the brain cell is a neuron or glial cell. In some embodiments, the cell is a DRG cell. In some embodiments, the cell is a hepatocyte. In some embodiments, the hepatocyte is a hepatic parenchymal cell, hepatic stellate cell, Kupffer cell, or hepatic sinusoidal endothelial cell.

[0320] In some embodiments, the cells are contacted with the AAV transduction regulator in vitro. In some embodiments, the cells are contacted with the AAV transduction regulator ex vivo. In some embodiments, the cells are contacted with the AAV transduction regulator in vivo.

[0321] In some embodiments, the cells are obtained from a subject. In some embodiments, the subject has a disorder or a symptom thereof, or is at risk of having a disorder or a symptom thereof. In some embodiments, the disorder is a neurodegenerative disorder. In some embodiments, the neurodegenerative disorder is Alzheimer's disease, Parkinson's disease, Huntington's disease, multiple sclerosis (MS), amyotrophic lateral sclerosis (ALS), or Batten disease. In some embodiments, the disorder is mild Alzheimer's disease, mild to moderate Alzheimer's disease, mild to severe Alzheimer's disease, early dementia, Parkinson's disease (e.g., idiopathic Parkinson's disease, bilateral idiopathic Parkinson's disease, intermediate to late stage Parkinson's disease), Huntington's disease (e.g., manifest Huntington's disease), SMA type 1, presymptomatic SMA, or amyotrophic lateral sclerosis (ALS) (e.g., familial ALS, SOD1-mutated ALS, or C9orf72-mutated ALS). In some embodiments, the disorder is an ocular disorder. In some embodiments, the ocular disorder is blindness, e.g., hereditary blindness or non-hereditary blindness. In some embodiments, the ocular disorder is Leber's congenital amaurosis, age-related macular degeneration, congenital choroideremia, or color vision deficiency. In some embodiments, the method reduces toxicity of a therapy, enhances efficacy of a therapy, or both.

[0322] In some embodiments, the modulator modulates (e.g., increases or decreases) a gene or gene product associated with AAV transduction efficiency, hi some embodiments, the gene or gene product is a mammalian (e.g., human) gene or gene product.

[0323] In some embodiments, the modulator inhibits a gene or gene product, e.g., a gene or gene product associated with decreased transduction efficiency of AAV particles, hi some embodiments, the modulator activates a gene or gene product, e.g., a gene or gene product associated with increased transduction efficiency of AAV particles.

[0324] In some embodiments, the gene or gene product is associated with increased transduction efficiency of AAV particles. In some embodiments, the gene or gene product is associated with increased transduction efficiency of AAV particles of a first serotype (e.g., AAV2), increased transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GPR108.

[0325] In some embodiments, the gene or gene product is associated with decreased transduction efficiency of AAV particles. In some embodiments, the gene or gene product is associated with decreased transduction efficiency of AAV particles of a first serotype (e.g., AAV2), decreased transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0326] In some embodiments, the gene or gene product, when modulated, increases the transduction efficiency of AAV particles, ie, the gene or gene product, when modulated, increases the transduction efficiency of AAV particles of a first serotype (e.g., AAV2), the transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both.

[0327] In some embodiments, the gene or gene product, when modulated, decreases the transduction efficiency of AAV particles, ie, the gene or gene product, when modulated, decreases the transduction efficiency of AAV particles of a first serotype (e.g., AAV2), the transduction efficiency of AAV particles of a second serotype (e.g., AAV9), or both.

[0328] In some embodiments, the gene product is RNA (e.g., mRNA). In some embodiments, the gene product is a protein. In some embodiments, the gene or gene product is selectively expressed in a target tissue (e.g., brain or liver). The following dependent claims describe AAV transduction regulators based on their mechanism. In some embodiments, the regulator alters (e.g., increases or decreases) the expression of a gene. In some embodiments, the regulator alters the structure of a gene. In some embodiments, the regulator alters (e.g., increases or decreases) the activity (e.g., enzymatic activity) of a gene product. In some embodiments, the regulator alters (e.g., increases or decreases) the level (e.g., abundance) of a gene product. In some embodiments, the regulator alters (e.g., increases or decreases) the stability of a gene product. In some embodiments, the regulator alters (e.g., increases or decreases) the transduction efficiency of AAV particles, e.g., as determined by an assay described herein (e.g., FACS analysis, e.g., as described in Example 1 or 2).

[0329] In some embodiments, the modulator increases the transduction efficiency of AAV particles. In some embodiments, the transduction efficiency is increased by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90%, or at least 1-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 60-fold, 70-fold, 80-fold, 90-fold, 100-fold, 200-fold, 300-fold, 400-fold, 500-fold, 600-fold, 700-fold, 800-fold, 900-fold, or 1000-fold compared to a baseline level of transduction efficiency. In some embodiments, the modulator increases transduction by at least 10, 20, 30, 40, 50, or 60 viral copies per genome. In some embodiments, the regulatory factor induces transduction at a rate of at least 10 per μg of DNA. 3 , 10 4 , 10 5 , 10 6 , or 10 7 The viral copy number increases to .

[0330] In some embodiments, the modulator reduces the transduction efficiency of AAV particles. In some embodiments, the transduction efficiency is reduced by at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% compared to a baseline level of transduction efficiency. In some embodiments, the modulator reduces transduction to 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 viral copies per genome or less. In some embodiments, the modulator reduces transduction to 10 copies per μg of DNA or less. 2 , 10 3 , or 10 4 Reduce the viral copy number to:

[0331] In some embodiments, the baseline level of transduction efficiency is the level of transduction efficiency in cells that have not been contacted with an AAV transduction regulatory agent, hi some embodiments, the baseline level of transduction efficiency is the level of transduction efficiency before the cells are contacted with an AAV transduction regulatory agent.

[0332] In some embodiments, the gene or gene product increases the transduction efficiency of AAV2 particles, and optionally, the gene or gene product does not increase or does not substantially increase the transduction efficiency of AAV9 particles. In some embodiments, the gene or gene product is essential for transduction of AAV2 particles, and optionally, the gene or gene product is not essential for transduction of AAV9 particles. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GRP108.

[0333] In some embodiments, the gene or gene product is selected from EXT1, EXT2, NDST1, BCL10, OAF, PDCD10, LMO4, MALT1, ZNF644, CHUK, GLCE, EP300, ARID4B, RAB21, MED13, DHX15, WASHC5, IKBKB, USP24, HSPA14, CXXC1, UBE2A, INTS8, CDC42, NFKB1, SIN3A, USP7, ARF5, CARD10, JAK1, SLC35C2, PAXK1, ZC3H11A, FAM20B, FAM72A, DHX36, INTS12, RPRD1B, or a combination thereof.

[0334] In some embodiments, the gene or gene product is associated with endosomal sorting (e.g., RAB21, WASHC5, or USP7). In some embodiments, the gene or gene product is associated with vesicle-mediated transport (e.g., CDC42 or ARF5). In some embodiments, the gene or gene product is associated with NFKB signaling (e.g., BCL10, MALT1, NFKB1, IKBKB, CHUK, or CARD10). In some embodiments, the gene or gene product is associated with heparan sulfate biosynthesis (e.g., EXT1, EXT2, NDST1, GLCE, or FAM20B). In some embodiments, the gene or gene product is associated with H3K9 methylation (e.g., ZNF644). In some embodiments, the gene or gene product is associated with pre-mRNA processing (e.g., DHX15). In some embodiments, the gene or gene product is associated with transcription (e.g., LMO4, EP300, MED13, SIN3, ARID4B, ZC3H11A, CXXC1, RPRD1B, or UBE2A). In some embodiments, the gene or gene product is associated with the Integrator complex and / or RNA polymerase II function (e.g., INTS8 or INST12). In some embodiments, the gene or gene product is associated with DNA repair and / or AAV genome degradation (e.g., DHX36, ARID4B, UBE2A, or USP24). In some embodiments, the gene or gene product is associated with cell proliferation and / or apoptosis (e.g., PDCD10). In some embodiments, the gene or gene product is associated with spinocarpal tarsal synostosis (e.g., OAF). In some embodiments, the gene or gene product is associated with protein folding (e.g., HSPA14). In some embodiments, the gene or gene product is associated with helicase activity (e.g., DHX36). In some embodiments, the gene or gene product is associated with fucosylation of Notch and / or transport of GCP-fucose (eg, SLC35C2).

[0335] In some embodiments, the gene or gene product increases the transduction efficiency of AAV9 particles, and optionally, the gene or gene product does not increase or does not substantially increase the transduction efficiency of AAV2 particles. In some embodiments, the gene or gene product is essential for transduction of AAV9 particles, and optionally, the gene or gene product is not essential for transduction of AAV2 particles. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GRP108.

[0336] In some embodiments, the gene or gene product is selected from TMPRSS11B, HTT, SNRNP70, BRD7, DMXL1, RAB10, CNGA1, KLHDC3, CHP1, CYP3A5, ELOVL4, PNISR, ZCCHC14, AZGP1, TPST1, SC5D, ELP2, ELP3, IPO9, RAB14, WDR7, XRCC4, GDI2, or a combination thereof.

[0337] In some embodiments, the gene or gene product is associated with microtubule-mediated transport or vesicle function (e.g., HTT). In some embodiments, the gene or gene product is an ion channel (e.g., CNGA1). In some embodiments, the gene or gene product is associated with nuclear protein import (e.g., IPO9). In some embodiments, the gene or gene product is associated with O-sulfation of tyrosine residues within acidic motifs of polypeptides (e.g., TPST1). In some embodiments, the gene or gene product is associated with protection of viral RNA (e.g., ZCCHC14). In some embodiments, the gene or gene product is associated with RNA binding by AAV proteins (e.g., PNISR). In some embodiments, the gene or gene product is associated with calcium ion-regulated exocytosis (e.g., CHP1). In some embodiments, the gene or gene product is associated with intracellular transport (e.g., RAB10, RAB14, GDI2, WDR7, or DMXL1). In some embodiments, the gene or gene product is a subunit (e.g., a catalytic tRNA acetyltransferase subunit) of an elongator complex, e.g., an RNA polymerase (e.g., RNA polymerase II) (e.g., ELP2 or ELP3). In some embodiments, the gene or gene product is chromatin-associated (e.g., KLHDC3). In some embodiments, the gene or gene product is associated with cholesterol biosynthesis (e.g., SC5D).

[0338] In some embodiments, the gene or gene product increases the transduction efficiency of AAV2 and AAV9 particles. In some embodiments, the gene or gene product is essential for transduction of AAV2 and AAV9 particles. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GRP108.

[0339] In some embodiments, the gene or gene product is selected from KIAA0319L, BAMBI, TM9SF2, PHIP, DCLRE1C, VPS35, GPR108, CYREN, ACP2, F8A2, F8A1, F8A3, RBPJ, ATP2C1, ICMT, RABIF, IER3IP1, RBM10, SMG7, GTF2I, ELAVL1, MEPCE, RAB4A, IER3IP1, SAMD1, or a combination thereof.

[0340] In some embodiments, the gene or gene product is associated with influenza infection (e.g., ACP2). In some embodiments, the gene or gene product binds to an unmethylated CGI (e.g., SAMD1). In some embodiments, the gene or gene product is associated with intracellular vesicle trafficking (e.g., RABIF). In some embodiments, the gene or gene product is associated with post-translational modification of a cysteine ​​residue (e.g., a C-terminal cysteine ​​residue) in, for example, a target protein (e.g., ICMT). In some embodiments, the gene or gene product binds to an AAV capsid protein (e.g., KIAA0319L). In some embodiments, the gene or gene product is associated with inhibition of a TLR (e.g., TLR9) (e.g., GPR108). In some embodiments, the gene or gene product is associated with endosomal trafficking of, for example, AAV-R (e.g., VPS35). In some embodiments, the gene or gene product is a calcium ATPase pump (e.g., ATP2C1). In some embodiments, the gene or gene product is associated with Notch signaling (e.g., RBPJ). In some embodiments, the gene or gene product is associated with HSPG metabolism (e.g., TM9SF2). In some embodiments, the gene or gene product is associated with inhibition of NHEJ (e.g., CYREN). In some embodiments, the gene or gene product is associated with viral hairpin degradation (e.g., DCLRE1C). In some embodiments, the gene or gene product is associated with Glc transporter translocation, and optionally, the gene or gene product binds to insulin receptor substrate 1 protein (e.g., PHIP).

[0341] In some embodiments, the gene or gene product reduces the transduction efficiency of AAV2 particles, and optionally, the gene or gene product, when regulated, does not reduce or does not substantially reduce the transduction efficiency of AAV9 particles. In some embodiments, the gene or gene product inhibits or prevents transduction of AAV2 particles, and optionally, the gene or gene product does not inhibit or prevent transduction of AAV9 particles. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0342] In some embodiments, the gene or gene product is GREB1L, BIRC2, TYMSOS, MSL3, SIK3, GTF2H5, PIGW, ATRAID, PPP4R1, ZFC3H1, SETDB1, SMCHD1, TMEM123, UHRF1, CLUL1, SMAD5, SETX, STEEP1, DENND6A, RTN4RL2, MTMR9, STRADA, PSIP1, BMPR1A, HIKESHI, AP3M1, MEN1, MYL12B, CREB1, RAB12, SMTNL1, MRGBP, WTAP, SUMO2, TCN 1, ALDH3B1, ARL14EP, MYL12A, RHOD, PGAP2, EIF4A1, PIGN, DAXX, HDLBP, GOLGA1, SARNP, UBE2L6, TRIM49, SIK2, SOX4, OR6Q1, OR4D6, UNC93B1, CATSPERZ, PIGT, PYM1, MICOS13, RIN1, DOT1L, TRIM49C, MAPK20, COL8A1, FASN, KDM3B, PIGF, PIGA, PIGY, GPC3, TRAPPC2L, RAB31, ELP3, or a combination thereof.

[0343] In some embodiments, the gene or gene product is associated with retinoic acid receptor activity (e.g., GREB1L). In some embodiments, the gene or gene product is thymidylate synthetase (e.g., TYMSOS). In some embodiments, the gene or gene product is associated with chromatin remodeling (e.g., SMCHD1). In some embodiments, the gene or gene product is associated with histone H4 acetylation (e.g., MSL3). In some embodiments, the gene or gene product is associated with transcription and / or DNA repair (e.g., GTF2H5). In some embodiments, the gene or gene product is a histone methyltransferase (e.g., SETDB1). In some embodiments, the gene or gene product is associated with exosomal degradation of polyadenylated RNA (e.g., ZFC3H1). In some embodiments, the gene or gene product is associated with recruitment of histone deacetylase to DNA (e.g., UHRF1). In some embodiments, the gene or gene product is associated with oxidative stress-induced DNA double-strand break response (e.g., SETX). In some embodiments, the gene or gene product is associated with histone modification (e.g., MEN1). In some embodiments, the gene or gene product is associated with nucleosome / DNA interactions (e.g., MRGBP). In some embodiments, the gene or gene product is associated with GPI biosynthesis (e.g., PIGW, PIGN, PIGT, PIGF, PIGA, or PIGY). In some embodiments, the gene or gene product is associated with GPI anchor maturation (e.g., PGAP2). In some embodiments, the gene or gene product is associated with vesicle-mediated endocytosis (e.g., DENND6A, GOLGA1, MTMR9, GPC3, PPP4R1, RAB12, RAB31, RHOD, RIN1, TMEM123, or TRAPPC2L). In some embodiments, the gene or gene product is associated with clathrin-coated vesicle-mediated endocytosis (e.g., AP3M1). In some embodiments, the gene or gene product is related to a BMP receptor kinase (eg, SMAD5, BMPR1A, or CREB1).In some embodiments, the gene or gene product is associated with transcription (e.g., PSIP1). In some embodiments, the gene or gene product is associated with nuclear import of HSP70 proteins (e.g., HIKESHI). In some embodiments, the gene or gene product is associated with Ser / Thr kinases (e.g., SIK2 or SIK3). In some embodiments, the gene or gene product is associated with protein sumoylation (e.g., SUMO2, UBE2L6).

[0344] In some embodiments, the gene or gene product reduces the transduction efficiency of AAV9 particles, and optionally, the gene or gene product does not reduce or substantially reduce the transduction efficiency of AAV2 particles. In some embodiments, the gene or gene product inhibits or prevents transduction of AAV9 particles, and optionally, the gene or gene product does not inhibit or prevent transduction of AAV2 particles. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0345] In some embodiments, the gene or gene product is selected from AP2A1, AP2B1, TM9SF4, ACTR5, PTMA, PAPOLA, PDHA1, PDHB, SLC25A19, GAK, AUNIP, FCHO2, ACTB, LIPT1, UCHL5, INO80E, ECHS1, NELFB, EDC4, PRMT1, PDS5B, PELI3, FBXL20, SLC35A1, or a combination thereof.

[0346] In some embodiments, the gene or gene product binds to ATP, chaperone proteins, and / or clathrin (e.g., GAK). In some embodiments, the gene or gene product is associated with the trafficking of clathrin-coated vesicles (e.g., AP2B1 or AP2A1). In some embodiments, the gene or gene product is associated with clathrin-mediated endocytosis (e.g., FCHO2). In some embodiments, the gene or gene product is associated with vesicle trafficking (e.g., ACTB). In some embodiments, the gene or gene product is associated with the innate immune response (e.g., PELI3 or FBXL20). In some embodiments, the gene or gene product is associated with glucose metabolism (e.g., PDHB or PDHA1). In some embodiments, the gene or gene product is associated with DNA resection and / or homologous recombination, e.g., after DNA damage (e.g., AUNIP). In some embodiments, the gene or gene product is associated with DNA repair, e.g., after DNA damage (e.g., UCHL5, INO80E, PDS5B, ACTR5, or PRMT1). In some embodiments, the gene or gene product is associated with transport of CMP sialic acid from the cytosol to Golgi vesicles (e.g., SLC35A1). In some embodiments, the gene or gene product is associated with localization of polypeptides containing a glycine-rich transmembrane domain, e.g., to the cell surface (e.g., TM9SF4). In some embodiments, the gene or gene product is associated with synthesis of poly(A) tails (e.g., PAPOLA). In some embodiments, the gene or gene product is PTMA. In some embodiments, the gene or gene product is associated with elongation of mRNA by RNA polymerase II (e.g., NELFB). In some embodiments, the gene or gene product is associated with mRNA degradation (e.g., EDC4). In some embodiments, the gene or gene product encodes a mitochondrial lipoyltransferase (e.g., LIPT1). In some embodiments, the gene or gene product is associated with mitochondrial fatty acid β-oxidation (e.g., ECHS1). In some embodiments, the gene or gene product encodes the mitochondrial thiamine pyrophosphate carrier (e.g., SLC25A19).

[0347] In some embodiments, the gene or gene product reduces the transduction efficiency of AAV2 and AAV9 particles. In some embodiments, the gene or gene product inhibits or prevents transduction of AAV2 and AAV9 particles. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0348] In some embodiments, the gene or gene product is selected from the group consisting of PITPNB, PITP, FAM91A1, WDR11, AP1G1, AP1M1, AP1S1, AP1S3, HEATR5B, STX16, AP1B1, PIAS1, DENR, ARL1, ZFAT, TBC1D23, LIN37, RALGAPB, B3GNT2, ELOVL1, AP2B1, KIAA2013, PTEN, MCTS1, NBN, HELZ, SLC38A10, FBXL20, TGIF1, KDSR, CPD, CHD7, USP9X, SIMC1, TAF11, VAPA, MTMR6, RAB1B, SLF2, MRE11, VTI1A, MBOAT7, PPP6R3, or a combination thereof.

[0349] In some embodiments, the gene or gene product is associated with the long-chain FA elongation cycle (e.g., ELOVL1). In some embodiments, the gene or gene product is associated with lipoic acid biosynthesis (e.g., PIAS1). In some embodiments, the gene or gene product is associated with a protein phosphatase catalytic subunit (e.g., PPP6R3). In some embodiments, the gene or gene product is associated with the WDR11 pathway (e.g., WDR11, FAM91A1, AP1G1, AP1S1, AP1M1, AP1S3, or TBC1D23). In some embodiments, the gene or gene product is associated with retrograde transport of, for example, PI and / or PC from the Golgi apparatus to the endoplasmic reticulum (e.g., PITP). In some embodiments, the gene or gene product is associated with vesicle transport from late endosomes to the trans-Golgi network (e.g., STX16). In some embodiments, the gene or gene product is associated with the activity or recruitment of golgin, arfaptin, and / or Arf-GEF to the trans-Golgi network (e.g., ARL1). In some embodiments, the gene or gene product encodes a component of clathrin-dependent vesicles and / or is involved in AP1G1 / AP-1 mediated protein transport (eg, HEATR5B).

[0350] In some embodiments, the regulatory element is (a) a gene editing system that targets one or more sites within a gene or its regulatory elements, (b) a nucleic acid encoding one or more components of the gene editing system, or (c) a combination thereof. In some embodiments, the gene editing system is a CRISPR / Cas system, a zinc finger nuclease system, a TALEN system, or a meganuclease system.

[0351] In some embodiments, the gene editing system binds to a target sequence in an early (e.g., first, second, or third) exon or intron of a gene. In some embodiments, the gene editing system binds to a target sequence of a gene, and the target sequence is upstream of exon 4, e.g., in exon 1, exon 2, or exon 3. In some embodiments, the gene editing system binds to a target sequence in a later exon or intron of a gene. In some embodiments, the gene editing system binds to a target sequence of a gene, and the target sequence is downstream of the penultimate exon, e.g., the third to last exon, the penultimate exon, or the last exon. In some embodiments, the gene editing system is a CRISPR / Cas system comprising a guide RNA (gRNA) molecule comprising a targeting sequence that hybridizes to the target sequence of the gene. In some embodiments, the CRISPR / Cas system is a CRISPR / Cas9 system. In some embodiments, the CRISPR / Cas system is a CRISPR / Cas12a system.

[0352] In some embodiments, the regulatory element is a small interfering RNA (siRNA) or small hairpin (shRNA) specific to the gene, or a nucleic acid encoding the siRNA or shRNA. In some embodiments, the siRNA or shRNA comprises a nucleotide sequence complementary to the nucleotide sequence of an mRNA encoded by the gene. In some embodiments, the regulatory element is a guide RNA (gRNA) specific to the gene, or a nucleic acid encoding the gRNA. In some embodiments, the gRNA comprises a nucleotide sequence complementary to the nucleotide sequence of the gene.

[0353] In some embodiments, the modulator is a gene-specific antisense oligonucleotide (ASO) or a nucleic acid encoding the ASO. In some embodiments, the ASO comprises a nucleotide sequence complementary to the nucleotide sequence of an mRNA encoded by the gene.

[0354] In some embodiments, the modulator is a small molecule (e.g., a compound described herein, e.g., in Figure 7). In some embodiments, the small molecule is a protein degradation inducer.

[0355] In some embodiments, the modulator is a protein or peptide, or a nucleic acid encoding the protein or peptide. In some embodiments, the modulator is an antibody molecule (e.g., an scFv or sdAb). In some embodiments, the modulator is a dominant-negative binding partner of the protein encoded by the gene, or a nucleic acid encoding the dominant-negative binding partner. In some embodiments, the modulator is a dominant-negative variant (e.g., catalytically inactive) of the protein encoded by the gene, or a nucleic acid encoding the dominant-negative variant.

[0356] In some embodiments, the AAV particles comprise an AAV genome. In some embodiments, the AAV particles comprise AAV-like particles. In some embodiments, the AAV particles comprise a capsid. In some embodiments, the AAV particles have a serotype of AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, or a combination thereof. In some embodiments, the AAV particles are AAV2 particles. In some embodiments, the AAV particles are AAV9 particles.

[0357] In some embodiments, the AAV particles have a tropism for the CNS (e.g., AAV1, AAV2, AAV4, AAV5, AAV8, or AAV9). In some embodiments, the AAV particles have a tropism for the heart (e.g., AAV1, AAV8, or AAV9). In some embodiments, the AAV particles have a tropism for the kidney (e.g., AAV2). In some embodiments, the AAV particles have a tropism for the liver (e.g., AAV7, AAV8, or AAV9). In some embodiments, the AAV particles have a tropism for the lung (e.g., AAV4, AAV5, AAV6, or AAV9). In some embodiments, the AAV particles have a tropism for the pancreas (e.g., AAV8). In some embodiments, the AAV particles have a tropism for photoreceptor cells (e.g., AAV2, AAV5, or AAV8). In some embodiments, the AAV particle has tropism for the retinal pigment epithelium (RPE) (e.g., AAV1, AAV2, AAV4, AAV5, or AAV8). In some embodiments, the AAV particle has tropism for skeletal muscle (e.g., AAV1, AAV6, AAV7, AAV8, or AAV9).

[0358] In some embodiments, the AAV particles comprise a nucleotide sequence encoding a therapeutic protein, e.g., a protein associated with a disorder described herein. In some embodiments, the AAV particles comprise a nucleotide sequence encoding NGF, APOE2 (e.g., hAPOE2), TERT (e.g., hTERT), MAPT, GAD, AADC, NTN, GDNF, GCase, HTT, SMN, SMN2, SOD1, or C9orf72. In some embodiments, the AAV particles comprise a nucleotide sequence encoding a therapeutic nucleic acid, e.g., a nucleic acid targeting a nucleotide sequence encoding a protein associated with a disorder described herein.

[0359] In some embodiments, the methods include contacting the cells with a plurality of AAV transduction regulators or AAV regulatory factors that regulate a plurality of genes or gene products associated with AAV transduction efficiency.

[0360] In another aspect, the present disclosure provides a cell produced by the methods described herein. In another aspect, the present disclosure provides a cell comprising an AAV regulatory element described herein and an AAV particle (e.g., an AAV particle described herein).

[0361] In another aspect, the present disclosure provides a pharmaceutical composition comprising an AAV modulator described herein and an AAV particle (e.g., an AAV particle described herein). In another aspect, the present disclosure provides a kit comprising an AAV modulator described herein and an AAV particle (e.g., an AAV particle described herein).

[0362] In another aspect, the disclosure provides AAV transduction modulators for use in methods of modulating the transduction efficiency of AAV particles in a cell or a subject, e.g., according to the methods described herein.

[0363] In another aspect, the disclosure provides an AAV transduction modulator for use in combination with an AAV genome or AAV particle in a method of treating a disorder in a subject, e.g., according to the methods described herein.

[0364] In another aspect, the disclosure provides an AAV transduction modulator for use in a method of conditioning a subject for a therapy comprising an AAV genome or AAV particles, e.g., according to the methods described herein.

[0365] In another aspect, the disclosure provides an AAV transduction modulator for use in a method of reducing toxicity of a therapy comprising an AAV genome or AAV particles in a subject, e.g., according to the methods described herein.

[0366] In another aspect, the disclosure provides an AAV transduction modulator for use in a method of increasing the efficacy of a therapy comprising an AAV genome or AAV particle in a subject, e.g., according to the methods described herein.

[0367] In another aspect, the disclosure provides for the use of an AAV transduction modulator in the manufacture of a medicament for modulating the transduction efficiency of AAV particles in a cell or a subject, e.g., according to the methods described herein.

[0368] In another aspect, the disclosure provides for the use of an AAV transduction modulator in the manufacture of a medicament in combination with an AAV genome or AAV particle to treat a disorder in a subject, e.g., according to the methods described herein.

[0369] In another aspect, the disclosure provides for the use of an AAV transduction modulator in the manufacture of a medicament for preparing a subject for therapy comprising an AAV genome or AAV particles, e.g., according to the methods described herein.

[0370] In another aspect, the disclosure provides for the use of an AAV transduction modulator in the manufacture of a medicament for reducing toxicity of a therapy comprising an AAV genome or AAV particles in a subject, e.g., according to the methods described herein.

[0371] In another aspect, the disclosure provides for the use of an AAV transduction modulator in the manufacture of a medicament for increasing the efficacy of a therapy comprising an AAV genome or AAV particles in a subject, e.g., according to the methods described herein.

[0372] In some embodiments of any of the above aspects, the gene or gene product is AAV-R, GPR108, WDR11, or MRE11. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GPR108. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0373] In some embodiments of any of the above aspects, the method results in high gene regulation (e.g., gene editing) efficiency in a first tissue (e.g., at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 98%) and limited effect in a second tissue (e.g., 20%, 15%, 10%, 5%, 2%, or less gene regulation (e.g., gene editing) efficiency). In some embodiments, the method results in high regulation (e.g., gene editing) efficiency in the liver (e.g., at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 98%) and limited effect in skeletal muscle, bone marrow, or both (e.g., 20%, 15%, 10%, 5%, 2%, or less gene regulation (e.g., gene editing) efficiency).

[0374] In some embodiments of any of the above aspects, the modulator is administered intravenously. [Brief explanation of the drawings]

[0375] [Figure 1-1] Figure 1: Figure 1A shows an exemplary pooled-screening next-generation sequencing (NGS) workflow for a genome-wide CRISPR / Cas9 screen for AAV transduction regulators. Figure 1B shows an overview of the AAV CRISPR screening method used to identify genetic regulators of AAV2 or AAV9 transduction in human (Huh-7) and mouse (AML-12) cells. [Figure 1-2] (As mentioned above.) [Figure 2-1]Figure 2: A series of diagrams showing the identification of common genes regulating AAV2 and AAV9 transduction. Results of a genome-wide CRISPR screen in Huh-7 cells using either AAV2 or AAV9 vectors are shown. Genes with a significant impact on transduction of each serotype are plotted based on their RSA score. Genes identified as significantly impacting AAV2 transduction are plotted on the Y-axis, and genes identified in the AAV9 screen are plotted on the X-axis. Data points highlighted in the upper right quadrants of A and C represent all genes shown to significantly promote (A) or inhibit (C) transduction of Huh-7 cells by both serotypes. The exact list of these host factors is shown in (B) (genes that promote AAV2 / AAV9 transduction) and (D) (genes that prevent AAV2 / AAV9 transduction). [Figure 2-2] (As mentioned above.) [Figure 2-3] (As mentioned above.) [Figure 2-4] (As mentioned above.) [Figure 3] Figure 1 shows a series of figures showing validation of selected hits across Huh-7 and SK-N-SH cell lines. AAV-R, GPR108, TM9SF2, WDR11, FAM91A1, and PITPNB genes were individually knocked down by CRISPR / Cas9 editing in Huh-7 cells (top panel) or SK-N-SH cells (bottom panel). After 21 days of cell selection, each modified cell line was transduced with either AAV2 or AAV9, and flow cytometry was performed on days 43 and 4 post-transduction, respectively. The MOI / titer of AAV used for transduction was based on historical titer curves, targeting approximately 20% GFP-positive cells for AAV2 and 60% GFP-positive cells for AAV9. The percentage of GFP-positive cells was calculated. [Figure 4-1]Figure 4: A series of diagrams showing genes promoting or preventing AAV9 transduction. Results of a genome-wide CRISPR screen in Huh-7 using either AAV2 or AAV9 vectors are shown. Genes that specifically increase or inhibit AAV9 transduction are highlighted in the lower right quadrants of graphs (A) and (C), respectively. The exact list of these host factors is shown in (B) (genes promoting AAV9 transduction) and (D) (genes preventing AAV9 transduction). [Figure 4-2] (As mentioned above.) [Figure 4-3] (As mentioned above.) [Figure 4-4] (As mentioned above.) [Figure 5-1] Figure 5: A series of diagrams showing genes that promote or prevent AAV2 transduction. Genes that specifically increase or inhibit AAV2 transduction are highlighted in the upper left quadrant of graphs A and C, respectively. The exact list of these host factors is shown in B (genes that promote AAV2 transduction) and D (genes that prevent AAV2 transduction). [Figure 5-2] (As mentioned above.) [Figure 5-3] (As mentioned above.) [Figure 5-4] (As mentioned above.) [Figure 6-1] Figure 6: A series of diagrams showing the identification of key host factors that promote or inhibit AAV9 transduction in mouse AML12 cells. Shown is a list of all mouse genes shown to significantly promote (A) or reduce (B) AAV9 transduction. Comparing the first 50 identified mouse genes to the results of a human screen with a similar vector identified few shared host factors between the two species. (C) Comparing the first 50 gene hits identified in the mouse screen with the results from a screen performed in Huh-7 cells revealed very limited overlap between the results. [Figure 6-2] (As mentioned above.) [Figure 6-3] (As mentioned above.) [Figure 7] This table shows the regulatory factors that can be used to increase or decrease the activity of candidate genes identified in CRISPR / AAV screens. A list of pharmacological compounds that target specific genes identified from CRISPR screens will be tested in vitro for their ability to regulate AAV transduction. Three concentrations (1 μM, 100 nM, 10 nM) will be first tested in Huh-7 cells, and then their effects will be evaluated on different cell lines and in vivo. [Figure 8-1] Figure 8: Schematic diagram showing a series of experiments to validate the impact of genes identified in a genome-wide CRISPR / Cas9 screen on AAV9 transduction in vivo using sgRNA-encapsulated nanoparticles. [Figure 8-2] (As mentioned above.) [Figure 9] Figure 1 shows the validation of mouse sgRNAs in the AML-12 cell line. The AAV-R, GPR108, WDR11, and MRE11 genes were individually knocked down in AML-12 by CRISPR / Cas9 editing. After 21 days of cell selection, each modified cell line was transduced with either AAV2 or AAV9, and fluorescence imaging was performed 4 days post-transduction. The vg / mL of AAV used for transduction targeted approximately 50% of GFP-positive cells. The percentage of GFP-positive cells was calculated and then compared to the parental, non-gene-edited AAV-treated cell line. For each gene, results for AAV2-transduced cells are shown on the left, and results for AAV9-transduced cells are shown on the right. [Figure 10] 1 shows a table showing the average percent gene editing efficiency in liver, skeletal muscle, and bone marrow. The percentage of editing is the average across animals for the gene of interest corresponding to the sgRNA / DLP used in the group. Data is not shown for the AAV-R, GPR108, WDR11, or MRE11 genes in animals not treated with the corresponding sgRNA / DLP, and no gene editing occurred. [Figure 11-1]Figure 11: A series of graphs showing the biodistribution of AAV in various tissues. The table shows a summary of viral copy number analysis in bone marrow, heart, liver, skeletal muscle, and spinal cord. Graph A presents the results as viral copies per µg of gDNA, while graph B presents the data as viral copies per diploid genome. [Figure 11-2] (As mentioned above.) [Figure 12-1] Figure 12: A series of graphs showing GFP mRNA expression in liver (A) and muscle (B) compared to sgSCR. Single muscle samples were available from the DLP1156 / sgAAV-R and DLP1156 / sgGPR108 groups. [Figure 12-2] (As mentioned above.) [Figure 13-1] Figure 13: A series of Western blots showing protein expression of AAV-R, MRE11, and GFP. Results of Western blot analysis of AAV-R (A), MRE11 (B), and GFP (C) in liver samples are shown. [Figure 13-2] (As mentioned above.) [Figure 13-3] (As mentioned above.) [Figure 14] 1 is a graph showing direct measurements of fluorescence intensity in liver protein extracts. Measurements of fluorescence intensity at 485 nm in liver homogenates are shown and are expressed in relative fluorescence units (RFU). [Figure 15]

[0023] Figure 1 is a series of diagrams showing immunohistochemical staining of GFP in liver tissue. Across the seven treatment groups in the study, all livers were examined for GFP expression using IHC. GFP staining is brown, and is very strong in animals treated with sgRNA scramble (Group 2). [Figure 16] This is a series of diagrams showing in situ hybridization to detect GFP antisense (AS) sequences in liver tissue. All animals were processed for GFP antisense sequences in the liver. Positive expression is designated in brown. This process captures single-cell GFP mRNA expression. This data reveals the diversity of mRNA expression levels per cell. [Figure 17] This is a series of diagrams showing in situ hybridization to detect GFP-sense (S) sequences in liver tissue. All animals were processed for GFP-sense sequences in the liver. Positive expression is designated in brown. This process captures single-cell GFP DNA expression. This data reveals the diversity of AAV transduction for each individual cell. [Figure 18-1] Figure 18: A series of graphs showing the percentage of GFP positive signal across a range of molecular localization endpoints. [Figure 18-2] (As mentioned above.) [Figure 18-3] (As mentioned above.) DETAILED DESCRIPTION OF THE INVENTION

[0376] This disclosure is based, at least in part, on a genome-wide CRISPR screen, which identified genes associated with AAV transduction. AAV is a platform for delivering gene therapy utilized across multiple therapeutic areas. Understanding transduction / tropism is important for both efficacy and safety, as ectopic expression or transgene overexpression by AAV-based gene therapy can result in cytotoxicity in some cases (e.g., liver, DRG neurons, cardiomyocytes, RPE). Cell tropism depends on the expression of AAV receptors and coreceptors, but also on additional pathways controlling, for example, intracellular trafficking, capsid nuclear translocation, uncoating, and episome formation. Further understanding of these mechanisms will inform the translational potential of preclinical studies and provide mitigation strategies to limit or prevent targeting and expression in suspect or "undesirable" cell types. The studies described in this disclosure aim to understand the key cellular processes that influence AAV transduction across serotypes, cell types, and species. Screens using AAV2 and AAV9 in human cells identified top hits important for infection, while highlighting genes that are specifically affected by either AAV2 or AAV9 transduction. Based on the identified genes, AAV transduction modulators can be designed, manufactured, and used in AAV-based gene therapy to treat various disorders.

[0377] definition Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs.

[0378] The terms "a" and "an" refer to one or to more than one (i.e., to at least one) of the grammatical referent of the article. By way of example, "an element" means one element or more than one element.

[0379] The term "about," when referring to a measurable value, such as an amount, length of time, or the like, is meant to encompass a ±20% variation, or in some cases a ±10% variation, or in some cases a ±5% variation, or in some cases a ±1% variation, or in some cases a ±0.1% variation from the specified value, as such variations are appropriate for practicing the methods of the present disclosure.

[0380] As used herein, the term "antibody" refers to a protein or polypeptide sequence derived from an immunoglobulin molecule that specifically binds to an antigen. Antibodies can be polyclonal or monoclonal, multi-chain or single-chain, or intact immunoglobulins, and can be derived from natural or recombinant sources. An antibody can be a tetramer of immunoglobulin molecules.

[0381] The term "antibody fragment" refers to at least a portion of an antibody that retains the ability to specifically interact with an epitope of an antigen (e.g., by binding, steric hindrance, stabilization / destabilization, spatial distribution). Examples of antibody fragments include, but are not limited to, Fab, Fab', F(ab'), Fv fragments, scFv antibody fragments, disulfide-linked Fv (sdFv), Fd fragments consisting of VH and CH1 domains, linear antibodies, single domain antibodies (either VL or VH) such as sdAb, camelid VHH domains, multispecific antibodies formed from antibody fragments such as bivalent fragments comprising two Fab fragments linked by a disulfide bridge at the hinge region, and isolated CDRs or other epitope-binding fragments of antibodies. Antigen-binding fragments can also be incorporated into single domain antibodies, maxibodies, minibodies, nanobodies, intrabodies, diabodies, triabodies, tetrabodies, v-NARs, and bis-scFvs (see, e.g., Hollinger and Hudson, Nature Biotechnology 23:1126-1136, 2005). Antigen-binding fragments can also be grafted onto scaffolds based on polypeptides such as fibronectin type III (Fn3) (see U.S. Pat. No. 6,703,199, which describes fibronectin polypeptide minibodies).

[0382] The term "scFv" refers to a fusion protein comprising at least one antibody fragment comprising a light chain variable region and at least one antibody fragment comprising a heavy chain variable region, wherein the light chain variable region and the heavy chain variable region are contiguously joined, for example, via a synthetic linker, e.g., a short flexible polypeptide linker, and can be expressed as a single-chain polypeptide, wherein the scFv retains the specificity of the intact antibody from which it is derived. Unless otherwise specified, as used herein, an scFv can have the VL and VH variable regions in either order, e.g., with respect to the N-terminus and C-terminus of the polypeptide, and can comprise a VL-linker-VH or a VH-linker-VL.

[0383] As used herein, the term "antibody molecule" or "binding domain" refers to a protein, e.g., an immunoglobulin chain or fragment thereof, comprising at least one immunoglobulin variable domain sequence. The term "antibody molecule" or "binding domain" encompasses antibodies and antibody fragments. In one embodiment, an antibody molecule is a multispecific antibody molecule, e.g., it comprises a plurality of immunoglobulin variable domain sequences, where a first immunoglobulin variable domain sequence of the plurality has binding specificity for a first epitope and a second immunoglobulin variable domain sequence of the plurality has binding specificity for a second epitope. In one embodiment, a multispecific antibody molecule is a bispecific antibody molecule. Bispecific antibodies have specificity for no more than two antigens. A bispecific antibody molecule is characterized by a first immunoglobulin variable domain sequence that has binding specificity for a first epitope and a second immunoglobulin variable domain sequence that has binding specificity for a second epitope.

[0384] The term "antibody heavy chain" refers to the larger of the two types of polypeptide chains present in antibody molecules in their naturally occurring conformations, which usually determines the class to which the antibody belongs.

[0385] The term "antibody light chain" refers to the smaller of the two types of polypeptide chains present in antibody molecules in their naturally occurring conformations. Kappa (κ) and lambda (λ) light chains refer to the two major antibody light chain isotypes.

[0386] The term "cancer" refers to a disease characterized by the rapid and uncontrolled growth of abnormal cells. Cancer cells can spread locally or to other parts of the body through the bloodstream and lymphatic system. Examples of various cancers are described herein and include, but are not limited to, breast cancer, prostate cancer, ovarian cancer, cervical cancer, skin cancer, pancreatic cancer, colorectal cancer, kidney cancer, liver cancer, brain cancer, lymphoma, leukemia, lung cancer, etc. Preferred cancers treated by the methods described herein include multiple myeloma, Hodgkin's lymphoma, or non-Hodgkin's lymphoma.

[0387] The terms "tumor" and "cancer" are used interchangeably herein, e.g., both terms encompass solid and liquid, e.g., diffuse or circulating, tumors. As used herein, the term "cancer" or "tumor" includes pre-cancerous as well as malignant cancers and tumors.

[0388] The terms "combination" or "in combination with" are not intended to imply that the therapies or therapeutic agents must be administered at the same time and / or formulated to be delivered together, although their delivery methods are within the scope described herein. Therapeutics in the combination can be administered simultaneously with, before, or after one or more other additional therapies or therapeutic agents. Therapeutics or therapeutic protocols can be administered in any order. Generally, each agent will be administered at a dose and / or time schedule determined for that agent. It will further be understood that additional therapeutic agents utilized in the combination can be administered together in a single composition or separately in different compositions. Generally, it is expected that additional therapeutic agents utilized in the combination will be utilized at levels that do not exceed the levels at which they are utilized individually. In some embodiments, the levels utilized in the combination will be lower than those utilized individually.

[0389] In some embodiments, the additional therapeutic agent is administered in a therapeutic or sub-therapeutic amount. In certain embodiments, the concentration of the second therapeutic agent required to achieve inhibition, e.g., growth inhibition, is lower when the second therapeutic agent is administered in combination with the first therapeutic agent than when the second therapeutic agent is administered individually. In certain embodiments, the concentration of the first therapeutic agent required to achieve inhibition, e.g., growth inhibition, is lower when the first therapeutic agent is administered in combination with the second therapeutic agent than when the first therapeutic agent is administered individually. In certain embodiments, the concentration of the second therapeutic agent required to achieve inhibition, e.g., growth inhibition, in combination therapy is lower than the therapeutic amount of the second therapeutic agent as a monotherapy, e.g., 10-20%, 20-30%, 30-40%, 40-50%, 50-60%, 60-70%, 70-80%, or 80-90% lower. In certain embodiments, in a combination therapy, the concentration of the first therapeutic agent required to achieve inhibition, e.g., growth inhibition, is lower than the therapeutic amount of the first therapeutic agent as a monotherapy, e.g., 10-20%, 20-30%, 30-40%, 40-50%, 50-60%, 60-70%, 70-80%, or 80-90% lower.

[0390] The terms "inhibition," "inhibitor," or "antagonist" include a decrease in a particular parameter, e.g., activity, of a given molecule. For example, at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99%, or more inhibition of activity is included within the term. Thus, inhibition need not be 100%.

[0391] The terms "activation," "activator," or "agonist" include an increase in a particular parameter, e.g., activity, of a given molecule. For example, an increase in activity of at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more, or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10-fold or more is encompassed by the term.

[0392] The term "derived from" indicates a relationship between a first molecule and a second molecule. It generally refers to the structural similarity between the first and second molecules and does not imply or include any process or source limitations on the origin of the first molecule from the second molecule.

[0393] The term "encode" refers to the inherent property of a specific nucleotide sequence in a polynucleotide, such as a gene, cDNA, or mRNA, to serve as a template for the synthesis of other polymers and macromolecules in biological processes having either a defined nucleotide sequence (e.g., rRNA, tRNA, and mRNA) or a defined amino acid sequence and the biological properties resulting therefrom. Thus, a gene, cDNA, or RNA encodes a protein when the protein is produced in a cell or other biological system by transcription and translation of mRNA corresponding to that gene. Both the coding strand, whose nucleotide sequence is identical to the mRNA sequence and usually provided in a sequence listing, and the non-coding strand used as a template for transcription of the gene or cDNA can be referred to as encoding the protein or other product of that gene or cDNA.

[0394] Unless otherwise specified, a "nucleotide sequence encoding an amino acid sequence" includes all nucleotide sequences that are degenerate versions of each other and that encode the same amino acid sequence. The phrase nucleotide sequence encoding a protein or RNA can also include introns, to the extent that the nucleotide sequence encoding the protein may, in some versions, contain one or more introns.

[0395] The terms "effective amount" or "therapeutically effective amount" are used interchangeably herein and refer to an amount of a compound, formulation, material, or composition as described herein that is effective to achieve a particular biological result.

[0396] The term "endogenous" refers to any material that is derived from or produced within an organism, cell, tissue, or system.

[0397] The term "exogenous" refers to any substance introduced from or produced outside an organism, cell, tissue or system.

[0398] The term "expression" refers to the transcription and / or translation of a particular nucleotide sequence driven by a promoter.

[0399] The term "expression vector" refers to a vector containing a recombinant polynucleotide comprising expression control sequences operably linked to a nucleotide sequence to be expressed. An expression vector contains sufficient cis-acting elements for expression; other elements for expression can be supplied by the host cell or in an in vitro expression system. Expression vectors include all those known in the art, including cosmids, plasmids (e.g., naked or contained in liposomes), and viruses (e.g., lentiviruses, retroviruses, adenoviruses, and adeno-associated viruses) that incorporate the recombinant polynucleotide.

[0400] The term "isolated" means altered or removed from the natural state. For example, a nucleic acid or peptide naturally occurring in a living animal is not "isolated," but the same nucleic acid or peptide partially or completely separated from the coexisting materials of its natural state is "isolated." An isolated nucleic acid or protein can exist in a substantially purified form, or can exist in a non-native environment, such as, for example, a host cell.

[0401] The term "operably linked" or "transcriptional regulation" refers to a functional linkage between a regulatory sequence and a heterologous nucleic acid sequence that results in expression of the latter. For example, a first nucleic acid sequence is operably linked with a second nucleic acid sequence when the first nucleic acid sequence is placed into a functional relationship with the second nucleic acid sequence. For example, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. Operably linked DNA sequences can be contiguous with each other and, for example, in the same reading frame, as necessary to link two protein coding regions.

[0402] The term "parenteral" administration of an immunogenic composition includes, for example, subcutaneous (sc), intravenous (iv), intramuscular (im) or intrasternal injection, intratumoral or infusion techniques.

[0403] The term "nucleic acid" or "polynucleotide" refers to deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) and polymers thereof in either single- or double-stranded form. Unless specifically limited, the term encompasses nucleic acids containing known analogs of natural nucleotides that have similar binding properties as the reference nucleic acid and are metabolized in a manner similar to naturally occurring nucleotides. Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions), alleles, orthologs, SNPs, and complementary sequences, as well as the sequence explicitly indicated. In particular, degenerate codon substitutions can be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and / or deoxyinosine residues (Batzer et al., Nucleic Acid Res. 19:5081 (1991); Ohtsuka et al., J. Biol. Chem. 260:2605-2608 (1985); and Rossolini et al., Mol. Cell. Probes 8:91-98 (1994)).

[0404] The terms "peptide," "polypeptide," and "protein" are used interchangeably and refer to compounds composed of amino acid residues covalently linked by peptide bonds. A protein or peptide must contain at least two amino acids, and there is no limit to the maximum number of amino acids that a protein or peptide sequence may contain. A polypeptide includes any peptide or protein containing two or more amino acids linked to each other by peptide bonds. As used herein, the term refers to both short chains, e.g., commonly referred to in the art as peptides, oligopeptides, and oligomers, and longer chains, which are commonly referred to in the art as proteins and exist in many varieties. "Polypeptide" includes, inter alia, biologically active fragments, substantially homologous polypeptides, oligopeptides, homodimers, heterodimers, variants of polypeptides, modified polypeptides, derivatives, analogs, and fusion proteins. A polypeptide includes natural peptides, recombinant peptides, or combinations thereof.

[0405] The term "promoter" refers to a DNA sequence recognized by the synthetic machinery of the cell, or introduced synthetic machinery, necessary to initiate the specific transcription of a polynucleotide sequence.

[0406] The term "promoter / regulatory sequence" refers to a nucleic acid sequence required for expression of a gene product operably linked to the promoter / regulatory sequence. In some cases, this sequence may be the core promoter sequence; in other cases, this sequence may also include an enhancer sequence and other regulatory elements required for expression of the gene product. The promoter / regulatory sequence may, for example, be one that expresses the gene product in a tissue-specific manner.

[0407] As used herein, "transient" refers to expression of a non-integrated transgene for a period of hours, days, or weeks, which is shorter than the period of expression of the gene when integrated into the genome of the host cell or contained within a stable plasmid replicon.

[0408] As used herein, the terms "treat," "treatment," and "treating" refer to a reduction or amelioration of the progression, severity, and / or duration of a proliferative disorder, or an amelioration of one or more symptoms (preferably one or more discernible symptoms) of a proliferative disorder, resulting from the administration of one or more therapies (e.g., one or more therapeutic agents, such as a CAR of the present disclosure). In certain embodiments, the terms "treat," "treatment," and "treating" refer to an improvement in at least one measurable physical parameter of a proliferative disorder, such as tumor growth, which is not necessarily discernible by the patient. In other embodiments, the terms "treat," "treatment," or "treating" refer to an inhibition of the progression of a proliferative disorder, either physically, e.g., by stabilization of a discernible symptom, physiologically, e.g., by stabilization of a physical parameter, or both. In other embodiments, the terms "treat," "treatment," or "treating" refer to a reduction or stabilization of tumor size or the number of cancerous cells.

[0409] The term "subject" is intended to include living organisms suitable for AAV-based gene therapy, eg, mammals, humans.

[0410] The term "therapeutic" as used herein means treatment. A therapeutic effect is achieved by the reduction, suppression, amelioration, or eradication of a disease state.

[0411] The term "prophylaxis" as used herein means the prevention or prophylactic treatment of a disease or disease state.

[0412] The terms "transfected" or "transformed" or "transduced" refer to the method by which exogenous nucleic acid is transferred or introduced into a host cell. A "transfected" or "transformed" or "transduced" cell is one that has been transfected, transformed, or transduced with exogenous nucleic acid. The cell includes the primary subject cell and its progeny.

[0413] The term "specifically binds" refers to an antibody or ligand that recognizes and binds to a binding partner (e.g., a tumor antigen) protein present in a sample, but that does not substantially recognize or bind to other molecules in the sample.

[0414] Ranges: Throughout this disclosure, various aspects of the present disclosure may be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as inflexibly limiting the scope of the present disclosure. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values ​​within that range. For example, description of a range such as 1 to 6 should be considered to have specifically disclosed subranges such as 1 to 3, 1 to 4, 1 to 5, 2 to 4, 2 to 6, 3 to 6, etc., as well as individual numerical values ​​within that range, e.g., 1, 2, 2.7, 3, 4, 5, 5.3, and 6. As another example, a range such as 95-99% identity includes those with 95%, 96%, 97%, 98%, or 99% identity, and includes subranges such as 96-99%, 96-98%, 96-97%, 97-99%, 97-98%, and 98-99% identity. This applies regardless of the breadth of the scope.

[0415] The term "gene editing system" is used herein to refer to a system, e.g., one or more molecules, that induces and achieves one or more nucleic acid alterations, e.g., deletions, at or near a site of genomic DNA targeted by the system. Gene editing systems are known in the art and are described in more detail below.

[0416] A "dominant-negative" gene product or protein is one that interferes with the function of another gene product or protein. The other affected gene product may be identical to or different from the dominant-negative protein. Dominant-negative gene products may be in a variety of forms, including truncations, full-length proteins or fragments thereof with point mutations, or fusions of full-length wild-type or mutant proteins or fragments thereof with other proteins. The level of inhibition observed may be very low. For example, this may require a large excess of the dominant-negative protein relative to the functional protein or proteins involved in the process to see an effect. The effect may be difficult to see under typical biological assay conditions. As used herein, the term "AAV particle" refers to a viral particle derived from or containing one or more nucleic acid sequences from an adeno-associated virus serotype, including, but not limited to, AAV-1, AAV-2, AAV-3, AAV-4, AAV-5, AAV-6, AAV-7, AAV-8, or AAV-9 viral vector. AAV particles can have one or more AAV wild-type genes, e.g., the rep and / or cap genes, deleted in whole or in part, while retaining, for example, functional flanking inverted terminal repeat ("ITR") sequences. In some embodiments, AAV particles can be packaged into a protein shell or capsid, e.g., comprising one or more AAV capsid proteins, which can provide a vehicle for delivering vector nucleic acid to the nucleus of a target cell. In some embodiments, AAV particles contain one or more AAV ITR sequences (e.g., AAV2 ITR sequences). In some embodiments, AAV particles contain one or more AAV ITR sequences (e.g., AAV2 ITR sequences) but do not contain any additional viral nucleic acid sequences. In some embodiments, components of the AAV particle (e.g., ITRs) are derived from a different serotype virus than the rAAV capsid (e.g., an AAV particle may contain ITRs from AAV2, or an AAV particle may be packaged in an AAV9 capsid).Embodiments of these viral particle constructs are provided, for example, in International Publication No. WO 2019 / 094253 (PCT / US2018 / 058744), which is incorporated by reference in its entirety.

[0417] Exemplary Genes and Gene Products Associated with AAV Transduction Efficiency The present disclosure provides genes and gene products associated with AAV transduction efficiency. The AAV regulatory factors described herein can be designed, manufactured, and used based on the discovery of these genes and gene products. In some cases, the AAV regulatory factors described herein modulate (e.g., increase or decrease) the activity and / or level of a gene or gene product (e.g., described herein) associated with AAV transduction efficiency. In some cases, exemplary genes or gene products associated with AAV transduction efficiency are depicted in any of Figures 2A-6B.

[0418] In some embodiments, the gene or gene product is AAV-R, GPR108, WDR11, or MRE11. In some embodiments, the gene or gene product is AAV-R. In some embodiments, the gene or gene product is GPR108. In some embodiments, the gene or gene product is WDR11. In some embodiments, the gene or gene product is MRE11.

[0419] Exemplary Genes and Gene Products That Specifically Promote AAV2 Transduction In some embodiments, the gene or gene product increases the transduction efficiency of AAV2 particles. In certain embodiments, the gene or gene product does not increase, or does not substantially increase, the transduction efficiency of AAV9 particles. In some embodiments, the gene or gene product is essential for transduction of AAV2 particles. In certain embodiments, the gene or gene product is not essential for transduction of AAV9 particles.

[0420] Exemplary genes or gene products include, but are not limited to, EXT1, EXT2, NDST1, BCL10, OAF, PDCD10, LMO4, MALT1, ZNF644, CHUK, GLCE, EP300, ARID4B, RAB21, MED13, DHX15, WASHC5, IKBKB, USP24, HSPA14, CXXC1, UBE2A, INTS8, CDC42, NFKB1, SIN3A, USP7, ARF5, CARD10, JAK1, SLC35C2, PAXK1, ZC3H11A, FAM20B, FAM72A, DHX36, INTS12, and RPRD1B.

[0421] In some embodiments, the gene or gene product is associated with endosomal sorting (e.g., RAB21, WASHC5, or USP7). In some embodiments, the gene or gene product is associated with vesicle-mediated transport (e.g., CDC42 or ARF5). In some embodiments, the gene or gene product is associated with NFKB signaling (e.g., BCL10, MALT1, NFKB1, IKBKB, CHUK, or CARD10). In some embodiments, the gene or gene product is associated with heparan sulfate biosynthesis (e.g., EXT1, EXT2, NDST1, GLCE, or FAM20B). In some embodiments, the gene or gene product is associated with H3K9 methylation (e.g., ZNF644). In some embodiments, the gene or gene product is associated with pre-mRNA processing (e.g., DHX15). In some embodiments, the gene or gene product is associated with transcription (e.g., LMO4, EP300, MED13, SIN3, ARID4B, ZC3H11A, CXXC1, RPRD1B, or UBE2A). In some embodiments, the gene or gene product is associated with the Integrator complex and / or RNA polymerase II function (e.g., INTS8 or INST12). In some embodiments, the gene or gene product is associated with DNA repair and / or AAV genome degradation (e.g., DHX36, ARID4B, UBE2A, or USP24). In some embodiments, the gene or gene product is associated with cell proliferation and / or apoptosis (e.g., PDCD10). In some embodiments, the gene or gene product is associated with spinocarpal tarsal synostosis (e.g., OAF). In some embodiments, the gene or gene product is associated with protein folding (e.g., HSPA14). In some embodiments, the gene or gene product is associated with helicase activity (e.g., DHX36). In some embodiments, the gene or gene product is associated with fucosylation of Notch and / or transport of GCP-fucose (eg, SLC35C2).

[0422] Exemplary Genes and Gene Products That Specifically Enhance AAV9 Transduction In some embodiments, the gene or gene product increases the transduction efficiency of AAV9 particles. In certain embodiments, the gene or gene product does not increase, or does not substantially increase, the transduction efficiency of AAV2 particles. In some embodiments, the gene or gene product is essential for transduction of AAV9 particles. In certain embodiments, the gene or gene product is not essential for transduction of AAV2 particles.

[0423] Exemplary genes and gene products include, but are not limited to, TMPRSS11B, HTT, SNRNP70, BRD7, DMXL1, RAB10, CNGA1, KLHDC3, CHP1, CYP3A5, ELOVL4, PNISR, ZCCHC14, AZGP1, TPST1, SC5D, ELP2, ELP3, IPO9, RAB14, WDR7, XRCC4, and GDI2.

[0424] In some embodiments, the gene or gene product is associated with microtubule-mediated transport or vesicle function (e.g., HTT). In some embodiments, the gene or gene product is an ion channel (e.g., CNGA1). In some embodiments, the gene or gene product is associated with nuclear protein import (e.g., IPO9). In some embodiments, the gene or gene product is associated with O-sulfation of tyrosine residues within acidic motifs of polypeptides (e.g., TPST1). In some embodiments, the gene or gene product is associated with protection of viral RNA (e.g., ZCCHC14). In some embodiments, the gene or gene product is associated with RNA binding by AAV proteins (e.g., PNISR). In some embodiments, the gene or gene product is associated with calcium ion-regulated exocytosis (e.g., CHP1). In some embodiments, the gene or gene product is associated with intracellular transport (e.g., RAB10, RAB14, GDI2, WDR7, or DMXL1). In some embodiments, the gene or gene product is a subunit (e.g., a catalytic tRNA acetyltransferase subunit) of an elongator complex, e.g., an RNA polymerase (e.g., RNA polymerase II) (e.g., ELP2 or ELP3). In some embodiments, the gene or gene product is chromatin-associated (e.g., KLHDC3). In some embodiments, the gene or gene product is associated with cholesterol biosynthesis (e.g., SC5D).

[0425] Exemplary Genes and Gene Products Facilitating AAV2 and AAV9 Transduction In some embodiments, the gene or gene product increases the transduction efficiency of AAV2 and AAV9 particles. In some embodiments, the gene or gene product is essential for transduction of AAV2 and AAV9 particles.

[0426] Exemplary genes and gene products include, but are not limited to, KIAA0319L, BAMBI, TM9SF2, PHIP, DCLRE1C, VPS35, GPR108, CYREN, ACP2, F8A2, F8A1, F8A3, RBPJ, ATP2C1, ICMT, RABIF, IER3IP1, RBM10, SMG7, GTF2I, ELAVL1, MEPCE, RAB4A, IER3IP1, and SAMD1.

[0427] In some embodiments, the gene or gene product is associated with influenza infection (e.g., ACP2). In some embodiments, the gene or gene product binds to an unmethylated CGI (e.g., SAMD1). In some embodiments, the gene or gene product is associated with intracellular vesicle trafficking (e.g., RABIF). In some embodiments, the gene or gene product is associated with post-translational modification of a cysteine ​​residue (e.g., a C-terminal cysteine ​​residue) in, for example, a target protein (e.g., ICMT). In some embodiments, the gene or gene product binds to an AAV capsid protein (e.g., KIAA0319L). In some embodiments, the gene or gene product is associated with inhibition of a TLR (e.g., TLR9) (e.g., GPR108). In some embodiments, the gene or gene product is associated with endosomal trafficking of, for example, AAV-R (e.g., VPS35). In some embodiments, the gene or gene product is a calcium ATPase pump (e.g., ATP2C1). In some embodiments, the gene or gene product is associated with Notch signaling (e.g., RBPJ). In some embodiments, the gene or gene product is associated with HSPG metabolism (e.g., TM9SF2). In some embodiments, the gene or gene product is associated with inhibition of NHEJ (e.g., CYREN). In some embodiments, the gene or gene product is associated with viral hairpin degradation (e.g., DCLRE1C). In some embodiments, the gene or gene product is associated with Glc transporter translocation. In particular embodiments, the gene or gene product binds to insulin receptor substrate 1 protein (e.g., PHIP).

[0428] Exemplary Genes and Gene Products that Specifically Inhibit AAV2 Transduction In some embodiments, the gene or gene product reduces the transduction efficiency of AAV2 particles. In certain embodiments, the gene or gene product, when regulated, does not reduce or does not substantially reduce the transduction efficiency of AAV9 particles. In some embodiments, the gene or gene product inhibits or prevents transduction of AAV2 particles. In certain embodiments, the gene or gene product does not inhibit or prevent transduction of AAV9 particles.

[0429] Exemplary genes and gene products include GREB1L, BIRC2, TYMSOS, MSL3, SIK3, GTF2H5, PIGW, ATRAID, PPP4R1, ZFC3H1, SETDB1, SMCHD1, TMEM123, UHRF1, CLUL1, SMAD5, SETX, STEEP1, PSIP1, DENND6A, RTN4RL2, MTMR9, STRADA, PSIP1, BMPR1A, HIKESHI, AP3M1, MEN1, MYL12B, CREB1, RAB12, SMTNL1, MR These include, but are not limited to, GBP, WTAP, SUMO2, TCN1, ALDH3B1, ARL14EP, MYL12A, RHOD, PGAP2, EIF4A1, PIGN, DAXX, HDLBP, GOLGA1, SARNP, UBE2L6, TRIM49, SIK2, SOX4, OR6Q1, OR4D6, UNC93B1, CATSPERZ, PIGT, PYM1, MICOS13, RIN1, DOT1L, TRIM49C, MAPK20, COL8A1, FASN, KDM3B, and ELP3.

[0430] In some embodiments, the gene or gene product is associated with receptor activity of retinoic acid (eg, GREB1L).

[0431] In some embodiments, the gene or gene product is thymidylate synthetase (e.g., TYMSOS). In some embodiments, the gene or gene product is associated with chromatin remodeling (e.g., SMCHD1). In some embodiments, the gene or gene product is associated with histone H4 acetylation (e.g., MSL3). In some embodiments, the gene or gene product is associated with transcription and / or DNA repair (e.g., GTF2H5). In some embodiments, the gene or gene product is a histone methyltransferase (e.g., SETDB1). In some embodiments, the gene or gene product is associated with exosomal degradation of polyadenylated RNA (e.g., ZFC3H1). In some embodiments, the gene or gene product is associated with recruitment of histone deacetylase to DNA (e.g., UHRF1). In some embodiments, the gene or gene product is associated with oxidative stress-induced DNA double-strand break response (e.g., SETX). In some embodiments, the gene or gene product is associated with histone modification (e.g., MEN1). In some embodiments, the gene or gene product is associated with nucleosome / DNA interactions (e.g., MRGBP). In some embodiments, the gene or gene product is associated with GPI biosynthesis (e.g., PIGW, PIGN, PIGT, PIGF, PIGA, or PIGY). In some embodiments, the gene or gene product is associated with GPI anchor maturation (e.g., PGAP2). In some embodiments, the gene or gene product is associated with vesicle-mediated endocytosis (e.g., DENND6A, GOLGA1, MTMR9, GPC3, PPP4R1, RAB12, RAB31, RHOD, RIN1, TMEM123, or TRAPPC2L). In some embodiments, the gene or gene product is associated with clathrin-coated vesicle-mediated endocytosis (e.g., AP3M1). In some embodiments, the gene or gene product is associated with BMP receptor kinase (e.g., SMAD5, BMPR1A, or CREB1). In some embodiments, the gene or gene product is associated with transcription (e.g., PSIP1).In some embodiments, the gene or gene product is associated with nuclear import of HSP70 proteins (e.g., HIKESHI). In some embodiments, the gene or gene product is associated with Ser / Thr kinases (e.g., SIK2 or SIK3). In some embodiments, the gene or gene product is associated with protein sumoylation (e.g., SUMO2, UBE2L6).

[0432] Exemplary Genes and Gene Products that Specifically Inhibit AAV9 Transduction In some embodiments, the gene or gene product reduces the transduction efficiency of AAV9 particles. In certain embodiments, the gene or gene product does not reduce or does not substantially reduce the transduction efficiency of AAV2 particles. In some embodiments, the gene or gene product inhibits or prevents transduction of AAV9 particles. In certain embodiments, the gene or gene product does not inhibit or prevent transduction of AAV2 particles.

[0433] Exemplary genes and gene products include, but are not limited to, AP2A1, AP2B1, TM9SF4, ACTR5, PTMA, PAPOLA, PDHA1, PDHB, SLC25A19, GAK, AUNIP, FCHO2, ACTB, LIPT1, UCHL5, INO80E, ECHS1, NELFB, EDC4, PRMT1, PDS5B, PELI3, FBXL20, and SLC35A1.

[0434] In some embodiments, the gene or gene product binds to ATP, chaperone proteins, and / or clathrin (e.g., GAK). In some embodiments, the gene or gene product is associated with the trafficking of clathrin-coated vesicles (e.g., AP2B1 or AP2A1). In some embodiments, the gene or gene product is associated with clathrin-mediated endocytosis (e.g., FCHO2). In some embodiments, the gene or gene product is associated with vesicle trafficking (e.g., ACTB). In some embodiments, the gene or gene product is associated with the innate immune response (e.g., PELI3 or FBXL20). In some embodiments, the gene or gene product is associated with glucose metabolism (e.g., PDHB or PDHA1). In some embodiments, the gene or gene product is associated with DNA resection and / or homologous recombination, e.g., after DNA damage (e.g., AUNIP). In some embodiments, the gene or gene product is associated with DNA repair, e.g., after DNA damage (e.g., UCHL5, INO80E, PDS5B, ACTR5, or PRMT1). In some embodiments, the gene or gene product is associated with transport of CMP sialic acid from the cytosol to Golgi vesicles (e.g., SLC35A1). In some embodiments, the gene or gene product is associated with localization of polypeptides containing a glycine-rich transmembrane domain, e.g., to the cell surface (e.g., TM9SF4). In some embodiments, the gene or gene product is associated with synthesis of poly(A) tails (e.g., PAPOLA). In some embodiments, the gene or gene product is PTMA. In some embodiments, the gene or gene product is associated with elongation of mRNA by RNA polymerase II (e.g., NELFB). In some embodiments, the gene or gene product is associated with mRNA degradation (e.g., EDC4). In some embodiments, the gene or gene product encodes a mitochondrial lipoyltransferase (e.g., LIPT1). In some embodiments, the gene or gene product is associated with mitochondrial fatty acid β-oxidation (e.g., ECHS1). In some embodiments, the gene or gene product encodes the mitochondrial thiamine pyrophosphate carrier (e.g., SLC25A19).

[0435] Exemplary Genes and Gene Products that Specifically Inhibit AAV2 and AAV9 Transduction In some embodiments, the gene or gene product reduces the transduction efficiency of AAV2 and AAV9 particles, hi some embodiments, the gene or gene product inhibits or prevents transduction of AAV2 and AAV9 particles.

[0436] Exemplary genes and gene products include, but are not limited to, PITPNB, PITP, FAM91A1, WDR11, AP1G1, AP1M1, AP1S1, AP1S3, HEATR5B, STX16, AP1B1, PIAS1, DENR, ARL1, ZFAT, TBC1D23, LIN37, RALGAPB, B3GNT2, ELOVL1, AP2B1, KIAA2013, PTEN, MCTS1, NBN, HELZ, SLC38A10, FBXL20, TGIF1, KDSR, CPD, CHD7, USP9X, SIMC1, TAF11, VAPA, MTMR6, RAB1B, SLF2, MRE11, VTI1A, MBOAT7, and PPP6R3.

[0437] In some embodiments, the gene or gene product is associated with the long-chain FA elongation cycle (e.g., ELOVL1). In some embodiments, the gene or gene product is associated with lipoic acid biosynthesis (e.g., PIAS1). In some embodiments, the gene or gene product is associated with a protein phosphatase catalytic subunit (e.g., PPP6R3). In some embodiments, the gene or gene product is associated with the WDR11 pathway (e.g., WDR11, FAM91A1, AP1G1, AP1S1, AP1M1, AP1S3, or TBC1D23). In some embodiments, the gene or gene product is associated with retrograde transport of, for example, PI and / or PC from the Golgi apparatus to the endoplasmic reticulum (e.g., PITP). In some embodiments, the gene or gene product is associated with vesicle transport from late endosomes to the trans-Golgi network (e.g., STX16). In some embodiments, the gene or gene product is associated with the activity or recruitment of golgin, arfaptin, and / or Arf-GEF to the trans-Golgi network (e.g., ARL1). In some embodiments, the gene or gene product encodes a component of clathrin-dependent vesicles and / or is involved in AP1G1 / AP-1 mediated protein transport (eg, HEATR5B).

[0438] As used herein, the terms "EXT1" and "exosin glycosyltransferase 1" refer to the gene EXT1 and the gene product encoded by the EXT1 gene. It is also known as "EXT," "LGS," "TTV," "LGCR," or "TRPS2." In the human genome, EXT1 is located on chromosome 8. Exemplary human EXT1 transcript sequences include, but are not limited to, the following NCBI reference sequences: NM_000127, GI:1777425437. Exemplary human EXT1 protein sequences include, but are not limited to, the following NCBI reference sequences: NP_000118.2 GI:46370066 and Q16394.2 GI:20141422. Without wishing to be bound by theory, in some embodiments, EXT1 is believed to be involved in the biosynthesis of heparan sulfate.

[0439] As used herein, the terms "EXT2" and "exosin glycosyltransferase 2" refer to the gene EXT2 and the gene product encoded by the EXT2 gene, which is also known as "SOTV" or "SSMS." In the human genome, EXT2 is located on chromosome 11. Exemplary human EXT2 transcript sequences include, but are not limited to, the following NCBI reference sequences: NM_207122.2 GI:1779821707, NM_000401.3 GI:296010872, NM_001178083.3 GI:1889698717, NM_001389628.1 GI:1953526484, NM_001389630.1 GI:1953526464, XM_024448383.1 GI:1370458892, and XM_011519950.1 GI:767965526. Exemplary human EXT2 protein sequences include, but are not limited to, the following NCBI reference sequences: NM_207122.2 GI:1779821707, NM_000401.3 GI:296010872, NM_001178083.3 GI:1889698717, NM_001389628.1 GI:1953526484, NM_001389630.1 GI:1953526464, XM_024448383.1 GI:1370458892, and XM_011519950.1 GI:767965526. NP_997005.1 GI:46370069, NP_000392.3 GI:296010873, NP_001171554.1 GI:296010875, NP_001376557.1 GI:1953526485, NP_001376559.1 GI:1953526465, XP_011518252.1 GI:767965527, and XP_024304151.1 GI:1370458893. Without being bound by theory, in some embodiments, EXT2 is believed to be involved in heparan sulfate biosynthesis.

[0440] As used herein, the terms "NDST1," "N-deacetylase and N-sulfotransferase 1," refer to the gene NDST1 and the gene product encoded by the NDST1 gene. It is also known as "HSST," "MRT46," or "NST1." In the human genome, NDST1 is located on chromosome 5. Exemplary human NDST1 transcript sequences include, but are not limited to, the following NCBI reference sequences: NM_001543.5 GI:1519314701 and NM_001301063.2 GI:1676319301. Exemplary human NDST1 protein sequences include, but are not limited to, the following NCBI reference sequences: NP_001534.1 GI:4505351 and NP_001287992.1 GI:666637969. Without wishing to be bound by theory, in some embodiments, NDST1 is believed to be involved in the biosynthesis of heparan sulfate.

[0441] As used herein, the terms "BCL10" and "BCL10 immune signaling adaptor" refer to the gene BCL10 and the gene product encoded by the BCL10 gene. It is also known as "CARMEN," "CIPER," "IMD37," "c-E10," or "mE10." In the human genome, BCL10 is located on chromosome 1. Exemplary human BCL10 transcript sequences include, but are not limited to, the following NCBI reference sequences: NM_003921.5 GI:1388742734, NM_001320715.2 GI:1676440509, XM_011542398.2 GI:1034563099, XM_011542397.3 GI:1370455114, and XM_011542399.2 GI:1034563100. Exemplary human BCL10 protein sequences include, but are not limited to, the following NCBI reference sequences: NP_003912.1 GI:4502379, NP_001307644.1 GI:1002639417, XP_011540699.1 GI:767906661, XP_011540700.1 GI:767906663, and XP_011540701.1 GI:767906666. Without wishing to be bound by theory, in some embodiments, BCL10 is thought to be involved in NFKB signaling.

[0442] As used herein, the terms "OAF" and "out at first homolog" refer to the gene OAF and the gene product encoded by the OAF gene, which is also known as "NS5ATP13TP2." In the human genome, OAF is located on chromosome 11. Exemplary human OAF transcript sequences include, but are not limited to, the following NCBI reference sequence: NM_178507.4. Exemplary human OAF protein sequences include, but are not limited to, the following NCBI reference sequence: NP_848602.1.

[0443] As used herein, the terms "PDCD10" and "programmed cell death 10" refer to the gene PDCD10 and the gene product encoded by the PDCD10 gene, which is also known as "CCM3" or "TFAR15." In the human genome, PDCD10 is located on chromosome 3. Exemplary human PDCD10 transcript sequences include, but are not limited to, the following NCBI reference sequences: NM_007217.4 GI:1520687835, NM_145859.2 GI:1890280404, NM_145860.2 GI:1890262549, XM_005247086.5 GI:1370483092, XM_005247087.5 GI:1370483093, XM_005247088.4 GI:1370483087, XM_006713485.4 GI:1370483091, GI:1370483089, XM_017005644.2 GI:1370483090, XM_017005645.2 GI:1370483096, XM_024453329.1 GI:1370483094, XM_024453330.1 GI:1370483097, and XM_024453331.1 GI:1370483099. Exemplary human PDCD10 protein sequences include, but are not limited to, the following NCBI reference sequences:NP_009148.2 GI:20127517, NP_665858.1 GI:22538792, NP_665859.1 GI:22538794, XP_005247143.1 GI:530373856, XP_005247144.1 GI:530373858, XP_005247145.1 GI:530373860, XP_006713548.1 GI:578807020, XP_011510670.1 GI:767925584, XP_011510671.1 GI:767925586,XP_016861133.1 GI:1034630983, XP_016861134.1 GI:1034630989, XP_024309097.1 GI:1370483095, XP_024309098.1 GI:1370483098, and XP_024309099.1 GI:1370483100. Without wishing to be bound by theory, in some embodiments, PDCD10 is thought to be involved in cell proliferation and / or apoptosis.

[0444] As used herein, the terms "LMO4" and "LIM domain only 4" refer to the gene LMO4 and the gene product encoded by the LMO4 gene. It is also known as "LIM-only 4 protein," "LMO-4," or "LIM domain transcription factor 4." In the human genome, LMO4 is located on chromosome 1. Exemplary human LMO4 transcript sequences include, but are not limited to, the following NCBI reference sequences: NM_006769.4 GI:1519245993 and NM_001369491.1 GI:1610577010. Exemplary human LMO4 protein sequences include, but are not limited to, the following NCBI reference sequences: NP_006760.1 GI:5803072 and NP_001356420.1 GI:1610577011. Without wishing to be bound by theory, in some embodiments, LMO4 is believed to be associated with transcription.

[0445] As used herein, the terms "MALT1" and "MALT1 paracaspase" refer to the gene MALT1 and the gene product encoded by the MALT1 gene, which is also known as "IMD12," "MLT1," "MLT," or "PCASP1." In the human genome, MALT1 is located on chromosome 18. Exemplary human MALT1 transcript sequences include, but are not limited to, the following NCBI reference sequences: NM_006785.4 GI:1393270561, NM_173844.3 GI:1675049238, XM_011525794.1 GI:767998143, XR_001753134.1 GI:1034603353, XR_001753135.1 GI:1034603354, and XR_001753136.1 GI:1034603355. Exemplary human MALT1 protein sequences include, but are not limited to, the following NCBI reference sequences: NP_006776.1 GI:5803078, NP_776216.1 GI:27886566, and XP_011524096.1 GI:767998144. Without being bound by theory, in some embodiments, MALT1 is thought to be involved in NFKB signaling.

[0446] As used herein, the terms "ZNF644" and "zinc finger protein 644" refer to the gene ZNF644 and the gene product encoded by the ZNF644 gene, which is also known as "BM-005," "MYP21," "ZEP-2," or "NatF." In the human genome, ZNF644 is located on chromosome 1. Exemplary human ZNF644 transcript sequences include, but are not limited to, the following NCBI reference sequences: NM_201269.3 GI:1519312808, NM_016620.4 GI:1890327857, NM_032186.5 GI:1890272283, XM_005271257.5 GI:1370454817, XM_005271260.5 GI:1370454818, XM_011542258.3 GI:1370454816, XM_011542259.3 GI:1370454819, GI:1370454822, XM_017002487.2 GI:1370454821, XM_017002488.2 GI:1370454823, XM_017002489.2 GI:1370454824, XM_017002490.2 GI:1370454825, XM_017002491.2 GI:1370454826, XM_017002492.2 GI:1370454827, XM_017002493.2 GI:1370454828, and XM_017002494.1 GI:1034562409. Exemplary human ZNF644 protein sequences include, but are not limited to, the following NCBI reference sequences:NP_958357.1 GI:41152093, NP_057704.2 GI:41152095, NP_115562.3 GI:41152091, XP_005271314.1 GI:530363442, XP_005271317.1 GI:530363448, XP_011540560.1 GI:767906309, XP_011540561.1 GI:767906312, XP_011540562.1 GI:767906314, XP_011540563.1 GI:767906317,XP_016857976.1 GI:1034562395, XP_016857977.1 GI:1034562398, XP_016857978.1 GI:1034562400, XP_016857979.1 GI:1034562402, XP_016857980.1 GI:1034562404, XP_016857981.1 GI:1034562406, XP_016857982.1 GI:1034562408, and XP_016857983.1 GI:1034562410. Without being bound by theory, in some embodiments, ZNF644 is thought to be involved in the methylation of H3K9.

[0447] As used herein, the term "CHUK" and "component of inhibitor of nuclear factor kappa B kinase complex" refer to the gene CHUK and the gene product encoded by the CHUK gene, which is also known as "BPS2," "IKBKA," "IKK-alpha," "IKK1," "IKKA," "NFKBIKA," or "TCF16." In the human genome, CHUK is located on chromosome 10. Exemplary human CHUK transcript sequences include, but are not limited to, the following NCBI reference sequences: NM_001278.5 GI:1519245267, NM_001320928.2 GI:1890265705, XM_017015611.1 GI:1034566253, XM_017015612.1 GI:1034566256, XM_017015613.1 GI:1034566258, XR_001747010.1 GI:1034566255, and XR_001747011.1 GI:1034566260. Exemplary human CHUK protein sequences include, but are not limited to, the following NCBI reference sequences: NP_001269.3 GI:62241001, NP_001307857.1 GI:1004170674, XP_016871100.1 GI:1034566254, XP_016871101.1 GI:1034566257, and XP_016871102.1 GI:1034566259. Without being bound by theory, in some embodiments, CHUK is thought to be involved in NFKB signaling.

[0448] As used herein, the terms "GLCE" and "glucuronic acid epimerase" refer to the gene GLCE and the gene product encoded by the GLCE gene, which is also known as "HSEPI." In the human genome, GLCE is located on chromosome 15. Exemplary human GLCE transcript sequences include, but are not limited to, the following NCBI reference sequences: NM_015554.3 GI:1519244225 NM_001324091.2 GI:1890343420, NM_001324092.2 GI:1675178323, NM_001324093.2 GI:1676317756, NM_001324094.2 GI:1675094819, XM_005254298.3 GI:1034590279, XM_017022073.1 GI:1034590277, and XM_017022074.2 GI:1370466481. Exemplary human GLCE protein sequences include, but are not limited to, the following NCBI reference sequences: NP_056369.1 GI:51317380, NP_001311020.1 GI:1022943262, NP_001311021.1 GI:1022943153, NP_001311022.1 GI:1022943120, NP_001311023.1 GI:1022943129, XP_005254355.1 GI:530405672, XP_016877562.1 GI:1034590278, and XP_016877563.1 GI:1034590281. Without being bound by theory, in some embodiments, GLCE is believed to be involved in the biosynthesis of heparan sulfate.

[0449] As used herein, the terms "EP300" and "E1A binding protein 300" refer to the gene EP300 and the gene product encoded by the EP300 gene. It is also known as "KAT3B," "MKHK2," "RSTS2," or "p300." In the human genome, EP300 is located on chromosome 22. Exemplary human EP300 transcript sequences include, but are not limited to, the following NCBI reference sequences: NM_001429.4 GI:1519315586 and NM_001362843.2 GI:1675014866. Exemplary human EP300 protein sequences include, but are not limited to, the following NCBI reference sequences: NP_001420.2 GI:50345997 and NP_001349772.1 GI:1384865987. Without wishing to be bound by theory, in some embodiments, EP300 is thought to be involved in transcription.

[0450] As used herein, the terms "ARID4B" and "AT-rich interacting domain 4B" refer to the gene ARID4B and the gene product e...

Claims

1. A method for adjusting the transduction efficiency of AAV particles, The cells were brought into contact with the AAV transduction regulator. This includes adjusting the trait introduction efficiency of the AAV particles; Selectively, the regulatory factor modulates (for example, increases or decreases) a gene or gene product related to AAV transduction efficiency. Selectively, the gene or gene product is (a) A mammalian (e.g., human) gene or gene product; (b) Related to increased transduction efficiency of AAV particles (e.g., AAV-R or GPR108); (c) Related to increased transduction efficiency of AAV particles of a first serotype (e.g., AAV2) and increased transduction efficiency of AAV particles of a second serotype (e.g., AAV9) (e.g., AAV-R or GPR108); (d) Related to a decrease in the transduction efficiency of AAV particles (e.g., WDR11 or MRE11); (e) This is associated with a decrease in the transduction efficiency of AAV particles of a first serotype (e.g., AAV2) and a decrease in the transduction efficiency of AAV particles of a second serotype (e.g., AAV9) (e.g., WDR11 or MRE11); (f) When regulated, it increases the transduction efficiency of AAV particles; (g) When regulated, it increases the transduction efficiency of AAV particles of the first serotype (e.g., AAV2) and the transduction efficiency of AAV particles of the second serotype (e.g., AAV9); (h) When regulated, it reduces the transduction efficiency of AAV particles; (i) When regulated, it reduces the transduction efficiency of AAV particles of the first serotype (e.g., AAV2) and the transduction efficiency of AAV particles of the second serotype (e.g., AAV9); and / or (j) Selectively expressed in target tissue (e.g., brain or liver); Selectively, the gene product may be RNA or the gene product may be a protein; Furthermore, the aforementioned regulatory factor may be selected at will. (a) Inhibit the gene or gene product, for example, a gene or gene product associated with a decrease in the transduction efficiency of AAV particles; (b) Activating the gene or gene product, for example, a gene or gene product related to increasing the transduction efficiency of AAV particles; (c) altering the expression of the gene (for example, increasing or decreasing it); (d) Modify the structure of the gene; (e) altering the activity (e.g., enzyme activity) of the gene product (e.g., increasing or decreasing it); (f) altering (e.g., increasing or decreasing) the level (e.g., abundance) of the gene product; and / or (g) alter the stability of the gene product (for example, increase or decrease it), method.

2. The method according to claim 1, wherein the regulatory factor alters (for example, increases or decreases) the transduction efficiency of AAV particles; optionally, (a) The regulatory factor increases the transduction efficiency of AAV particles, Selectively, the regulatory factor increases the transduction to at least 10, 20, 30, 40, 50, or 60 viral copies per genome. Selectively, the regulator increases transduction to at least 10³, 10⁴, 10⁵, 10⁶, or 10⁷ viral copies per 1 μg of DNA. Optionally, the transduction efficiency is increased by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% compared to a baseline level of transduction efficiency, or by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000 times; or (b) The regulatory factor reduces the transduction efficiency of AAV particles, Selectively, the regulatory factor reduces transduction to a viral copy number of 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 or less per genome. Selectively, the regulatory factor reduces transduction to a viral copy number of 10², 10³, or 10⁴ or less per 1 μg of DNA. Selectively, the transduction efficiency is reduced by at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% compared to a baseline level of transduction efficiency; Furthermore, optionally, (c) A method wherein the reference level of transduction efficiency is the level of transduction efficiency in cells that have not come into contact with the AAV transduction regulator; or the reference level of transduction efficiency is the level of transduction efficiency before the cells come into contact with the AAV transduction regulator.

3. The gene or gene product is: (I) Increase the transduction efficiency of AAV2 particles, Selectively, the gene or gene product does not increase the transduction efficiency of AAV9 particles, or does not substantially increase it. Selectively, the gene or gene product is AAV-R or GRP108; Selectively, the gene or gene product is (i) The gene or gene product is essential for the transduction of the AAV2 particle, and optionally, is not essential for the transduction of the AAV9 particle; and / or (ii) Selected from the group consisting of AAV-R, GRP108, EXT1, EXT2, NDST1, BCL10, OAF, PDCD10, LMO4, MALT1, ZNF644, CHUK, GLCE, EP300, ARID4B, RAB21, MED13, DHX15, WASHC5, IKBKB, USP24, HSPA14, CXXC1, UBE2A, INTS8, CDC42, NFKB1, SIN3A, USP7, ARF5, CARD10, JAK1, SLC35C2, PAXK1, ZC3H11A, FAM20B, FAM72A, DHX36, INTS12, and RPRD1B, or combinations thereof; Furthermore, optionally, the gene or gene product may be related to the following: (a) Endosome sorting (e.g., RAB21, WASHC5, or USP7); (b) Vesicular transport (e.g., CDC42 or ARF5); (c) NFKB signaling (e.g., BCL10, MALT1, NFKB1, IKBKB, CHUK, or CARD10); (d) Biosynthesis of heparan sulfate (e.g., EXT1, EXT2, NDST1, GLCE, or FAM20B); (e) Methylation of H3K9 (e.g., ZNF644); (f) Processing of mRNA precursors (e.g., DHX15); (g) Transcription (e.g., LMO4, EP300, MED13, SIN3, ARID4B, ZC3H11A, CXXC1, RPRD1B, or UBE2A); (h) Function of the integrator complex and / or RNA polymerase II (e.g., INTS8 or INST12); (i) DNA repair and / or AAV genome degradation (e.g., DHX36, ARID4B, UBE2A, or USP24); (j) Cell proliferation and / or apoptosis (e.g., PDCD10); (k) Spinocarpal-tarsal fusion syndrome (e.g., OAF); (l) Protein folding (e.g., HSPA14); (m) helicase activity (e.g., DHX36); or (n) Fucosylation of Notch and / or transport of GCP-fucose (e.g., SLC35C2); (II) Increase the trait transfer efficiency of AAV9 particles, Selectively, the gene or gene product does not increase, or substantially does not increase, the transduction efficiency of AAV2 particles. Selectively, the gene or gene product is AAV-R or GRP108; Selectively, the gene or gene product is (i) The gene or gene product is essential for the transduction of the AAV9 particle, and optionally, is not essential for the transduction of the AAV2 particle; and / or (ii) Selected from the group consisting of AAV-R, GRP108, TMPRSS11B, HTT, SNRNP70, BRD7, DMXL1, RAB10, CNGA1, KLHDC3, CHP1, CYP3A5, ELOVL4, PNISR, ZCCHC14, AZGP1, TPST1, SC5D, ELP2, ELP3, IPO9, RAB14, WDR7, XRCC4, and GDI2, or combinations thereof; Furthermore, optionally, the gene or gene product is (a) Related to microtubule-mediated transport or vesicle function (e.g., HTT); (b) It is an ion channel (e.g., CNGA1); (c) Related to nuclear protein import (e.g., IPO9); (d) Related to the O-sulfation of tyrosine residues within the acidic motif of polypeptides (e.g., TPST1); (e) related to the protection of viral RNA (e.g., ZCCHC14); (f) Related to RNA binding by AAV proteins (e.g., PNISR); (g) related to calcium ion-controlled exocytosis (e.g., CHP1); (h) Those involved in intracellular transport (e.g., RAB10, RAB14, GDI2, WDR7, or DMXL1); (i) A subunit of the elongator complex, for example, RNA polymerase (e.g., RNA polymerase II) (e.g., catalytic tRNA acetyltransferase subunit) (e.g., ELP2 or ELP3); (j) Chromatin-binding (e.g., KLHDC3); or (k) related to cholesterol biosynthesis (e.g., SC5D); or (III) Increase the transduction efficiency of AAV2 and AAV9 particles, Selectively, the gene or gene product is AAV-R or GRP108; Selectively, the gene or gene product is (i) Essential for the transduction of AAV2 and AAV9 particles; and / or (ii) Selected from the group consisting of AAV-R, GRP108, KIAA0319L, BAMBI, TM9SF2, PHIP, DCLRE1C, VPS35, GPR108, CYREN, ACP2, F8A2, F8A1, F8A3, RBPJ, ATP2C1, ICMT, RABIF, IER3IP1, RBM10, SMG7, GTF2I, ELAVL1, MEPCE, RAB4A, IER3IP1, and SAMD1, or combinations thereof; Furthermore, optionally, the gene or gene product is (a) Related to influenza infection (e.g., ACP2); (b) Binding to unmethylated CGI (e.g., SAMD1); (c) Related to intracellular vesicular transport (e.g., RABIF); (d) Related to post-translational modifications of cysteine ​​residues (e.g., C-terminal cysteine ​​residues) in target proteins (e.g., ICMT); (e) Binding to the AAV capsid protein (e.g., KIAA0319L); (f) Inhibition of TLRs (e.g., TLR9) (e.g., GPR108); (g) For example, those related to the endosomal transport of AAV-R (e.g., VPS35); (h) A calcium ATPase pump (e.g., ATP2C1); (i) Related to Notch signaling (e.g., RBPJ); (j) Related to the metabolism of HSPG (e.g., TM9SF2); (k) Inhibition of NHEJ (e.g., CYREN); (l) Related to viral hairpin degradation (e.g., DCLRE1C); or (m) In relation to the translocation of the Glc transporter, the gene or gene product optionally binds to the insulin receptor substrate 1 protein (e.g., PHIP). The method according to claim 1 or 2.

4. The AAV particles are (a) containing the AAV genome; (b) containing AAV-like particles; (c) containing a capsid; (d) Having a serotype of AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, or a combination thereof; (e) It is an AAV2 particle; (f) It is an AAV9 particle; (g) Having orientation toward CNS (e.g., AAV1, AAV2, AAV4, AAV5, AAV8, or AAV9); (h) Having a directional orientation toward the heart (e.g., AAV1, AAV8, or AAV9); (i) Having tropism towards the kidney (e.g., AAV2); (j) Having a hepatic orientation (e.g., AAV7, AAV8, or AAV9); (k) Having tropism towards the lungs (e.g., AAV4, AAV5, AAV6, or AAV9); (l) Having a tropism toward the pancreas (e.g., AAV8); (m) Having tropism toward photoreceptor cells (e.g., AAV2, AAV5, or AAV8); (n) Having tropism toward the retinal pigment epithelium (RPE) (e.g., AAV1, AAV2, AAV4, AAV5, or AAV8); (o) Having a orientation toward skeletal muscle (e.g., AAV1, AAV6, AAV7, AAV8, or AAV9); (p) Contains a nucleotide sequence encoding a therapeutic protein; (q) comprising a nucleotide sequence encoding NGF, APOE2 (e.g., hAPOE2), TERT (e.g., hTERT), MAPT, GAD, AADC, NTN, GDNF, GCase, HTT, SMN, SMN2, SOD1, or C9orf72; and / or (r) containing a nucleotide sequence encoding therapeutic nucleic acid, The method according to claim 1 or 2.

5. The cell is (a) brain cells, hepatocytes, spinal cord cells, dorsal root ganglion (DRG) cells, spleen cells, lymph node cells, kidney cells, lung cells, cardiac cells, muscle cells (e.g., skeletal muscle cells, e.g., thigh muscle cells), diaphragmatic cells, bone marrow cells, or gonadal cells; (b) Central nervous system (CNS) cells; optionally, the CNS cells are astrocytes, oligodendrocytes, micronephrine cells, or ependymal cells; (c) a brain cell; further optionally, the brain cell is a nerve cell or a glial cell; (d) DRG cells; (e) Hepatocytes; (i) Selectively, the regulator increases the transduction to at least 10, 20, 30, 40, 50, or 60 viral copies per hepatocyte genome, (ii) Optionally, the regulator increases the transduction to at least 10⁵, 10⁶, or 10⁷ viral copies per 1 μg of DNA in the hepatocytes. (iii) Optionally, the hepatocytes are hepatic parenchymal cells, hepatic stellate cells, Kupffer cells, or hepatic sinusoidal endothelial cells; (f) Contact with the AAV transduction regulator in vitro; (g) Contact with the AAV transduction regulator exovivo; or (h) Contacting the AAV transduction regulator in vivo, and optionally, the method yields high gene regulation (e.g., gene editing) efficiency in a first tissue (e.g., liver) (e.g., at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 98%) and limited effects in a second tissue (e.g., skeletal muscle, bone marrow, or both) (e.g., 20%, 15%, 10%, 5%, 2%, or less gene regulation (e.g., gene editing) efficiency). The method according to claim 1 or 2.

6. A pharmaceutical composition comprising an AAV transduction modifier for adjusting the transduction efficiency of AAV particles in a target.

7. Use of an AAV transduction modifier in the manufacture of a drug for adjusting the transduction efficiency of AAV particles in a target.

8. A pharmaceutical composition comprising an AAV genome or AAV particles for use in treating a disorder in a subject, wherein a gene or gene product related to AAV transduction efficiency is regulated in the subject.

9. A pharmaceutical composition comprising an AAV transduction regulator for treating a disorder in a subject in combination with a therapy comprising an AAV genome or AAV particles.

10. Use of an AAV genome or AAV particles in the manufacture of a drug for treating a disorder in a subject, wherein a gene or gene product related to AAV transduction efficiency is regulated in the subject.

11. Use of an AAV transduction regulator in the manufacture of a drug for treating a disorder in a subject in combination with a therapy comprising an AAV genome or AAV particles.

12. A pharmaceutical composition for use according to claim 8 or 9, or a use according to claim 10 or 11, (a) When the AAV transduction regulator is administered, the subject has never been administered the therapy or is not currently being administered it; (b) The subject was administered the AAV transduction modifier for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, or 1, 2, 3, 4, 5, or 6 months prior to the administration of the therapy; (c) The subject was administered the AAV transduction regulator for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, or 1, 2, 3, 4, 5, or 6 months or less prior to the administration of the therapy; (d) When the AAV transduction regulator is administered, the subject has previously received or is currently receiving the therapy; (e) Before the administration of the AAV transduction regulator, the subject was administered the therapy for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, or 1, 2, 3, 4, 5, or 6 months; (f) Before the administration of the AAV transduction regulator, the subject was administered the therapy for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, or 1, 2, 3, 4, 5, or 6 months or less; (g) The subject has a disability or symptoms thereof, or is at risk of having a disability or symptoms thereof; optionally, the disability is (i) a neurodegenerative disorder; further optionally, the neurodegenerative disorder is Alzheimer's disease, Parkinson's disease, Huntington's disease, multiple sclerosis (MS), amyotrophic lateral sclerosis (ALS), or Batten's disease; (ii) mild Alzheimer's disease, mild to moderate Alzheimer's disease, mild to severe Alzheimer's disease, early dementia, Parkinson's disease (e.g., idiopathic Parkinson's disease, bilateral idiopathic Parkinson's disease, mid to late-stage Parkinson's disease), Huntington's disease (e.g., manifest Huntington's disease), type 1 SMA, pre-symptomatic SMA, or amyotrophic lateral sclerosis (ALS) (e.g., familial ALS, SOD1 mutation ALS, or C9orf72 mutation ALS); or (iii) an eye disorder; optionally, the eye disorder is blindness, for example, hereditary blindness or non-hereditary blindness; or the eye disorder is Leber congenital amaurosis, age-related macular degeneration, congenital choroidal absence, or color blindness; and / or (h) The use reduces the toxicity of the therapy, enhances the effectiveness of the therapy, or both. A pharmaceutical composition for the aforementioned use, or the aforementioned use.

13. A pharmaceutical composition comprising an AAV transduction regulator for preparing a target for a therapy comprising an AAV genome or AAV particles.

14. Use of an AAV transduction regulator in the manufacture of a drug for preparing a target for a therapy containing an AAV genome or AAV particles.

15. A pharmaceutical composition comprising an AAV regulatory factor for reducing the toxicity of a therapy containing an AAV genome or AAV particles in a subject.

16. Use of an AAV regulator in the manufacture of a drug for reducing the toxicity of a therapy containing an AAV genome or AAV particles in a subject.

17. A pharmaceutical composition for use according to claim 15, or a use according to claim 16, (a) When the AAV transduction regulator is administered, the subject has never been administered the therapy or is not currently being administered it; (b) The subject was administered the AAV transduction modifier for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, or 1, 2, 3, 4, 5, or 6 months prior to the administration of the therapy; (c) The subject was administered the AAV transduction regulator for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, or 1, 2, 3, 4, 5, or 6 months or less prior to the administration of the therapy; (d) When the AAV transduction regulator is administered, the subject has previously received or is currently receiving the therapy; (e) Before the administration of the AAV transduction regulator, the subject was administered the therapy for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, or 1, 2, 3, 4, 5, or 6 months; (f) Before the administration of the AAV transduction regulator, the subject was administered the therapy for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, or 1, 2, 3, 4, 5, or 6 months or less; (g) The toxicity is reduced by at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% compared to the reference toxicity level; (h) The toxicity level of the above standard is the toxicity level of a subject that has never been administered the AAV transduction modulator; (i) The toxicity level of the standard is the toxicity level before the subject is administered the AAV transduction modifier; (j) The use described above reduces toxicity to the dorsal root ganglia (DRG); (k) The use described above reduces liver toxicity; (l) The use thereof reduces the toxicity of cardiomyocytes; and / or (m) The use described above reduces the toxicity of the retinal pigment epithelium (RPE), A pharmaceutical composition for the aforementioned use, or the aforementioned use.

18. A pharmaceutical composition comprising an AAV transduction regulator for use in enhancing the efficacy of a therapy comprising an AAV genome or AAV particles in a subject.

19. Use of an AAV transduction regulator in the manufacture of a drug for enhancing the efficacy of a therapy containing an AAV genome or AAV particles in a subject.

20. A pharmaceutical composition for use according to claim 18, or a use according to claim 19, (a) When the AAV transduction regulator is administered, the subject has never been administered the therapy or is not currently being administered it; (b) The subject was administered the AAV transduction modifier for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, or 1, 2, 3, 4, 5, or 6 months prior to the administration of the therapy; (c) The subject was administered the AAV transduction regulator for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, or 1, 2, 3, 4, 5, or 6 months or less prior to the administration of the therapy; (d) When the AAV transduction regulator is administered, the subject has previously received or is currently receiving the therapy; (e) Before the administration of the AAV transduction regulator, the subject was administered the therapy for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, or 1, 2, 3, 4, 5, or 6 months; (f) Before the administration of the AAV transduction regulator, the subject was administered the therapy for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours, 1, 2, 3, 4, 5, or 6 days, 1, 2, 3, or 4 weeks, or 1, 2, 3, 4, 5, or 6 months or less; (g) The effectiveness is increased by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% compared to the standard, or by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000 times; (h) The reference level of effectiveness is the level of effectiveness in subjects who have not been administered the AAV transduction modifier; and / or (i) The reference level of effectiveness is the level of effectiveness before the subject is administered the AAV transduction regulator. A pharmaceutical composition for the aforementioned use, or the aforementioned use.

21. A method for producing cells with increased AAV transduction efficiency, By bringing one cell into contact with the AAV transduction regulator, This includes producing the aforementioned cells, The aforementioned method.

22. Cells produced by the method of Claim 21; or cells, pharmaceutical composition, or kit comprising an AAV regulator and AAV particles.

23. The following: (a) Controlling the transduction efficiency of AAV particles in cells or subjects; (b) A combination of AAV genome or AAV particles in a method for treating the target disorder; (c) Adjustment of the subject for therapies containing AAV genome or AAV particles; (d) Reduction of the toxicity of therapies containing AAV genome or AAV particles in the subject; or (e) Increased effectiveness of therapies containing AAV genome or AAV particles in the subjects A pharmaceutical composition containing an AAV transduction regulator for use in [the specified field].

24. The following: (a) Controlling the transduction efficiency of AAV particles in cells or subjects; (b) For use in combination with AAV genomes or AAV particles in methods for treating disorders in subjects; (c) To tailor therapies containing AAV genomes or AAV particles; (d) To reduce the toxicity of therapies containing AAV genomes or AAV particles in subjects; or (e) Use of AAV transduction regulators in the manufacture of agents to increase the efficacy of therapies containing AAV genome or AAV particles in a subject.

25. The method according to any one of claims 1, 2, or 21, a pharmaceutical composition for use according to any one of claims 6, 8, 9, 13, 15, 18, or 23, or a use according to any one of claims 7, 10, 11, 14, 16, 19, or 24, (a) The method or use results in a high gene regulation (e.g., gene editing) efficiency (e.g., at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 98%) in a first tissue (e.g., liver) and a limited effect (e.g., 20%, 15%, 10%, 5%, 2%, or less gene regulation (e.g., gene editing) efficiency) in a second tissue (e.g., skeletal muscle, bone marrow, or both); and / or (b) The AAV transduction regulator is administered by intravenous contact or administration. The method, the pharmaceutical composition for the use, or the use.

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