WO2020041498A1 - Compositions and methods for modulating transduction efficiency of adeno-associated viruses - Google Patents

Abstract

Methods and compositions for modulating the transduction efficiency of an adeno-associated virus (AAV) into a cell or tissue are provided.

Description

COMPOSITIONS AND METHODS FOR MODULATING

TRANSDUCTION EFFICIENCY OF ADENO-ASSOCIATED

VIRUSES

TECHNICAL FIELD

This disclosure generally relates to modified adeno-associated viruses (AAV) and methods of modulating the transduction efficiency of such viruses.

BACKGROUND

Previous methodologies have been insufficient to identify major AAV entry factors or to characterize subfamily-wide receptor and entry factor requirements. Previous studies have primarily focused on cDNA overexpression in poorly permissive cell lines to identify factors that increase transduction of a particular serotype (76. 80, 81 >, most often AAV2 (74, 75, 77). These studies have identified several proteins that increase AAV transduction, yet the mechanism by which they influence transduction has been poorly characterized aside from often demonstrating increased attachment at the cell surface upon overexpression (78). There is a disconnect in the data however, as knock-down and knock-out studies of these factors often do not show a major defect in AAV transduction, and thus cannot be defined as a required entry receptor.

SUMMARY

The present disclosure relates to the mechanism by which adeno-associated virus (AW) transduces celts. Having an understanding of this mechanism allows a person of skill in the art to modulate the entry and, hence, the transduction efficiency, of AAVs into cells.

As described herein, methods of modulating the transduction efficiency of an adeno-associated virus (AAV) into a cell are provided. Such methods typically include introducing a genetically-modified adeno-associated vims (AAV) into the cell, where the AAV capsid has been genetically modified to comprise a heterologous VP l polypeptide sequence and where the heterologous VP1 polypeptide sequence requires the presence of a GPR108 receptor for transduction or does not require the presence of a GPR108 receptor for transduction of the cell. In some embodiments, the heterologous VPi polypeptide or portion thereof includes the sequence shown in SEQ ID NO: 1. In these instances, the heterologous VPI polypeptide sequence does not require the presence of a GPR108 receptor for transduction of the cell. One example of a VPI polypeptide that includes the sequence shown in SEQ ID NO: 1 is the amino acid sequence of an AAVS VPI protein or a portion thereof.

in some embodiments, the heterologous VPI polypeptide or portion thereof includes the sequence shown in SEQ ID NO;2. In these instances, the heterologous VPI polypeptide sequence requires (he presence of a GPR108 receptor for transduction.

Examples of VPI polypeptide that includes the sequence shown in SEQ ID NO:2 are the amino acid sequences of a VPI protein or a portion thereof from AAVi, AAV2, AAV3, AAV4, AAV6.2, AAV7, AAVS, AAV9, Anc80, AncSl, Anc82, Anc83, Anc84, And 10, And 13, rh8c, rhIO, PHP-B, 8BPV2, or 7M8.

Also as described herein, methods of modifying the cell entry of an adeno- associated virus (AAV) are provided. Such methods typically include genetically engineering an AAV to be GPR 108-independent, where the genetically engineered GPR 108-independent AAV includes a VPI polypeptide sequence having the sequence

wherein each of Xi i2 is any amino acid. Alternatively, such methods can include genetically engineering an AAV to be GPR 108-dependent, where the genetically engineered GPR 108-dependent AAV includes a VPI polypeptide sequence having tire sequence

NO:2), wherein each of X1-12 is any amino acid, thereby modifying the cell tropism of (he AAV.

An exemplary genetically engineered GPR 108-independent AAV includes a VPI polypeptide sequence having the sequence

wherein Xi is

S or A or T; Xx is F or A or T: X.» is P; X4 is D; Xi is W; Xd is L; X? is E; Xs is E; X» is G; Xio is L or l orV; Xn is R; and/or Xi 2 is E or Q. In one embodiment, the genetically engineering GPR 108-independenl AAV includes a VPI polypeptide sequence derived from an AAV5 VPI protein.

Similarly, an exemplary genetically engineered GPR 108-dependent AAV includes a VPI polypeptide sequence having the sequence MXt¾DGYLX.iX₄X5X6X7D(T/N)LSX5iX<_iXioXitXi₂WW(KA/D)L(K/Q)P (SEQ ID NO.2), wherein X₁ is S or A or T; X2 is F or A or T; X: is P; X₄ is D; X$ is W; X<s is L; X? is E; X» is E; X₉ is G; X10 is L or I or V; Xn is R; and/or Xu is E or Q. in some embodiments, the genetically engineering GPR 108-dependent AAV comprises a VP1 polypeptide sequence derived from a VP1 protein of AAV1 , AAV2, AAV3, AAV4, AAV6.2, AAV7, AAV8, AAV9, Anc80, AncSl. Anc82, Anc83, Anc84, And 10,

And 13, rh8c, rhIO, PHP-B, 8BPV2, or 7M8.

In addition, methods of increasing the transduction efficiency of an adeno- assoeiated virus (AAV) into a cell are provided. Such methods typically include contacting the cell with a compound that increases the expression or activity of GPR108 in the cell, thereby increasing the transduction efficiency of the AAV into the cell.

A representative compound that can be used to increase the expression of GPR108 in the cell is an expression construct including a GPR 108 transgene. In some

embodiments, the AAV is AAV 1 , AAV2, AAV3, AAV4, AAV6.2, AAV7, AAV8, AAV9. Anc80, Anc8l , Anc82, Anc83, Anc84, And 10, And 13, rh8c, rhIO, PHP-B, 8BPV2, or 7M8. In some embodiments, the AAV is a genetically-engineered AAV.

Also as described herein, methods of decreasing the transduction efficiency of an adeno-associated virus (AAV) into a cell are provided. Such methods typically include contacting the cell with a «impound that decreases the expression or activity of GPR 108 in the cell, thereby decreasing the transduction efficiency of the AAV into the cell.

A representative compound that can be used to decrease the expression of GPR 108 in the cell is an interfering RNA molecule. In some embodiments, the interfering RNA molecule is siRNA or R.N Ai.

The cells used in any of the methods described herein can be in vivo.

Representative cells include liver cells, kidney cells, heart cells, lung cells, epithelial cells, endothelial cells, bone marrow cells (including hematopoietic stem cells).

In addition, methods of increasing the uptake of a therapeutic agent into a cell are provided. Such methods typically include contacting the cell with the therapeutic agent linked to an AAV VPl polypeptide, where the VP I polypeptide includes the sequence MXiXtVDHPXiXiXsXeXrEVGXaXeXteXuXiiFLGLEA (SEQ ID NO: l ), wherein each of XMJ is any amino acid.

Representative therapeutic agents include proteins or protein complexes. In some embodiments, the therapeutic agent is further linked to a binding factor that binds to G PR 108. Representative binding factors that bind to GPR108 include, without limitation, an antibody, an aptamer, and an antibody domain.

Further, compositions including a therapeutic agent linked to a VP I polypeptide comprising SEQ ID NO.1 or SEQ ID NO:2 are provided. In some embodiments, the therapeutic agent is a protein or protein complex.

In addition, AAV capsid sequences are provided that include a heterologous VP1 sequence that includes SEQ ID NO:l. A representative heterologous VP1 sequence includes the sequence shown in SEQ ID NO: 18.

AA V capsid sequences also are provided (hat include a heterologous VP1 sequence that includes SEQ ID NO: 2. A representative heterologous VP I sequence includes the sequence shown in SEQ ID NO: 19.

In one aspect, the disclosure provides methods of modulating the transduction efficiency of an adeno-associated virus (AA V) into a cell. Such methods include introducing a genetically-modified adeno-associated virus (AAV) into the cell, where the AAV capsid has been genetically modified to comprise a heterologous VP l polypeptide or portion thereof, and where the heterologous VPI polypeptide or portion thereof is involved in GPR 108-dependent or GPR108-independent transduction of (he cell, depending on die sequence of the VPI polypeptide. In some embodiments, the heterologous VPI polypeptide or portion thereof is a VPI polypeptide or portion thereof from AAV5, in which case the AAV is GPR 108-independent. In some embodiments, the genetically modified AAV is an AAV that is AAV Receptor (AAVR)-independent.

In another aspect, the disclosure features methods of modulating the uptake of a non-AA V compound into a cell. Such methods include contacting the cell with the non- AAV compound linked to a GPR 108-dependent AAV VPI polypeptide or portion thereof. In some embodiments, the non-AAV compound is a protein or protein complex. In some embodiments, the GPR 108-dependent AAV VPI polypeptide or portion thereof originates from A A VI , AAV2, AAV3, AAV4, AAV6.2. AAV7, AAV8, AAV9, Anc80, Anc81, Anc82, Anc83, Anc84, And 10, And 13, rh8c, rhIO, PHP-B, 8BPV2, and 7M8.

In some embodiments, the non-AAV compound is further linked to a binding factor that binds GPR 108. Representative binding factors that bind GPR108 include, without limitation, an antibody, an aptamer, and an antibody domain.

In still another aspect, the disclosure features methods of increasing the transduction efficiency of an adeno-associated virus (AAV) into a cell. Such methods include contacting the cell with a compound that increases the expression or activity of GPR 108 in the cell, thereby increasing the transduction efficiency of the AAV into the cell. In some embodiments, the compound (bat increases the expression of GPR108 in the cell is an expression construct comprising a GPR 108 transgene.

In yet another aspect, the disclosure provides methods of decreasing tire transduction efficiency of an adeno-associated virus (AAV) into a cell. Such methods include contacting the cel) with a compound that decreases tire expression or activity of GPR 108 in the cell, thereby decreasing the transduction efficiency of the AAV into the cell. In some embodiments, the compound that decreases the expression of GPR 108 in the cell is an interfering RNA molecule. Representative interfering RN A molecules include, without limitation, siRNA and RNAi. In some embodiments, the compound that decreases the activity of GPR 108 in the cell is an antibody that specifically binds to GPR 108 (i.e., an anti-GPR 108 antibody).

The cells in any of die methods described herein can be in vivo cells.

Representative cells include, widiout limitation, liver cells, kidney cells, heart cells, lung cells, epithelial cells, endothelial cells, bone marrow cells (including hematopoietic stem cells).

This disclosure enables the creation of novel capsids with unique cell and tissue targeting properties, which can be used to target novel tissue or cell types not previously accessible to the AAV serotypes in current use. Specifically, the methods and compositions described here allow for AAV vectors to be altered to either engage a cellular receptor, GPR108, or lose dependency on the use and need for GPR108, leading to AAV vectors to either gain access to GPR 108-expressing cells or not be restricted by GPR 108 expression in the target cell type.

As used herein, transduction efficiency refers to the proportion of a plurality of viruses that are able to gain entry and infect a cell.

As used herein,“derived^’’ in the context of a VP1 polypeptide sequence refers to the serotype from which the VP! polypeptide sequence arose or originated. The VP1 polypeptide can be expressed, generated, or synthesized in any manner.

A genetically-engineered vims refers to a virus in which a nucleic acid sequence has been changed. Methods of genetically engineering viruses are known in the an and are discussed further herein. A“heterologous” polypeptide or portion thereof refers to a polypeptide or a portion thereof that is not native to the rest of the polypeptide or to the organism in which the heterologous polypeptide resides.

A“GPR l US-dependent” AAV refers to an AAV that requires the presence of GPR 108 for transduction into a cell. On the other hand, a“GPR 108-independent” AAV refers to an AAV that does not require the presence of GPRI 08 for transduction into a cell.

A“VPI protein” is typically a VPi protein or a portion thereof from a particular AAV serotype exhibiting either GPR 108-independence or GPRi 08-dependence. A“VPI polypeptide” is a molecule derived from a VPI protein or a portion thereof that is incorporated into the capsid of an AAV to impart a GPR 108 dependence to the AAV. As described herein, the GPR 108 dependence imparted to the AAV by the VPi polypeptide is usually different compared to the GPR108 dependence of the wild type VPI protein normally found in that AAV. A representative GPRI 08-independent sequence is MX!XVDHPX>XtX<X<,X7EVGX*X?XiflX! iXuFLGLEA (SEQ ID NO: 1 , wherein each of X i-12 can be any amino acid), while a representative GPR108-dependenl sequence is MX i X~DG Y LX iXiX sX*X7D(T/N)LSX *XsX i oX i iXi„»WW(K,'A/D)L(K/Q)P (SEQ ID NO:2. wherein each of Xi-p can be any amino acid).

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 the methods and compositions of matter belong. Although methods and materials similar or equivalent to those described herein can be used in the pract ice or testing of (he methods and compositions of matter, suitable methods and materials are described below'. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety.

DESCRIPTION OF DRAWINGS

FIG. 1 is a model of the usage of AAV cellular entry receptors, by serotype.

FIG. 2A is a schematic of a two-vector lentiviral GeCKO system.

FIG. 2B is a schematic demonstrating that Huh7 AAVR KO cells undergo leniiCRISPR mutagenesis using vectors described in FIG. 2 A. FIG. 3A is a dot plot showing FACS selection of GFP* and GFP- cells in the V2A half of a Genome-Scale CR1SPR Knock-Out (GeCKO) library.

FIG. 3B is a dot plot showing FACS selection of GFP+ and GFP- cells in the V2B half of a Genome-Scale CR1SPR Knock-Out (GeCKO) library.

FIG. 3C is a dot plot showing FACS selection of GFP- cells expanded and subjected to a second round of high MOl transduction for the V2A half of the GeCKO library.

FIG. 3D is a dot plot showing FACS selection of GFP- cells expanded and subjected to a second round of high MOI transduction for the V2B half of the GeCKO library.

FIG. 4A is the Robust Rank Aggregation (RRA) analysis to identify genes enriched in cells highly expressing GFP, suggestive of potential AAV restriction factors.

FIG. 4B is a bar graph showing the fold increase in transduction of

rh32.33.CMV.Luciferase.SVPA into CRISPR-ediled polyclonal cell populations generated by transducing Huh7 AAVR KO Cas9 cells with lentivirus encoding sgRNAs targeting individual genes identified in rh32.33 GFP* cell population.

FIG. 5A is the RRA of the first round of GFP- transduction, grouped by functionality.

FIG. 5B is the RRA of the second round of GFP- transduction, grouped by functionality.

FIGs. 6A · 6F are graphs of the luminescence observed in WT (wild type), Neuraminidase 1 (NEU 1) knock-out |KO|, cathepsin A (CTSA) heterozygous (HEX) or CTSA knock-out (KO) cells transduced with AAVR independent serotypes rh.32.33 or AAV4 (6A, 6B) or AAVR independent serotypes AAV5. Anc80, AAV9, or AAV9.PHP- B (6C - 6F) in the presence of hAd5 helper virus.

FIG. 6G is a graph of the luminescence observed in various human cell lines expressing Cas9 transduced with a lentivirus containing CTSA- or NEU 1 -specific sgRNA followed by transduction of different AAV capsids expressing the

C.MV.Luciferase.SVPA transgene.

FIGs. 7A and 7B are graphs of the luminescence observed in Huh? cells pretreated with the indicated concentrations of neuraminidase inhibitors, Zanamivir (7A) or DANA (7B), followed by transduction of the indicated capsid serotype encapsidating a luciferase-encoding transgene (dark: AAVR -dependent serotypes; light: AAVR- independent serotypes; solid line: unknown g!ycan attachment factor; dotted line sialic acid used for attachment).

FIGs. 8A - 8D are graphs of the luminescence observed in Huh7 cells pre-treated with 2 mM of the indicated compound, followed by a 2 h treatment with Neuraminidase from Vibrio cholera before transduction with rh32.33 <8A), AAV4 (8B\ AAV5 (8C), or Anc80 (8D) encapsidating a luciferase-encoding transgene.

FIG. 8E is a bar graph of cell-bound viral genomes in WT and mutant MEF cell lines for the indicated serotypes.

FIG. 5/A is a phylogenetic tree of extant and putative evolutionary intermediate AAV serotypes.

FIG. 9B is a graph of the luminescence observed in WT or GPR108 KO Huh7 cells transduced with a CMV.Luciferase.SVPA (AAVrhlO, AAV8, AAVAnc82, AAV9. AAVAnc81 , AAVAncSO, AAV3, AAV6.2, AAV I. AAVA32.33, AAV4, AAV5) or a CMV.eGFP.T2A.Luciferase.SVPA (AAVAnc83, AAV And 10, AAV2) transgene.

FIG. 9C is a graph of the transduction level of indicated serotypes in AAVR KO, GPR 108 KO, or double KO cells relative to WT Huh? cells.

FIG. 10A is a graph of the luminescence observed in HI HeLa cells deleted for GPR 108, then stably transduced with GPR 108 lentivirus, followed by transduction of the indicated serotypes expressing a luciferase-encoding transgene with and without helper vims.

FIG. 10B is a graph of the luminescence observed in Huh7 WT or GPRI08 KO cells transfected with flag-tagged human CPR107 or GPR 108 followed by transduction of the indicated serotype expressing a luciferase-encoding transgene.

FIG. IOC is a graph of the luminescence observed in Huh7 WT or GPR108 KO cells transfected with flag-tagged mouse GPR107 or GPR108 followed by transduction of the indicated serotype expressing a luciferase-encoding transgene.

FIGs. 11 A - 1 IB are graphs of the luminescence observed in Hepa WT or GPR108 KO cells transfected with flag-lagged human or mouse GPR107 or GPR108 and transduced with rh32.33, AAV4, AAV5, (1 1 A) and Anc80, AAV9. and AAV9.PHP-B (I IB) expressing a luciferase-encoding transgene.

FIG. 12A is a schematic of the membrane orientation of non-functional GPR107.

FIG. 12B is a schematic of the predicted membrane orientation of GPR108. FIG. 12C is an image of a Western blot that demonstrates the expression of human and mouse GPR 107 and GPR 108 constructs in Huh7 cells, visualized by a flag-tag at the C-terminus.

FIG. 12D is an image of a Western blot (probed with an anti-flag antibody) to demonstrate expression ofhnman and moose GPR107 and GPR108 in Hepa cells.

FIG. 13A is a graph of the luminescence observed in WT or GPR108 KO Hnh7 or H 1 HeLa cells transduced with parental capsid AAV9 or surface exposed peptide- insertion capsid AAV9.PHP-B.

FIG. 13B is a graph of the luminescence observed in WT or GPR 108 KO Huh7 or HI HeLa cells transduced with a glycan-binding defective AAV2HSPG- or parental AAV2 capsid.

FIG. 13C is a graph of a binding assay for cell-bound viral genomes in I Iuh7 WT. AAVR KO, GPR 108 KO, or double KO ceils, assessed for the indicated capsid serotype.

FIG. 14A is a schematic showing the chimeric capsids used to determine the GPR 108 usage domain.

FIG. 14B is a graph of the luminescence observed in Huh7 WT. AAVR KO,

GPR 108 KO, or double KO cells transduced with the indicated WT or chimeric capsids expressing a luciferase-eneoding transgene.

FIG. 15A is a schematic of chimera swaps between portions of AAV 5 and AAV2.

FIG. 15B is a graph showing luciferase expression (RLU/s) in Huh7 and Huh7 GPR 108 KO transduced with the indicated AAV 48 hours after transduction. Data are shown as mean ± SEM of five technical replicates.

FIG. 16 is an alignment of the region known to confer GPR108 dependency (AAV5 (SEQ ID NO:8): AAV2 (SEQ ID NO:9); AAV4 (SEQ ID NO:10); AAVrh32.33 (SEQ ID NO: I I); AAVanc80L6S (SEQ ID NO: 12): AAV1 (SEQ ID NO: 13); AAV6.2 (SEQ ID NO: 14); AAV8 (SEQ ID NO:15); AAV3 (SEQ ID NO: 16); and AAV9 (SEQ ID NO: 17)).

FIG. 17A is a graph of in vivo luciferase expression (p/s/cm2/$r) during 6-week follow-up of C57BL/6J mice treated with tel l gc/mouse of version 1 of cap 2-5 chimeras in AAV2, AAV5, AAV2.5, AAV5.2 or PBS (control). Data is shown as mean ± SEM of 5 animals per group. FIG. 17B is a graph of luciferase (RLU/s) m wild lype MEF or GPR 108 KO MEF transduced with the indicated AAV expressing a luciferase transgene 48 h after transduction. Data are shown as mean * SEM of three independent experiments.

FIG. 17C is a graph ofluciferase (RLU/s) in Huh7, Huh? AAVR KO, Huh7 GPR 108 KO or Huh 7 double KO transduced with the indicated AAV expressing luciferase 48 h after transduction. Data are shown as mean ± SEM of three independent experiments.

FIG. 18A is a graph of in vivo luciferase expression (p/s/cm2/sr) over 8-weeks following treatment of C57BU6J and GPR 108 KO mice with lei Igc/mouse of the indicated AAV carrying a luciferase transgene. Data is shown as mean * SEM of three animals per group.

FIG. 18B are images of a representative mice per group at day 14 after the administration of the vectors.

DETAILED DESCRIPTION

The work described in this disclosure is one of the first instances of a highly stringent genome-wide screen to identify viral entry factors being used to understand die entty pathway of a gene therapy vector. Three novel host cell entry factors are identified and characterized, and lest results for both AAVR-independent and AAVR-dcpendcnt AAV serotypes are described. The highly conserved usage of two entry factors, AAVR and G protein-coupled receptor 108 (GPR 108), demonstrate that most AAVs appear to share the same entry pathway. A novel multi-factor entry mechanism is presented in which most AAVs bind and require AAVR for proper trafficking, followed by a requirement of GPR108 for endosomal escape (FIG. 1 ).

FIG 1 is a schematic of a model, based on the work described herein, of AAV cellular entry receptors. For example, most AAV serotypes (e.g., AAVL AAV2, AAV3, AAV4, AAV6.2, AAV7. AAV8, AAV9, AncSO, Anc81 , Anc82. Anc83, Anc84, And 10, And 13. rh8c, rhlO, PHP-B, 8BPV2, and 7M8) require both AAVR and GPR108 for cellular entry (e g., in both human and mouse); both AAVR and GPR108 are reported to be ubiquitously expressed. On the other hand, AAV5 uniquely uses an alternate domain of AAVR, and not GPR108, as well as a currently unknown co-receptor for endosomal escape, and AAV4 and rh32.33 use a minimal receptor complex of neuraminidase 1 (NEU 1 ) and calhepsin A (CTS A), as well as the GPR 108 receptor for endosomal escape. As described herein, the AAV sequences involved in cellular entry can be engineered to produce novel capsids with unique cell and tissue targeting properties, allowing targeting of specific tissues or cell types not previously accessible to the current AAV serotypes. AAV, like any virus, engages host proteins and other co-factors for entry and several other steps that allow for a productive infection. Here, we describe a generali/able method that allows AAV vectors to be modified to depend on GPR108, thereby allowing access to GPR 108-expressing cells and tissues, or conversely, to be relieved of GPR108 dependency, thereby allowing vectors not to be restricted by the need for GPR108 expression in (he target cell. In addition, based on the mechanism of entry described herein, the transduction efficiency of an AAV into cells can be modulated or altered using a number of different methods. For example, the methods described herein can be used to modify the cell entry of an adeno-associated virus (AAV).

The ability to manipulate or control, at least in pan, the entry of an AA V into a cell has far-reaching therapeutic implications, AAVs can be used therapeutically to treat a large number of different diseases or deficiencies, and the methods described herein can be used to modulate the transduction efficiency of one or more cells by those AAVs. For example, AAVs can be used to deliver therapy (e.g., gene therapy) to cells for the treatment of a wide variety of disorders including hemophilia, retinitis pigmentosa, cystic fibrosis, !eber congenital amaurosis, lysosomal storage disorders, inborn errors of metabolism (e.g., inborn errors of amino acid metabolism including phenylketonuria, inborn errors of organic acid metabolism including propionic academia, inborn errors of fatty acid metabolism including medium-chain acyl-CoA dehydrogenase deficiency (MCAD)), cancer, achromatopsia, cone-rod dystrophies, macular degenerations (e.g., age-related macular degeneration), !ipopo!ypeptide lipase deficiency, familial hypercholesterolemia, spinal muscular atrophy, Duchenne's muscular dystrophy, Alzheimer's disease. Parkinson's disease, obesity, inflammatory bowel disorder, diabetes, congestive heart failure, hypercholesterolemia, hearing loss, coronary heart disease, familial renal amyloidosis, Marfan’s syndrome, fatal familial insomnia, Creutzfe!dt-Jakob disease, sickle-cell disease, Huntington’s disease, fronto-temporal lobar degeneration, Usher syndrome, lactose intolerance, lipid storage disorders (e.g., Niemann-Pick disease, type C), Batten disease, choroideremia, glycogen storage disease type II (Pompe disease), ataxia telangiectasia (Louis-Bar syndrome), congenital hypothyroidism, severe combined immunodeficiency (SCID), and/or amyotrophic lateral sclerosis (ALS). Genetically Engineered Adeno-Associated Viruses ( A A Vs )

As described herein, the transduction efficiency of an adeno-associated virus ( AAV) into a cell can be modulated or altered by generating a non-naturally occuning, genetically modified adeno-associated virus (AAV) and introducing a plurality of the genetically modified AAVs into the cell. A VP1 polypeptide or portion thereof refers to the VP1 unique N-lerminal portion within the AAV sequence. VP1, VP2, and VP3 are overlapping C-terminal proteins, which result in a VP12 unique domain at the N terminus of VPl and VP2 (referred to as“VP12u”) and a unique VPi domain (referred to as “VP1 u”). As demonstrated herein, GPR108 engagement has been mapped to the VPlu domain.

As described herein, the AAV capsid protein can be genetically engineered to include a heterologous VP1 polypeptide sequence that imparts a requirement for the presence of a GPR 108 receptor for transduction of a cell to an AAV that otherwise, in a non-genetically engineered form, does not require the presence of a GPR 108 receptor for transduction of the cell. Alternatively, the AAV capsid protein can be genetically engineered to include a heterologous VP1 polypeptide sequence that removes the requirement for the GPR108 receptor for transduction of a cell to an AAV that otherwise, in a non-genetically engineered form, requires the presence of a GPR 108 receptor for transduction of the cell.

For example, an AAV can be genetically engineered to include a VP1 sequence having the sequence MX iXiVDHPXsX4XjX«XrEVGXeX9X wXi i Xt ;FLGLE A (SEQ ID NO.l , wherein the Xs can be any amino acid), which imparts GPR 108-independence to the AAV (e.g., removing die requirement for GPR 108). In some embodiments, Xi can be S or A or T; X* can be F or A or T; X.< can be P: X* can be D; Xs can be W; Xs can be L: X? can be E; Xs can be E; X* can be G; Xto can be L or 1 or V; Xu can be R; and/or X)2 can be E or Q.

A representative GPR 108-independent VP1 sequence is

MAAVDHPPDWLEEVGEGIREFLGLEA (SEQ ID NO: 18).

Alternatively, an AAV can be genetically engineering to include a VP1 sequence having the sequence

MXiXiDGYLXrX«XsX6X7D(T/N)LSX*XsXioXi iXi2WW(K/A/DML(10Q)P (SEQ ID NO:2, wherein die Xs can be any amino acid), which imparts GPR 108-dependence to the AAV (e.g., requiring the presence of GPR 108). In some embodiments, X i can be S or A or T; XJ can be F or A or T; X:, can be P; X₄ can be D; can be W: X<. can be L; X? can be E; XH can be E: X$> can be G; XJO can be L or l or V; Xu can be R; and/or Xiz can be E or Q.

A representative GPR108-dependent VPI sequence is

M SF DGY LPDWLEDTLSEGLRE W WKLKP (SEQ ID NO: 19).

In other embodiments, SEQ ID N0.8 (shown in FIG. 16, and which is a portion of the VP1 sequence from AAV5) is an example ofa GPR 108-independent sequence, while SEQ ID NOs: 9-17 (shown in FIG. 16 and each corresponding to a portion of the VPI sequence from AAV2. AAV4, fh.32.33, AAVanc80L65, AAV1, AAV6.2, AAV8, AAV3, and AAV9, respectively) are examples of GPR 108-dependent sequences, although it would be appreciated that VPI sequences other than those shown here can impart GPR 108-independence or GPR 108-dependence. For example, a homologous VP 1 polypeptide (e.g., the corresponding portion of the VPI protein) from AAV7, AncSl, Anc82 Anc83, Anc84, Aucl 10, And 13, rh8c, rhlO, PIIP-B, 8BPV2, or 7M8 also can impart GPR 108-dependence.

As described herein, the VPI polypeptide is involved in either GPR108-dependem or GPR108-independent transduction of a cell, depending on the VP! protein of an AAV serotype from which the VPI polypeptide was derived. Therefore, an AAV can be genetically engineered to include a heterologous VPI polypeptide to modify the cell entry and ultimate transduction efficiency of the genetically engineered AAV.

For example, a normally GPR 108-dependent AAV can be genetically modified to include a heterologous VPI polypeptide that will cause an AAV to exhibit GPR108- independent transduction into cells, or a normally GPR108-independenl AAV can be genetically modified to include a heterologous VPI polypeptide that causes the AAV to exhibit GPRK)8-dependeut transduction into cells.

In some instances, the heterologous VPI polypeptide is derived from a VPI protein or portion thereof from AAV5. As demonstrated herein, the AAV5-derived VPI polypeptide can impart GPR 108-independence to an otherwise GPR108-dependent AAV. In some instances, the AAV that is genetically modified to include a heterologous VPI polypeptide is an AAV that is AAV Receptor (AAVR)-independent. AAVR-independent AAVs are known in the art and include, for example, AAV4 and rh32.33. For example, an AAVR-ittdependent AAV can be genetically-engineered to also be GPR 108- independent using the methods described herein.

Methods oj Modulating the Transduction Efficiency of AAV

Based on the understanding of the AAV cellular entry mechanism provided by this disclosure, it may be desirable, in some instances, to increase the transduction efficiency of an adeno-associated virus (AAV) into a cell by increasing the expression or activity of GPR108 in the cell. Similarly, based on the understanding of the AAV cellular entry mechanism provided by this disclosure, it may be desirable, in some instances, to decrease the transduction efficiency of an adeno-associated virus (AAV) into a cell by contacting the cell with a compound that decreases the expression or activity 0I GPRIO8 in the cell.

Methods of increasing the expression or activity' of a protein in a cell are generally known and typically include, for example, introducing an expression construct into the cells, where die expression construct expresses, or over-expresses, a transgene encoding the desired protein (e.g. , a GPR 108 transgene). Similarly, methods of decreasing the expression or activity of a protein are generally known and typically include, for example, expressing an interfering RNA in the cell. Interfering RNAs are known in the art and include, without limitation, small interfering RNAs (siRNAs) and RNA interference (RNAi) molecules.

Human GPR 108 sequences as well as mouse and rat GPR 108 sequences are known in the art. See, for example, NM_001080452 (human GPR108 transcript variant 1 ); NM_020171 (human GPR 108 transcript variant 2); NP_001073921 (human GPR 108 protein isoform 1): AF376726 (mouse GPR 108 transcript); and BC061996 (rat GPR108 transcript). Such sequences can be used to generate an expression construct for expressing a GPR 108 transgene, or such sequences can be used to generate one or more interfering RNAs, A representative interfering RNA sequence toward GPR108 has the sequence of CGG AC’A AGC CCA UUU GGA A (SEQ ID NO:20) (designated siRNA3 in Kaur. 2018, Ph.D. Thesis for National University of Singapore; available at scholarbank.nus.edu.sg/handle/ 10635/142828 on the World Wide Web).

Expression constructs are known in the art and are commercially available or can be produced by recombinant DNA techniques routine in the art. Expression constructs typically include one or more regulatory elements operably linked to a transgene, and further can include sequences such as those encoding a selectable marker (e.g., an antibiotic resistance gene). A construct designed to express a nucleic acid can encode a chimeric or fusion polypeptide (i.e., a polypeptide operatively linked to a heterologous polypeptide, which can be at either the N-terminus or C-lerminus of the polypeptide). Representative heterologous polypeptides are those that can be used in purification of the encoded polypeptide (e.g., 6xHi$ tag, glutathione S-transferase (GST))

Regulatory elements include nucleic acid sequences that direct and regulate expression of nucleic acid coding sequences. One example of a regulatory element is a promoter sequence. Regulatory elements also can include introns, enhancer sequences, response elements, or inducible elements that modulate expression of a nucleic acid (e.g., a transgene). Regulatory elements can be of bacterial, yeast, insect, mammalian, or viral origin and constructs can contain a combination of regulatory elements from different origins. As used herein, operab!y linked means that elements for expression are positioned in a construct relative to a coding sequence (e.g., a transgene) in such a way as to direct or regulate expression of the coding sequence. In some instances, operably linked means in-frame.

Constructs as described herein can be introduced into a host cell. As used herein, “host cell” refers to tire particular cell into which the nucleic acid is introduced and also includes the progeny or potential progeny of such a cell. A host cell can be any prokaryotic or eukaryotic cell. For example, nucleic acids can be expressed in bacterial cells such as K. coli, or in insect cells, yeast or mammalian cells (such as Chinese hamster ovary cells (CHO) or COS cells). Other suitable host cells are known to those skilled in the art.

The cells that are contacted as described herein (e.g., with a compound (hat increases or decreases the expression or activity of GPR108 or with a genetically modified AAV) can be cells cultured in vitro or cells in vivo , e.g., in a portion of tissue in an animal mode! or in a human or animal subject. Representative cell types include, without limitation, liver cells, kidney cells, heart cells, muscle cells, brain cells, lung cells, epithelial cells, endothelial cells, and bone marrow' cells (including hematopoietic stem cells) or cells in the eye or inner ear. The cells that are contacted as described herein can be, for example, tumor cells or engineered cells.

Many methods for introducing nucleic acids into host cells, both in vivo and in vitro, are known to those skilled in the art and include, without limitation, electroporation, calcium phosphate precipitation, polyethylene glycol (PEG) transformation, heat shock, !ipofeciion, microinjection, and viral-mediated nucleic acid transfer.

Delivery of Therapeutic Agents

The methods and compositions described herein also can be used to modulate the uptake of a therapeutic agent into a cell. For example, a therapeutic agent such as a protein fe.g., an antibody, e.g., a monoclonal antibody) or a protein complex can be linked to a GPR108-dependent AAV VP1 polypeptide or portion thereof. In this manner, a therapeutic agent can be engineered to utilize the GPR108 uptake mechanism usually used by AAVs. Based on the disclosure herein, it would be understood that (he GPR 108- dependent AAV VP1 polypeptide can include the consensus sequence shown in SEQ ID NO:2 or the GPR 108-dependent AAV VP1 polypeptide can be derived from the VP1 protein or portion thereof from any AAV that requires GPR108 for uptake (e.g., AAVl, AAV2, AAV3, AAV4, AAV6.2, AAV7, AAV8, AAV9. Anc80, Anc8I, Anc82, Anc83, Anc84, And 10, And 13, rh8c, rhlO, PHP-B, 8BPV2, or 7M8).

In some instances, it may be desirable to further link an additional binding factor to the therapeutic agent that has affinity to GPR 108. Such a binding factor can be any molecule or agent that binds to GPR 108 including, without limitation, an antibody, an antibody domain, or an aptamer. For example, the N-termmus of a therapeutic agent can be linked to a VP I polypeptide that includes the consensus sequence,

NO:2), to allow delivery of a therapeutic agent to cells.

In accordance with the present disclosure, there may be employed conventional molecular biology, microbiology, biochemical, and recombinant DNA techniques within the skill of the art. Such techniques are explained fully in the literature. The disclosure will be further described in the following examples, which do not limit the scope of the methods and compositions of matter described in the claims.

EXAMPLES

Materials and Methods

All cell lines were maintained in Dulbecco’s modified Eagle’s minimal medium DMEM (Corning) supplemented with 10% FBS (GE Healthcare) and 100 lU/mL penicillin/strepiomycin (Coming) in a humidified incubator with 5% CO’ at 37°C. All cell lines were a gift from Jan Carrette lab and were previously published (Pillay et al., 2016, Nature, 530:108-12). Cells were transfected using Poly Jet/» Vitro DNA

Transfection Reagent (SignaGen, CattfSL 100688) using the standard protocol.

Primary cell MEFs were cultured in Iscove Modified Dulbecco Media IMDM (Gibco) supplemented with 10% FBS (GE Healthcare), 55 mM beta-mercaptoethanol (Gibco), 15 pg'mL gentamicin sulfate (Thermo Fisher) and non-essential amino acids (Thermo Fisher). WT and GPR108 KO MEFs were a gift from Brian Seed and Guoling Zhou and were previously described (Dong et al., 2018, Plos One, 13(K»:e0205303).

NCBI sequences used for synthesis were as follows: mouse GPR107, BAC26961; mouse GPR108, NP_084360; human GPRI07, AAK57695; human GPR108,

XP 290854.Capsid chimeras were generated from AAV2 and AAV5 nucleotide sequence at the VP1 junction demonstrated in (Excoffon et al., 200?), PNAS USA, 106:3865-70). Capsid chimeras were synthesized by Genewiz and subcloned into pAAVector2 using Htndill and Spel restriction sites.

High titer vectors were produced, purified, and titrated by the MEEl/SERI Gene Transfer Vector Core ( vector meei.harvard.edu on the World Wide Web). Large scale vector preparations were generated by polyethy!enimine (Polysciences, Cat#24765-2) triple transfection of pHe!p, pAAVector2(Cap], and pCMV.Lucifeiase.SVPA, pCMV.eGFP.T2A.Lucifera.se, or pCMV.eGFP. WPRE.bGH transgenes in a 2:1 :1 ratio. 520 pg total DNA was transfected in ten-layer hyperflasks using a PEI Max: DNA ratio of 1.375: 1 (w/w). Three days after transfection, vectors were concentrated by tangential flow filtration and purified by iodixanol gradient uitracentrifugation as previously described (Lock et al., 2010, Hum. Gene Ther., 21 :1259-71).

Chimeric and point mutant viral vectors were produced on a smaller scale as crude viral preparations by same transfection method in 10 cm cell culture plates. Three days after transfection, cells Mid supernatant were collected, subjected to three freeze-thaw cycles, then crude virus preparation was clarified by centrifugation for 10 min at 10,000 RPM in a ThermoScientific FIBER/. to? FI 5-8x50cy rotor at 4°C.

All !uciferase transduction assays were done by seeding 10,000 cells per well in black -bottom 96 well plates overnight. When indicated, cells were pie-incubated with 200 pfu/cel! of WT hAd5 (University of Pennsylvania Vector com) in D 10 for two hours, then hAd5-coniaining medium was removed prior to transduction. Cells were transduced with either AAV at IxlO⁴ VG/cell in 50 pL serum-free DMEM (AAVR rescue experiments) for Ih at 37"C, then DIO was added to a total volume of 200 pL, or 100 m! per well of crude virus prep (chimeric and point mutant capsid experiments) was added for 1h at 37°C, removed, then DIO was added. Transduction levels were analyzed by luciierase assay 48 hours post-transduction.

Two days post-transduction, cell culture medium was removed and cells were lysed in 20 pL per well of l x Reporter Lysis Buffer (Promega, Cat#), then frozen at - 80°C. After thaw, ffLuc expression was measured in Relative Light Units/s on a Synergy HI Hybrid Mu!i-Mode Microplate reader using 100 mϊ., luciferin buffer [200 mM Tris pH 8, 10 mM MgCI2, 300 mM ATP, lx Firefly Luciferase signal enhancer (Thermo

Cat# 16180), and 150 pg/mL D-Luciferin).

Example 1— Entry Screen and Analysis

Lenlivirus was produced from HEK293T cells (ATCC, Manassa, VA), by transient transfection using PolyJet In Vitro DNA Transfection Reagent (SignaGen, Cat#SL 100688) using manufacturer's protocol for lentiviral production. LentiCas9-b1ast and individual sgRNA-containing lentivinises were produced in HEK293T cells seeded overnight at 4x10* cells per 10 cm dish. 1 h prior to transfection, medium was changed to fresh pre-warmed D10, followed by transiection of psPAX2, pLentiCas9-Blast or LV04, and pCMV-VSV-G at a 10: 10:1 ratio. Medium was changed to fresh D106 hours after transfection, mid supernatant virus was harvested 48 hours later, clarified by

centrifugation at 2,000 RPM for 5 min in Sorvali tabletop centrifuge, and filtered through a 0.45 micron filter. Large-scale GeCKO lenlivirus was produced as previously described (Joung el al„ 20) 7, Nat. Proloc., 12:828-63).

Briefly, V2A and V2B were produced as individual lentiviral library preps using a large scale transfection of the protocol described herein, in Coming HYPER flask culture vessels. Supernatant virus was collected at Day 2 and Day 3 post transfection, filtered through a 0.45 micron filter, and concentrated by ultracentrifugation at 24,000 PRM for 2 hours at 4"C in SW-28 rotor.

Cell lines were seeded at I x 10⁶ cells per well of a 6 well plate the night prior to transduction. Cells were transduced by spinfeclion for 30 min at 25^L0 and 2,500 RPM in tabletop using I ml, per well of supernatant lentivirus in the presence of 8 pg/pl, Polybrene (ThermoFisher Scientific, Cat#TR1003G). Medium wits changed to fresh D10 following spinfeciion, and one day later, stably transduced cells were selected using 5 pg/pL puromycin (Sigma Aldrich, Cat#P9620) for 2 days.

Cas9 cells were transduced with lentivims expressing individual targeting sgRNA (LV04 constructs) as described herein. After at least 1 week of puromycin selection, individual cell clones were plated by limiting dilution in 96-w'ell plates in DMEM 20% FBS plus non-essential amino acids and Pen'Strep to increase cell survival. 2-3 weeks after plating single-cell clones were expanded and screened for knock-out.

Concentrated lentiCRISPR library was tittered on Hub? AAVR KO Cas9 cells by determining % transduced celt survival after 2 days of puromycin selection, relative to untransduced control cells in the absence of puromycin.

Huh? AAVR KO Cas9 cells were transduced with concentrated V2A or V2B lentivims at an MOl of 0.3 in 6-well plates by spinfection as described above for 30 min at 25°C with 8 pg/pL polybrene, followed by incubation at 37°C and 5% CO: for 1.5, after which fresh DIO media was added. Puromycin was added at a concentration of 5 pg/pL 24h post-transduction to select sgRNA expressing cells. Cells were cultured with puromycin for 1 week to carry out selection and allow editing to occur before selection with AAV. 30 million cells from each half of the mutagenized library (V2A and V2B cells) were transduced with 100,000 VG/celi rh32.33CMV.eGFP.WPRE. Cells were transduced in a total volume of 10 mL serum-free DMEM in each of two 15 cm plates for 1 hour followed by addition of 10 mL DMEM 20% FBS and cells were split the following day.

Cells were collected for FACS sorting by trypsim^'/ation, spun in a table-top centrifuge at 2,000 R.PM for 5 min, then resuspended in PBS (without calcium and magnesium) with 5 mM EDTA. FACS sorting was done at the Massachusetts General Hospital Flow Cytometry Core (Simches Research Building) on a BD FACSAria Fusion Cell Sorter instrument. Cells were collected into DMEM supplemented with 20% FBS and Pen/Sirep. Selected cells were expanded and genomic DNA was extracted from a total of !0⁷ cells per sample. GFP negative cells from each half of the library were split in half and either sequenced or subjected to a second transduction and FACS son using the same transduction protocol.

After sequencing, raw reads were mapped to known sgRNA sequences using the MaGECK. analysis pipeline. Significance values were determined for the entire library after normalization to control population within each half of the library (V2A and V2B), and data is reported as raw p-value without multiple test correction.

These genetically modified cells served as a library of cells that were next interrogated whether the genetic modification affected AAV efficiency of targeting. The sequencing of the sgRNA then permitted tracking the genetic modifications that let! to an increase or decrease of AAV efficiency of targeting. This correlation was then statistically challenged for robustness. Significant hits were further validated for their role in AAV transduction. In addition, as described in Example 2. a second round of selection was performed on the library', to fimher increase the robustness of the findings.

Example 2— Entry Screen Identifies rh32.33 Entry Factors

A CRlSPR-based entry screen was designed to identify cellular entry factors required for the alternate AAV entry pathway. A two-vector lentiviral GeCKO system introduced Cas9 in a single vector into the cell line of interest, followed by the introduction of a library of sgRNAs and miRNAs spanning the entire human genome (FIG. 2A) (Shalem et al., 2014, Science, 343:84-7). Briefly, cells were transduced with Vector 1 [lentiCas9-Bla$f| followed by blaslicidin selection, for stable expression of Cas9. Cas9 was then transduced with Vector 2 (lentiGuide-Puro) in a library format containing sgRNAs targeting the entire human genome to generate a cell line knock-out library.

Lentiviral plasmids were purchased from Addgene or Sigma. LentiCas9-blast (52962), psPAX2 (12260). pCMV-VSV-G (8454), GeCKO V2A and GeCKO V2B (1000000048 and 1000000049) were purchased from Addgene. Individual sgRNA lentivirus constructs targeting an individual gene used for screen validation and knock-out experiments were purchased from Sigma as QuickPick glycerol stock clones in Sigma LV04 vector backbone.

Lentivirus was produced from HEK293T cells (ATCC, Manassa, VA) by transient transfection using PolyJet In Vitro DNA Transfection Reagent (SiguaGen.

Cat#SLl00688) using manufacturer’s protocol for lentiviral production. LenliCas9-blast and individual sgRNA-containing !entiviruses were produced in HEK293T cells seeded overnight at 4x 10⁶ cells per 10 cm dish. 1 h prior to transfection, medium was changed to fresh pre-warmed DIO, followed by transfection of psPAX2, pLentiCas9-Blast or LV04, and pCMV-VSV-G at a 10:10:1 ratio. Medium was changed to fresh DIO 6 hours after transfection, and supernatant virus was harvested 48 hours later, clarified by

centrifugation at 2,000 RPM for 5 min in Sorvall tabletop centrifuge, and filtered through a 0.45 micron filter. Large-scale GeC KO lenfivirus was produced as previously described (Jotmg et al., 2017, Nat. Protoc., 12:828-63).

Briefly, V2 A and V2B were produced as individual lenti viral library preps using a large scale tranfection of the protocol described above, in Coming HYPERfiask culture vessels. Supernatant virus was collected at Day 2 and Day 3 post transfection, filtered through a 0.45 micron filter, and concentrated by ultracentrifugalion at 24,000 PRM for 2 hours at 4°C in SW-28 rotor. Concentrated lentiCRISPR library was tittered on Huh7 AAVR KO Cas9 cells by determining % transduced cell survival after 2 days of puromycin selection, relative to untransduced control cells in the absence of puromycin.

Huh7 AAVR KO cells were used for this screen to assure that any possible redundancy with AAVR-dependenl entry would not cause false negatives in the screen. Multiple rounds of transduction of lentiCRISPR mulagenized cells transduced with a rh32.33.CMV.eGFP.WPRE vector and FACS sorting followed by Illumina deep sequencing of sgRNA prevalence were used to identify cellular factors involved in either AAV restriction or AAV entry (FIG. 2B).

Genomic DN A from control (unselected) or selected cells was extracted using a Qiagen Blood & Cell Culture DNA Midi Kit (Cal. No. 13343). Barcode addition and illumina adapter addition was carried out as previously described (Joung el at., 2017, Nat. Protoc., 12:828-63). Briefly, a two-step PCR was carried out using sample-specific primers to specifically amplify sgRNA sequence and distinguish samples during multiplexed sequencing on an Illumina MiSeq machine as described (Joung el al., 2017, Nat, Protoc., 12:828-63).

30 million cells mutagenized with each half of the lentiCRISPR (GeCKO) library (V2A ceils and V2B cells) (Sanjana et al.. 2014, Nat. Methods, 1 1 :783-4) were transduced with a high MOl ofrh32.33.CMV.eGPF.WPRE. The cells with the highest ~15% mean fluorescence intensity (MFI) were selected and sgRNA prevalence was deep sequenced to identify cellular factors that may be restricting AAV entiy or gene expression (FIG. 3A, 3B). Cells that were GFP negative (FIG. 3A, 3B) were selected, split in half and either deep sequenced or subjected to another round of transduction. These cells were transduced at the same MOl and GFP negative cells were sorted and sequenced for further enrichment of rh32.33 entry factors (FIG. 3C, 3D). The second round of transduction, although done at the same MOl, had a higher percentage of cells that remained GFP negative (FIG. 3C. 3D) relative to the first round of transduction (FIG. 3A. 3B), suggesting that selection enriched for deleted genes required for rh32.33 entry. The genomic DNA was extracted from the different selected cell populations, and the sgRNAs were amplified by a two-step nested-PCR strategy that added sample-specific barcodes and Illumina adaptors (Joung et al, 2017, Nat. Proloc.. 12:828-63) for deep sequencing

The samples were multiplexed and sequenced, followed by combining the V2A and V2B samples to analyze the sgRNA prevalence in the full library, and reads were mapped back to known sequences within the lentiCRISPR V2 library. A two-step nested PCR strategy was used to amplify sgRNA 's for sequencing from unselected (Ctrl) or first round GFP+ or GFP- cell populations, adding a unique sample barcode and illumina adaptors in the NGS amplicon. Each selection condition produced more than 7 million total raw reads and more than 3.7 million reads mapped perfectly to the known input sgRNA sequence, enough to maintain greater than 300-fold coverage of the sgRNA library.

In (his second round of selection for cells that were made refractory to AAV infection by genetic perturbation, a more rigorous selection was performed to identify, through this multiplex library approach, which cellular factors are associated wilh reduced AAV infection. These co-factors, identified by the sequencing of sgRNA markers in the host genome, are (hen considered potential required genes and proteins involved in AAV transduction.

Example 3. Identification of Potential AAV Restriction Factors

Robust Rank Aggregation (RRA) analysis and MAGeCK analysis (Li el al., 2014, Genome Biol., 15:554; and Li et al., 2015. Genome Biol., 16:281) of the GFP positive cells identified several factors enriched in the celts with high mean fluorescence intensity (FIG. 4A):

ACSL6. Acyl-CoA Synthetase Long Chain Family Member 6, catalyzes the formation of Acy!-CoA from fatty acids and may playing a major role in lipid metabolism. • LETMD l : LETM 1 Domain Containing 1 , has been suggested to have a role in p53 regulation and tumorigenesis.

• CALN1 : Calneuron 1 , negatively regulates golgi-to plasma membrane transport, deletion of which could potentially alter the trafficking pathways upon AAV transport to the nucleus.

• SSH3. Slingshot Protein Phosphatase 3, plays a role in act in dynamics by activating ADF/cofilin proteins, which may also influence and alter the AAV entry trafficking pathways.

The most significant hit in the GFP positive subset was TMEM 125, an uncharacterized transmembrane protein. Individual sgRNA(s) targeting several of the top hits from the GFP positive selection were introduced to Huh7 AAVR KO Cas9 cells using a lentivira! vector, then puromycin-selected cells were assessed for fh32.33 transduction level using a luciferase assay.

Data presented are fold increase in RLIJ from transduction of 10,000 VG/cell with rh32.33.CMV.Luciferase.SVPA in CR1SPR edited polyclonal cell population relative to parental cell line (Huh7 AAVR KO Cas9). Polyclonal cell lines were generated by transduction of Huh7 AAVR. KO Cas9 cells with lentivirus encoding sgRNAs targeting individual genes identified in rh32.33 GFP+ cell population. Several sgRNA transduced cell lines demonstrated increased transduction relative to the parental cell line, most notably TMEM 125 and GMEB2 (glucocorticoid modulatory element binding protein 2). which each showed roughly a 100-fold increase in transduction (FIG. 4B).

This results demonstrate that GeCKO-based entry screen is able to identify potential cellular restriction factors for AAVrh32.33.

Example 4— Identification of Potential AAV Entry Factors

Analysis of (he GFP- cell population produced as described herein identified several genes that were enriched in the GFP- population, one of the most significant of which was GPR108 (FIG. 5A). This gene was even further enriched in the analysis of the second round of transduction (FIG. 5B), as well as other genes that were highly enriched such as neuraminidase 1 (NEUl) and cathepsin A (CTSA). The X-axis indicates the individual genes within the GeCKO library grouped by functionality, and the Y-axis indicates the significance of each hit based on RRA analysis. The bubble diameter corresponds to the number of individual sgRNAs per gene enriched in the selected population, relative to the unseleeted control. Importantly, the significance of tire (op hits increased to a p- value of near 10⁶, while other genes stayed the same, around a significance value of HP. This suggests that the second round of transduction was extremely important for (he enrichment of rh32.33 entry factors. The identification of GPR108 as an entry factor led to the investigation and mapping of the VP1 region involved in GPR108 dependence.

Example 5-—NEU1 and CTSA are Required for Entry of Alternate Entry Pathway Serotypes rh32.33 and AAV4

Since NED 1 and CfSA exist in a complex together, and NEUl stability and conformation is dependent on CTSA (Galijart et at., 1988, Cell. 54:755-64; and Bonten et al„ 1995, J. Biol. Chera., 270:26441-5), these proteins were tested to determine whether both are important for (he alternate AAV entry route. TWO AAVR independent serotypes were tested, rh32.33 and AAV4, in previously published Mouse Embryonic Fibroblast (MEF) cell lines derived from either NEUl WT or KO mice, or CTSA WT, Heterozygous (HET), or KO mice. Both rh32.33 and AA V4 showed a loss of transduction in the NEU 1 and C TSA KO cells, with little or no effect being observed in the CTSA heterozygous cells (FIG. 6A, 6B).

Several other AAV serotypes were tested, including AAV5, which uses sialic acid as an attachment factor. Although NEU l is involved in sialic acid glycan biology, no difference in transduction of any AAVR dependent serotypes was observed (FIG. 6C-6F). This demonstrates that NEUl and CTSA are specifically required for AAVR independent entry, and that rh.32.33 and AAV4 appear to use the same alternate entry pathway. The effect of NEUl loss in human cells was further evaluated by introducing either an NEU I- or CTSA-specific sgRNA into a variety of Cas9 cell lines. Although a monoclonal celt line with complete NEUl knock-out functionality was not identified, when celts were tested after puromycin selection in a polyclonal context, a large decrease in rh32.33 transduction was observed in multiple NEUl sgRNA transduced cell lines but no decrease was observed for any other serotypes tested (FIG. 6G). This suggests that NEU l is required for AAVR independent entry in both human and mouse cells.

Example 6. Enzymatic Activity of NEUl is Required for Alternate Pathway Entry Because N EU 1 is an enzyme and CTSA, also identified in the entry screen (FIG. 5C), is required for maintaining the catalyticaily active conformation of NEU l (D’Azzo et al., 1982, PNAS USA, 79:4535-9; and Vinogradova et al., 1998, Biochem. J„ 330(Pt 2):641 -50), whether enzymatic activity of NEU 1 is required for its function was tested in rh32.33 and AAV4 entry. Two different sialic acid analog neuraminidase inhibitor compounds were used, Zanamivir (von It/stein el al., 15193, Nature, 363:418-23) and DANA (Meind! et al., 1974, Virology, 58:457-63), to do a dose response on Hull? cells and assess the effect on entry of different AAVR dependent and AAVR independent serotypes. Two different AAVR-dependent serotypes, A A V5 and Anc8(), and (wo AAVR-independent serotypes, rh.32.33 and AAV4, were tested. Importantly, AAV4 and AAV5 were examined because both AAVs use sialic acid as an attachment factor (Kaludov et al., 2001, 3. Virol., 75:6884-93; and Waiters et al., 2001, J. Biol. Chem., 276:20610-6) yet differ in their AAVR dependence.

Briefly, 10,000 celts per ivell were plated in 96-well plates I day prior to inhibitor treatment. Cells were incubated with the indicated concentration of Zanamivir (Sigma SML0492) or DANA (PAID Millipore 252926) for 24 hours prior to transduction in a total volume of 100 pL D10. When indicated, control or inhibitor treated cells were treated with 50 mU/ml, Neuraminidase from Vibrio cholera Type III (Sigma Aldrich, Cat#N7885) in serum-free DMEM, followed by AAV transduction as described.

A short, 1 hour pre-treatment of cells did not show any decrease in transduction. However, pre-treatment of Hull? cells for 24 hours with the indicated concentrations of the neuraminidase inhibitors. Zanamivir (FIG. 7A) or DANA (FIG. 7B) followed by transduction of 10,000 VG/cel! of the indicated capsid serotype encapsidating a

CM V . Luci ferase. S VPA transgene drastically decreased rh32.33 transduction by roughly ten-fold, as well as slightly decreased AAV4 entry (black: AAVR-dependent serotypes: green: AAVR-independent serotypes; solid line: unknown glycan attachment factor: dotted line: sialic acid used for attachment). The requirement for long pre-incubation with neuraminidase inhibitors to show a decrease in AAVR-independent entry suggests that the entry defect may be secondary to NEU 1 and CTSA ftmction, in the sense that NEU 1 activity may be regulating activity of another protein or cellular process required for entry'. Neither of the AAVR-dependent serotypes, AAV5 or Anc80, showed a decrease in transduction, demonstrating that the activity of NEU1 is specifically' required for entry' of AAVR-independent serotypes. Because N EU 1 and CTSA play a role in cellular glycosylation states, confirmation was desired that the entry defect was not due to an overall alteration in glycosylation at the cell surface, leading to an attachment defect. To do this, cells were first pre- treated for 24 h with Zanatnivir or DANA, followed by treatment with a recombinant neuraminidase from Vibrio cholera to remove any sialic acid that may have accumulated at the cell surface due to NEU 1 inhibition.

The indicated pre-chilled vector was then added to cells on ice, incubated for 1 hour for the vectors to undergo attachment, unbound vector was washed away using ice- cold PBS, then transduction was allowed to proceed and vector transduction assessed in the different treatment conditions by fold-change relative to untreated control cells via luciferase assay.

The same four vectors used in FIG. 7 were examined, to tease apart the function of NEU 1 on attachment verses entry of these different serotypes, The indicated cell lines were plated on 24-well plates at 5x 10⁴ cells per well overnight. Cells were placed on ice for 10 minutes, then 10⁹ VG per well pre-chil!ed vector was added in a total volume of 200 pL per well. Vectors were allowed to bind cells on ice on an orbital shaker platform for lh. Following binding, cells were washed 3x with ice-cold PBS with Mg·²’ and Ca-‘ then either 100 pL PBS per well was added and plates were frozen at -80°C. Binding assay plates underwent 3 iree/e-thaw cycles, prior to resuspension and viral genome quantification by qPCR as described herein using CMV primer/probe.

DNase l -resistant viral genomes of iodixanol purified vector preps were quantified by TaqMan qPCR (ThermoFisher, Cat# 4304449) using a primer and probe set detecting CMV promoter. Vector purity was assessed by SDS-PAGE electrophoresis.

Huh7 cells were pre-treated for 24 h with 2 mM of Zanamivir or DANA, followed by a 2 h treatment with Neuraminidase from Vibrio cholera before transduction with rh32.33 (FIG. 8A), AAV4 (FIG. 8B), AAV5 (FIG. 8C), or Anc80 (FIG. 8D)

encapsulating a CMV.Luciferase.SVPA transgene. FIG. 8E are the results of qPCR of cell-bound viral genomes on WT and mutant MEF cell lines for the indicated serotypes.

After neuraminidase treatment of Zanamivir- or DANA-treated cells, a reversal of entry inhibition was not observed (FIG. 8A), suggesting that the rh32.33 entiy defect is not due to altered glycan structure at the cell surface. In contrast, AAV4 and AAV5 both showed a drastic drop in transduction after treatment with exogenous neuraminidase, as expected due to a loss of their preferred glycan attachment factor, a terminal sialic acid moiety (FIG. 8B, 8C). Because Anc80 has no known attachment factor and uses AAVR, no effect of NEU 1 inhibition or neuraminidase treatment was observed on overall transduction of Anc80, as expected (FIG. 8D). These data suggest that the NEU 1 and CTSA entry defect is likely not due to global perturbation of glycan structure on the cell surface. To assay vector attachment directly, a qPCR based cellular binding assay was used to measure vector attachment to NEU I and CTSA WT or KO MEF cells.

While differences in attachment of the different vectors was demonstrated (e.g., roughly 100-fold increase in attachment of AAV4 compared to rh32.33 (FIG. 8E)), a major difference in WT vs. NEUl or CTSA KO cells was not observed for any of the vectors tested. This binding assay demonstrates that a loss of transduction in NEUl and CTSA KO cells is not due to a defect in attachment of the vector at the cell surface and that these proteins likely play a post-attachment role as an entry receptor or part of a multi-protein entry-receptor complex. Example 7— GPRI08 is Requited for Entry of AAVR Dependent and AAVR

Independent Serotvnes in Multiple Cell Types

The most significantly enriched gene identified in this screen was an

uncharacterized 7 transmembrane G-prolein coupled receptor-like protein, GPR108 (FIGs. 5A, 5B). GPR108 is required for entry of all serotypes but AAV5, and is independent of helper virus.

Interestingly, this protein was also identified as a potential entry factor in the initial haploid screen that identified AAVR (Pillay et al., 2016, Nature, 530:108-12). This suggested to us that GPR 108 may be important not only for rh32.33 entry, but for entry of other AAV serotypes as well. A GPR 108 KO Huh7 cell line was generated and a panel of extant serotypes as well as putative ancestral intermediate capsids were tested (FIG.

9A ) for GPR 108 usage via luciferase assay.

Transduction of all tested serotypes (CMV .Luci ferase.S VP A (AAVrhlO, AAV8, AAVAnc82, AAV9, AAVAnc81, AAVAncSO, AAV3, AAV6.2, AAVl , AAVrh32.33, AAV4. AAV5) or CMV.eGFP.T2A.Lucifetase.SVPA (AAVAnc83, AAVAucl 10, AAV2)) in WT or GPR 108 KO Huh? cells at 10,000 VG/cell with hAd5 helper virus except AAV5 was greater than 10 to 100-fold decreased in the GRP108 KO cells compared to WT Huh7 cells (FIG. 9B). In cells deleted for both AAVR andGPR!08 (i.e., AAVR KO, GPR108 KO, or double KO cells relative to WT Huh7 cells in the presence or absence of helper virus) there was a complete loss of transduction of all serotypes, whether cells were pre-infected with a helper virus or not (FIG. 9C).

Loss of transduction upon GPR 108 KO also was observed in H 1 HeLa cells (FIG. 10A), suggesting that requirement of this cellular entry factor is conserved in all AAV transducib!e cell lines.

Example 8— AAV Entry Can Be Rescued bv Stable or Transient Transfection of GPR108

To confirm (he GPR108 KO defect is due to a loss of GPR108 protein expression, the GRP 108 cDNA was stably re-introduced into HI HeLa GPR108 KO cells using a lentiviral vector.

HI HeLa cells were generated in which GPR108 was deleted, then the KO cells were stably transduced with GPR 108 lentivirus, followed by transduction of the indicated serotypes at 10,000 VG/cell with and without helper virus. Stable re-introduction was able to rescue transduction of all tested GPR 108-dependent vectors, but KO and rescue had no effect on the overall transduction level of the GPR 108-independent AA V5 (FIG. 10A}. There are no functional antibodies available for detection of GPR108, so a construct containing a 3x alanine-glycine linker at the c-terminus. followed by a flag-tag for detection of GPR 108 protein expression, was designed. This construct as well as a flag tagged homolog, GPR 107. were sub-cloned into pcDNA3. l(-) and transiently transfected into WT or GPR 108 KO Huh7 cells, followed by transduction with a variety of GPR108-dependent and independent serotypes. Expression of flag-tagged constructs was determined by Western blotting of whole-cell lysates using mouse anti-flag clone M2 antibody (Sigma FI 804) and rabbit anti-beta-actin loading control (Abeam ab8227). Flag-tagged GPR107 and GPR108 constructs containing flanking Noil and BamHI restriction sites were synthesized by Genewiz, followed by restriction enzyme subcloning into pcDNA3.1 (-) plasmid using Noil and BamHI (NEB) restriction sites.

Huh7 WT or GPR 108 KO cells were transfected with flag-tagged human or mouse GPR 107 or GPR 108 followed by transduction of the indicated serotype in the presence of hAd5 helper vims (10,000 VG/cell CMV.Luciferase.SVPA transgene).

Although there was not a full rescue of transduction to wild type levels, there was a clear rescue phenotype observed from transfection of GPR108, but not GPR107 (FIG. 10B, 10C) for all GPR 108-dependent serotypes. These data demonstrate that GPR108 protein expression is required for the entry pathway of most A AVs, aside from the most evolutionarily divergent serotype, A A V5.

Example 9— GPR 108 Usage Is Conserved in Mouse

As human and mouse GPR107 and GPR 108 are highly similar sequences, we wanted to determine whether GPR 108 was similarly used for AAV entry in mouse cells. Hepa cells, a mouse hepatoma cell line, were used as an analogous mouse in vitro system to the human Huh7 cells. Transduction of rh32.33, AAV4, AAV5, [Fig. 4.1 1 A| and Aoc80, AAV9, and AAV9.PHP-B [Fig. 4.1 l.Bj in Hepa WT or GPR108 KO cells transfected with flag-tagged human or mouse GPR 107 or GPR 108 ( 10,000 VG/cell CMV.Luci ferase. SVPA transgene). Interestingly, AAV5 is able to transduce Hepa cells to a high level, while other serotypes such as rh32.33 and AAV4 are not (FIG. 1 1 A).

This suggests that the alternate factor AAV5 uses in place of GPR 108 is likely highly conserved in mouse, yet mouse GPR 108 may not be as highly functional as human GPR 108 for some serotypes. An sgRNA against mouse GPR 108 was additionally used to generate a Hepa GPR108 KO cell line. Of the GPR 108-dependent serotypes tested that transduced Hepa cells, all demonstrated a 10- to 100-fold decrease in transduction in the hepa GPR 108 KO cells compared to wild type (FIG. I IB). Flag-tagged human or mouse cDNAs of GPR 108 or a homologous protein GPR 107 (Edgar. 2007, DNA Seq., 18:235- 41) were re-introduced into hepa GPR 108 KO cells, and a slight increase in AAV transduction was observed (FIG. 1 1 B).

Interestingly, in human cells, mouse GPR108 is able to rescue transduction to similar levels as the human GPR108 construct (FIG. 10B, 10C). It is possible that these constructs were not successful to rescue transduction due to low' protein expression levels. Therefore, expression of each of these constructs was assessed using an anti-flag Western blot from transfected cell lysates in human and mouse cells.

GPR 107 and GPR 108 are both relatively uncharacteri/.ed proteins predicted to have 7 transmembrane domains, with a large luminal N terminus and short cytoplasmic C terminus (FIG. 12 A. 12B). GPR 107 has been shown to have both a disulfide bond and a furin cleavage site in the luminal N -terminal domain required for its function (Tafesse el at., 2014. J. Biol. Chem., 289:24005-18), and the alanine-glycine linker and flag tag also are shown (FIG. 12 A). Furin cleavage of GPR108 produces two peptide fragments of roughly 28 and 34 kDa, the larger of which is visualized by anti-flag Western blot after transient transfection in Huh? cells (FIG. 12C). The bela-actin loading control is shown in (FlG. 12D). These data demonstrate that GPR 108 and GPR 107 were expressed and post-translationally modified as expected.

Example 10·— OPR 108 Does Not Facilitate AAV Attachment

The current understanding of factors involved in AAV transduction primarily exists surrounding factors involved in AAV attachment, and there is little known about the presence and mechanism of intracellular AAV entry receptors. Therefore, we wanted to test whether GPR 108 is playing a role in AAV attachment or further downstream in the entry pathway. Two different capsid surface mutants that have altered tropism or binding properties were tested, alongside their parental AAV capsid, in Huh7 and H 1 HeLa GPR 108 KO celts.

First, a luciferase assay demonstrated that a peptide insertion variant of AAV9, AAV9.PMP-B (Deverman et al., 2016, Nat. Biotechnol., 34:204-9), transduced into WT or GPR 108 KO Huh? or HI HeLa cells, was dependent on GPR 108, similar to the parental capsid, AAV9 (FIG. 13 A). Additionally, an AAV2 variant containing point mutations that ablate binding to the primary AAV2 attachment factor, heparin sulfate (Vandenberghe et al, 2006, Nat. Med., 12.967-71 ), was tested. While the HSPG- variant (glycan-binding defective AAV2HSPG- or parental capsid AAV2) had overall decreased transduction in all cell lines tested (WT or GPR 108 KO Huh7 or HI HeLa cells) (FIG. 13B). transduction of the GPR108 KO cells were 10- to 100-fold decreased compared to their wild-type counterpart, suggesting that GPR 108 usage is independent of AAV attachment. While these data suggest that GPR 108 does not facilitate attachment, it was desired to test this directly.

Therefore, a binding assay was employed as described to assess attachment of GPR 108-dependent and -independent serotypes. Huh7 WT and GPR108 KO cells were tested, as well as AAVR KO cells and the double KO cells, since AAVR was previously suggested to play a role at the plasma membrane (Pillay et al., 2016. Nature. 530:108-12) (FIG. 13Cj. No difference was observed in the number of bound viral genomes per cell in any of the knock-out cell lines for any vector tested, yet differences in the number of bound viral genomes for different serotypes were detected, demonstrating that GPR108 is not facilitating attachment. Example 1 1— GPR 108 Independence is Transferable and is Dependent on the

Phospholipase-Containinu VP1 Domain of the AAV Capsid

To further understand the function of GPR 108 for entry and how it engages the capsid, chimeric capsids were used to identify the capsid domain that dictates GPR108 usage. Because AAVS and AAV2 differ in their GPR108 usage, chimeras generated between these two serotypes were used. A set of reciprocal chimeras with and without the analogous point mutation were designed to determine which region of capsid dictates GPR 108 usage (FIG. 14A). These chimeras then were tested in Huh7 WT, AAVR KO, GPR 108 KO, or double KO cells with the indicated WT or chimeric capsids {100 pL erode vector prep, plus hAd5 helper virus, CMV.eGPF.T2 A. Luciferase transgene). As AAV2 and AAVS both require AAVR, the expected loss of transduction was observed for all tested serotypes in the AAVR KO and double KO cell lines (FIG. 14B).

Interestingly, both of the chimeras containing the VP1 unique region of AAVS were able to transduce GPR 108 KO Huh? ceils to a similar level as WT cells. Residue 581 did not appear to play a major role in GPR108 usage, although it did have a small effect on overall transduction levels. These experiments demonstrate that the VP1 unique region of AAV dictates GPR108 usage, and that this cellular functionality is transferrable to other AAV serotypes.

Example 12— Further Refined Mapping of the GPR 108 Domain

Domain swapping experiments were performed to map the GPR108 domain. Specifically, the indicated domains within VP l from AA5 and AAV2 were exchanged to produce the indicated chimeric AAVs (FIG. 15A). Three different capsid chimeras were synthesized, in which the sequence previously identified to confer GPR 108 dependency was broken down into three parts using conserved regions as break points. The GPR 108- dependent regions from AAVS capsid were swapped into the AAV2 capsid and vectors were produced.

Huh? cells were transduced with equal volumes of crude vims preparations of wild type AAVs (i.e., AAV2 or AAVS) or chimeric AAVs (i.e., AAV5-2-2.2 (SEQ ID NO:S), AAV2-5-2.2 (SEQ ID NO:6) or AAV2-2-5.2 (SEQ ID NO:?)) expressing a GFP.T2A.luciferase transgene as described herein and shown below. The amount of luciferase (RLU's) in the transformed Huh? cells was determined 48 hours after transduction and compared with luciferase expression in an Huh? cell line in which GPR 108 has been knocked out (Huh? G PR 10.8 KO). The results are shown in FIG. 15B (mean .¾ SEM of 5 replicates).

The analysis of transduction in Hub7 and Huh7 GPR 108 KO showed that the new capsids were able to transduce wild type cells at similar levels, while the only chimera able to transduce GPR108 KO cells was the one containing the first 41 amino acids of AAVS.

An alignment between die relevant region from the capsid sequence of AAV2 and the relevant region from the capsid sequence of AAV5 was created.

15

The region responsible for GPR 108 dependency was aligned from a number of different AAVs (FIG. 16), including amino acid sequences from AAV5 as well as a number of GPR 108-dependenl serotypes (i.e., AAV2, AAV4, AAVrh32.33,

this N-termiual sequence is highly conserved among GPR 108 -dependent serotypes, while AAVS differs in three main regions (boxed). These regions are likely involved in the dependency to GPR108, and were used to generate a GPR 108-in depen deni consensus sequence (SEQ ID NO: 1) and a GPR 108-dependent consensus sequence (SEQ ID NO:2). Thus, a GPR108-independeut AAV includes the following VP1 consensus sequence:

wherein each of X1-12 can be any amino acid; and

a GPR108-dependent AAV includes the following VP1 consensus sequence;

ID NO: 2),

wherein each of X _{1 - 1} can be any amino acid. Example 13— Stability and Performance Experiments

The stability and performance of AAV2, AAV5, and chimeras of the two were examined in vivo and in vitro.

C57BL/6J mice (5 animals per group) were treated with lei 1 gc/mouse of AAV2, AAV5, AAV2.5, AAV5.2 or PBS (control) carrying the CMV-EGPF.T2A.luciferase transgene. Luciferase expression was examined in the mice (p/s/cnr/$r) for 6 weeks following transformation. FIG. 17A shows the results of these experiments (mean ··± SEM).

Wild type MEF cells (WT MEF) or MEF cells derived from GPR 108 KO mice (CPR108 KO MEF) were transduced with AAV2, AAV5, AAV2.5 or AAV5.2 viruses carrying the GFP.T2A.luciferase transgene. Cells were treated with 200 pfu/cell of AdS for 2 hours before infecting with the AAVs (MOI le4). The amount of luciferase (RLU/s) was examined 48 hours after transduction. FIG. 17B show's the results of three independent experiments (mean ± SEM).

Muh7, Huh7 A AYR KO, Huh7 GPR108 KO or Huh7 double KO were transduced with AAV2, AAVS, AAV2.5 or AA V5.2 viruses carrying the GFP.T2A.loeiferase transgene. A set of cells were treated with 200 pfu/cell of Ad5 for 2 hours before infecting with foe AAVs (M01=Te4), while the others were directly treated with the AAVs. The amount of luciferase (RLU/s) was measured 48 hours after transduction. FIG. 17C shows the results of three independent experiments (mean .÷ SEM).

These results demonstrate that AAVs produced using VP1 polypeptides that alter GPR 108 dependence are stable structures that can transduce murine MEFs in vitro and mouse tissues in vivo at similar level of the parental wild type vectors.

Example 14 In Vivo Requirement for GPR 108

C57BL/6J mice and GPR108 KO mice (3 animals per group) were transduced with lei Igc/mouse of AAV8, AAVrh32.33, AAV5 viruses (or PBS as a control) carrying the CMV -Luciferase transgene. The amount of luciferase was measured (p/s/cm2/sr: mean ± SEM) over a period of 8 weeks following transduction (FIG. 18A). A

representative mice from each group was imaged 14 days alter transduction with the indicated vector (FIG. 18B). The results shown in FIG. 18A and FIG. 18B demonstrate that GPR 108 is a required entry factor for in vivo transduction by AAV. OTHER EMBODIMENTS

It is to be understood that, while the methods and compositions of matter have been described herein in conjunction with a number of different aspects, the foregoing description of the various aspects is intended to illustrate and not limit the scope of the methods and compositions of matter. Other aspects, advantages, and modifications are within the scope of the following claims.

This disclosure features methods and compositions that can be used for. can be used in conjunction with, can be used in preparation for. and are products of the disclosed methods and compositions. These and other materials are disclosed herein, and it is understood that combinations, subsets, interactions, groups, etc. of these methods and compositions are disclosed. That is, while specific reference to each various individual and collective combinations and permutations of these compositions and methods may not be explicitly disclosed, each is specifically contemplated and described herein. For example, if a particular composition of matter or a particular method is disclosed and discussed and a number of composi tions or methods are discussed, each combination and permutation of the compositions and the methods are specifically contemplated unless specifically indicated to the contrary. Likewise, any subset or combination of these is also specifically contemplated mid disclosed.

Claims

WHAT IS CLAIMED IS:

1. A method of modulating the transduction efficiency of an adeno- associated virus (AAV) into a cell, the method comprising

introducing a genetically-modified adeno-associated vims (AAV) into the cell, wherein the AAV capsid has been genetically modified to comprise a heterologous VP I polypeptide sequence, wherein the heterologous VP1 polypeptide sequence requires the presence of a GPR l 08 receptor for transduction or does not require the presence of a GPR 108 receptor for transduction of (he cell.

2. The method of claim 1 , wherein the heterologous VP1 polypeptide or portion thereof comprises the sequence shown in SEQ ID NO: 1.

3. The method of claim 1 , wherein the heterologous VP1 polypept ide or portion (hereof comprises the sequence shown in SEQ ID NO:2.

4. The method of claim I , wherein the heterologous VP1 polypeptide comprises an amino acid sequence of an AAV5 VP1 protein or a portion thereof.

5. The method of claim 1. wherein the heterologous VP1 polypeptide comprises an amino acid sequence of a VP1 protein or a portion thereof from AAV1 , AAV2, AAV3, AAV4, AAV6.2, AAV7, AAV8, AAV9, Anc80, Anc8l , Anc82, Anc83, Anc84, And 10, And 13, rhSc, rhlO, PHP-B, 8BPV2, or 7M8.

6. The method of claim I , wherein the heterologous VP1 polypeptide sequence requires the presence of a GPR 108 receptor for transduction.

7. The method of claim 1 , wherein the heterologous VP1 polypeptide sequence does not require the presence of a GPR 108 receptor for transduction of the cell.

8. A method of modifying the cell entry of an adeno-associated vims (AAV), the method comprising. genetically engineering an AAV to be GPRI 08-independent, wherein the genetically engineered GPR 108-independent AAV comprises a VPI polypeptide sequence having the sequence

(SEQ ID NO: I ), wherein each of Xi-n is any amino acid, or

genetically engineering an AAV to be GPRl08-dependent, wherein the genetically engineered GPRI 08-dependent AAV comprises a VPI polypeptide seqtience having the sequence

NO:2), wherein each ofXt-12 is any amino acid,

thereby modifying the cell entry of die AAV.

9. The method of claim 8, wherein the genetically engineered GPR 108- independent AAV comprises a VPi polypeptide sequence having the sequence

MXtX?VDHPXsX4XiX<5X7EVGXsX->XioXi i X* ?FLGLEA (SEQ ID NO: I K wherein Xt is S or A or T; X2 is F or A or T; Xu is P; X4 is D; X? is W; Xc. is L; X? is E; Xs is E; X» is G; X so is L or I or V; Xi 1 is R; and/or Xi > is E or Q.

10. Tire method of claim 8, wherein lire genetically engineered GPR 108- dependent AAV comprises a VPI polypeptide sequence having the sequence

MXt X iDG YIJG XaXs X&X ?D( T/N)LSXsX>iX IOXI iXt2WW(K/A/D)L(K/Q)P (SEQ ID NO:2), wherein Xi is S or A or T; X2 is F or A or T; Xs is P; X» is D; Xs is W: X* is L; X? is E; Xs is E; Xy is G; X10 is L or 1 or V; X» is R; and/or Xu is E or Q.

1 1. The method of claim 8, wherein the genetically engineering GPR 108- independent AAV comprises a VPI polypeptide sequence derived from an AAV5 VPI protein.

12. The method of claim 8, wherein the genetically engineering GPR108- depcndent AAV comprises a VPI polypeptide sequence derived from a VPI protein of AAV1 , AAV2, AAV3, AAV4, AAV6.2, AAV7, AAV8, AAV9, Anc80, Anc81 , Anc82, Anc83, Anc84, And 10, And 13, rh8c, rhlO, PHP-B, 8BPV2, or 7M8.

13. A method of increasing the transduction efficiency of an adeno-associated virus (AAV) into a cell, the method comprising contacting the cell with a compound that increases the expression or activity of GPR108 in the cell, thereby increasing the transduction efficiency of the AAV into the cell.

14. The method of claim 13, wherein the compound that increases the expression of GPRI08 in die cel) is an expression construct comprising a GPR108 transgene.

15. The method of claim 13, wherein the AAV is selected from the group consisting of AAV 1, AAV2, AAV3, AAV4. AAV6.2. AAV7, AAV8, AAV9, Anc80, Anc81, Anc82, Anc83, Anc84, And 10, And 13, rh8c. rhIO, PHP-B, 8BPV2, and 7M8.

16. The method of claim 13, wherein the AAV is a genetically-engineered AAV.

17. A method of decreasing the transduction efficiency of an adeno-associated virus (AAV) into a cell, the method comprising contacting the cell with a compound that decreases the expression or activity of GPR108 in the cell, thereby decreasing the transduction efficiency of the AAV into the cell.

18. The method of claim 17, wherein the compound that decreases the expression of GPR108 in the cell is an interfering RNA molecule.

19. The method of claim 18, wherein the interfering RNA molecule is selected from the group consisting of siRNA and RNAi.

20. The methods of any of claims 1-19, wherein the cells are in vivo.

21. The methods of any of claims 1-19. wherein the cells are liver cells, kidney cells, heart cells, lung cells, epithelial cells, endothelial cells, bone marrow cells (including hematopoietic stem cells).

22. A method of increasing the uptake of a therapeutic agent into a cell, the method comprising contacting the cell with the therapeutic agent linked to an AAV VP l polypeptide, wherein the VPI polypeptide comprises the sequence

wherein each

of Xi.ii is any amino acid.

23. The method of claim 22, wherein the therapeutic agent is a protein or protein complex.

24. The method of claim 22, wherein the therapeutic agent is further linked to a binding factor that binds to GPR 108.

25. The method of claim 24, wherein the binding factor that binds to GPR108 is selected from the group consisting of an antibody, an aptamer, and an antibody domain.

26. A composition comprising a therapeutic agent linked to a VP 1 polypeptide comprising SEQ ID NO: 1 or SEQ ID NO:2.

27. The composition of claim 26. wherein the therapeutic agent is a protein or protein complex.

28. An AAV capsid sequence comprising a heterologous VP1 sequence that comprises SEQ ID NΌ.Ί .

29. The AAV capsid sequence of claim 28, wherein the heterologous VP1 sequence comprises SEQ ID NO: 18.

30. An AAV capsid sequence comprising a heterologous VP 1 sequence that comprises SEQ ID NO:2.

31. The AAV capsid sequence of claim 30, wherein the heterologous VP1 sequence comprises SEQ ID NO: 19.