NOVEL AAV LIBRARY

Abstract
An AAV library, comprising AAV variants having an amino acid sequence corresponding to the position amino acids 585 to 597 or 598 of AAV8 or the position amino acids 583 to 595 or 596 of AAV9, and the polynucleotide, host cells, thereof. A method of generating and screening an AAV library and its use.
Description
TECHNICAL FIELD

The present invention relates to gene therapy, especially refers to adeno-associated virus (AAV) and AAV library.


BACKGROUND OF THE INVENTION

It is shown that the transduction efficiencies and tissue tropism are dictated by the AAV capsid. The capsid plays roles throughout the viral life cycle from the initial binding to cell-surface receptors, intracellular trafficking, and entry into the nucleus which all determine the ability of AAV for gene transfer. AAV capsid library-based screen has been used to select AAV capsids with enhanced transduction efficiency and specificity for target cells and tissues.


The method involves genetic diversification to create a library, repeated rounds of screening or selection which enable the enrichment of key mutations or motifs that help to achieve the user-defined goal. For AAV, this process includes creating viral particle libraries which contain mutations in the cap open reading frame (ORF) with large genetic diversity. Then, a selective pressure is applied to the AAV library to promote the emergence of variants capable of surviving under the pressure which are then recovered and used as enriched sub-library for the next cycle of selection. After rounds of selection, the resulting AAVs can be tested clonally for the desired property.


Currently, four different techniques have been applied to create genetic diversity in cap ORF. First, random point mutations can be introduced into the cap ORF and amplified by error-prone PCR. However, this method gives rise to a large amount of dead-end AAV variants derived from random mutagenesis. Second, chimeric cap gene can be generated by mixing multiple AAV capsid sequences for DNA shuffling, a PCR-based method for genetic recombination. However, the level of chimerism and the genetic diversity depend on the input parental AAV capsid sequences which are usually limited. Third, peptide library sequences can be inserted into the AAV capsid usually the receptor binding domain of AAV2 capsid, at R588 position or corresponding position of AAV9. Finally, genetic diversification can focus on the variable regions (VRs) of the AAV2 capsid. It was first introduced to four VRs. Recently, this has been extended to eight VRs, except VR II (due to its overlapping with AAP ORF), either individually or combinatorically.


Due to historical reasons, AAV2 is the mostly studied AAV serotype. Therefore, the design and modifications of the AAV capsid library were largely based on AAV2 capsid backbone. However, the clinical results based on AAV2-mediated gene delivery are sub-optimal. For example, in a clinical trial using AAV2 vector expressing human FIX for the treatment of hemophilia B, the duration of factor expression was limited to approximately 8 weeks due to the cell-mediated immunity against AAV2 capsid.


With an increasing number of clinical stage gene therapy studies, AAV8 and AAV9, another two naturally-occurring serotypes, have demonstrated more powerful gene delivery capability. AAV8 is a leading research and clinical tool for liver-directed gene transfer. AAV9 is able to bypass the blood-brain-barrier (BBB), making it a leading capsid for transduction of central nervous system (CNS). However, the primary cellular receptor for AAV8 and AAV9 remain unknown. The primary glycan receptor for AAV9 is galactose (GAL). The binding of AAV9 to GAL is determined through five critical residues. Both AAV8 and AAV9 were reported to use laminin receptor (LamR) as co-receptor for internalization into cells. At present, the engineering of AAV8 and AAV9 vectors for both basic understanding as well as gene delivery applications are limited.


For previous AAV capsid library, it was aimed to be as diverse as possible. However, based on observations from next generation sequencing (NGS) of barcoded AAV capsid libraries, it is estimated that when a single position of the capsid is modified to a random amino acid that less than one of five mutants will be viable at forming a capsid. This simple benchmark illustrates the challenge of building diverse libraries. If less than ⅕ sequences with a single mutation are viable, then assuming rare epistatic rescue events, less than 1/25 of double mutants and 1/125 of triple mutants will be viable, etc. The conclusion is that as purely random libraries become more diverse that the quality of these libraries decreases exponentially. This tradeoff between diversity and quality is critical to library design. To this end, we need more effective strategies to design alternative AAV capsid library for selecting improved AAV variants.


SUMMARY

The present invention provides an AAV library comprising a multitude of adeno-associated virus (AAV) variants, the AAV variants comprises a variant AAV capsid protein comprising one or more amino acid substitutions, the capsid protein comprise a substituted amino acid sequence corresponding to VR VIII region of the native AAV 8 or AAV9 capsid protein.


The present invention provides an AAV library comprising a multitude of adeno-associated virus (AAV) variants, the AAV variants comprises a variant AAV capsid protein comprising a substitution at one or more of amino acid residues N585, L586, Q587, Q588, Q589, N590, T591, A592, P593, Q594, 1595, G596, T597, V598, corresponding to amino acid sequence of the native AAV 8 (SEQ ID NO:1), the substitution of amino acid residues is selected from N585Y, L586N, L586Q, L586K, L586H, L586F, Q587N, Q588 N, Q588S, Q588A, Q588D, Q588G, Q589T, Q589A, Q589G, Q589S, Q589N, N590A, N590S, N590D, N590T, N590Q, T591S, T591A, T591R, T591E, T591G, A592Q, A592D, A592G, A592R, A592T, P593A, P593T, Q594T, Q594A, Q594I, Q594S, Q594D, I595A, I595T, I595V, I595T, I595S, I595Y, G596Q, G596S, G596A, G596E, T597A, T597L, T597D, T597S, T597N, T597V, T597W, T597M, V598D.


In one specific embodiment, the capsid protein comprises a substituted amino acid sequence of Formula I at the amino acids corresponding to amino acid position 585 to 597 or 585 to 598 of the native AAV 8 (SEQ ID NO:1).


In one specific embodiment, the capsid protein comprise a substituted amino acid sequence of Formula I at the amino acids corresponding to amino acid position 585 to 598 of the native AAV 8 (SEQ ID NO:1): X1X2X3X4X5X6X7X8X9X10X11X12X13X14, wherein

    • X1 is selected from Asn and Tyr,
    • X2 is selected from Leu, Asn, Gln, Lys, His, and Phe,
    • X3 is selected from Gln and Asn,
    • X4 is selected from Gln, Asn, Ser, Ala, Asp, and Gly,
    • X5 is selected from Gln, Thr, Ala, Gly, Ser, and Asn,
    • X6 is selected from Asn, Ala, Ser, Asp, Thr, and Gln,
    • X7 is selected from Thr, Ser, Ala, Arg, Glu, and Gly,
    • X8 is selected from Ala, Gln, Asp, Gly, Arg, and Thr,
    • X9 is selected from Pro, Ala, and Thr,
    • X10 is selected from Gln, Thr, Ala, Ile, Ser, and Asp,
    • X11 is selected from Ile, Ala, Thr, Val, Thr, Ser, and Tyr
    • X12 is selected from Gly, Gln, Ser, Ala, and Glu,
    • X13 is selected from Thr, Ala, Leu, Asp, Ser, Asn, Val, Trp, and Met,
    • X14 is selected from Val and Asp,
    • the sequence doesn't comprise a amino acids sequence of SEQ ID NO:2 (native AAV8 VR VIII).


In one embodiment, the capsid protein comprise a substituted amino acid sequence of Formula IV at the amino acids corresponding to amino acid position 585 to 597 of the native AAV 8 (SEQ ID NO:1): X1X2X3X4X5X6X7X8X9X10X11X12X13, wherein

    • X1 is Asn,
    • X2 is selected from Leu, Asn, His, and Phe,
    • X3 is Gln,
    • X4 is selected from Gln, Asn, Ser, and Ala,
    • X5 is selected from Gln, Thr, Ala, Gly, Ser, and Asn,
    • X6 is selected from Asn, Thr, and Gln,
    • X7 is selected from Thr, Ser, and Ala,
    • X8 is selected from Ala, Gln, Gly, and Arg,
    • X9 is selected from Pro and Ala,
    • X10 is selected from Gln, Thr, Ala, Ile, Ser, and Asp,
    • X11 is selected from Ile, Ala, Thr, and Val
    • X12 is selected from Gly, Gln, Ser, Ala, and Glu,
    • X13 is selected from Thr, Ala, Leu, Asp, Asn, Val, Trp, and Met,
    • the sequence doesn't comprise a amino acids sequence of SEQ ID NO:2 (native AAV8 VR VIII).


In one embodiment, the capsid protein comprise a substituted amino acid sequence of Formula II at the amino acids corresponding to amino acid position 585 to 597 of the native AAV 8 (SEQ ID NO:1): X1X2X3X4X5X6X7X8X9X10X11X12X13, wherein

    • X1 is Asn,
    • X2 is selected from Leu, Asn, and Phe,
    • X3 is Gln,
    • X4 is selected from Gln, Asn, Ser, and Ala,
    • X5 is selected from Thr, Ala, and Ser,
    • X6 is selected from Asn, Ser, and Thr,
    • X7 is selected from Thr, Ala, and Gly,
    • X8 is selected from Ala, Gln, Gly, and Arg,
    • X9 is selected from Pro and Ala,
    • X10 is selected from Gln, Ala, and Ile,
    • X11 is selected from Thr and Val,
    • X12 is selected from Gly and Gln,
    • X13 is selected from Thr, Leu, Asn, and Asp.


In the invention, the NCBI Reference Sequence of WT AAV8 capsid protein is YP_077180.1 (GenBank: AAN03857.1), as shown in SEQ ID NO:1.









(Amino Acid Sequence of WT AAV8 capsid)


SEQ ID NO: 1


MAADGYLPDWLEDNLSEGIREWWALKPGAPKPKANQQKQDDGRGLVLPGY





KYLGPFNGLDKGEPVNAADAAALEHDKAYDQQLQAGDNPYLRYNHADAEF





QERLQEDTSFGGNLGRAVFQAKKRVLEPLGLVEEGAKTAPGKKRPVEPSP





QRSPDSSTGIGKKGQQPARKRLNFGQTGDSESVPDPQPLGEPPAAPSGVG





PNTMAAGGGAPMADNNEGADGVGSSSGNWHCDSTWLGDRVITTSTRTWAL





PTYNNHLYKQISNGTSGGATNDNTYFGYSTPWGYFDFNRFHCHFSPRDWQ





RLINNNWGFRPKRLSFKLFNIQVKEVTQNEGTKTIANNLTSTIQVFTDSE





YQLPYVLGSAHQGCLPPFPADVFMIPQYGYLTLNNGSQAVGRSSFYCLEY





FPSQMLRTGNNFQFTYTFEDVPFHSSYAHSQSLDRLMNPLIDQYLYYLSR





TQTTGGTANTQTLGFSQGGPNTMANQAKNWLPGPCYRQQRVSTTTGQNNN





SNFAWTAGTKYHLNGRNSLANPGIAMATHKDDEERFFPSNGILIFGKQNA





ARDNADYSDVMLTSEEEIKTTNPVATEEYGIVADNLQQQNTAPQIGTVNS





QGALPGMVWQNRDVYLQGPIWAKIPHIDGNFHPSPLMGGEGLKHPPPQIL





IKNTPVPADPPTTENQSKLNSFITQYSTGQVSVEIEWELQKENSKRWNPE





IQYTSNYYKSTSVDFAVNTEGVYSEPRPIGTRYLTRNL*





The DNA sequence of WT AAV8 capsid is


atggctgccgatggttatcttccagattggctcgaggacaacctctctga





gggcattcgcgagtggtgggcgctgaaacctggagccccgaagcccaaag





ccaaccagcaaaagcaggacgacggccggggtctggtgcttcctggctac





aagtacctcggacccttcaacggactcgacaagggggagcccgtcaacgc





ggcggacgcagcggccctggagcacgacaaggcctacgaccagcagctgc





aggcgggtgacaatccgtacctgcggtataaccacgccgacgccgagttt





caggagcgtctgcaagaagatacgtcttttgggggcaacctcgggcgagc





agtcttccaggccaagaagcgggttctcgaacctctcggtctggttgagg





aaggcgctaagacggctcctggaaagaagagaccggtagagccatcaccc





cagcgttctccagactcctctacgggcatcggcaagaaaggccaacagcc





cgccagaaaaagactcaattttggtcagactggcgactcagagtcagttc





cagaccctcaacctctcggagaacctccagcagcgccctctggtgtggga





cctaatacaatggctgcaggcggtggcgcaccaatggcagacaataacga





aggcgccgacggagtgggtagttcctcgggaaattggcattgcgattcca





catggctgggcgacagagtcatcaccaccagcacccgaacctgggccctg





cccacctacaacaaccacctctacaagcaaatctccaacgggacatcggg





aggagccaccaacgacaacacctacttcggctacagcaccccctgggggt





attttgactttaacagattccactgccacttttcaccacgtgactggcag





cgactcatcaacaacaactggggattccggcccaagagactcagcttcaa





gctcttcaacatccaggtcaaggaggtcacgcagaatgaaggcaccaaga





ccatcgccaataacctcaccagcaccatccaggtgtttacggactcggag





taccagctgccgtacgttctcggctctgcccaccagggctgcctgcctcc





gttcccggcggacgtgttcatgattccccagtacggctacctaacactca





acaacggtagtcaggccgtgggacgctcctccttctactgcctggaatac





tttccttcgcagatgctgagaaccggcaacaacttccagtttacttacac





cttcgaggacgtgcctttccacagcagctacgcccacagccagagcttgg





accggctgatgaatcctctgattgaccagtacctgtactacttgtctcgg





actcaaacaacaggaggcacggcaaatacgcagactctgggcttcagcca





aggtgggcctaatacaatggccaatcaggcaaagaactggctgccaggac





cctgttaccgccaacaacgcgtctcaacgacaaccgggcaaaacaacaat





agcaacttgcctggactgctgggaccaaataccatctgaatggaagaaat





tcattggctaatcctggcatcgctatggcaacacacaaagacgacgagga





gcgtttttttcccagtaacgggatcctgatttttggcaaacaaaatgctg





ccagagacaatgcggattacagcgatgtcatgctcaccagcgaggaagaa





atcaaaaccactaaccctgtggctacagaggaatacggtatcgtggcaga





taacttgcagcagcaaaacacggctcctcaaattggaactgtcaacagcc





agggggccttacccggtatggtctggcagaaccgggacgtgtacctgcag





ggtcccatctgggccaagattcctcacacggacggcaacttccacccgtc





tccgcgatgggcggctttggcctgaaacatcctccgcctcagatcctgat





caagaacacgcctgtacctgcggatcctccgaccaccttcaaccagtcaa





agctgaactctttcatcacgcaatacagcaccggacaggtcagcgtggaa





attgaatgggagctgcagaaggaaaacagcaagcgctggaaccccgagat





ccagtacacctccaactactacaaatctacaagtgtggactttgctgtta





atacagaaggcgtgtactctgaaccccgccccattggcacccgttacctc





acccgtaatctgtaa






In one specific embodiment, the AAV variant comprises a substituted sequence corresponding to the position amino acids 585 to 597 of SEQ ID NO:1 (AAV8); preferably, the sequence comprises a amino acids sequence selected from the groups consisting of SEQ ID NO:3-42 as shown in Table 6, preferably selected from the groups consisting of SEQ ID NO: 2-3, 6-7, 9-11, 13-14, 16, 20-22, 24, 25, 32-33, 37, 39, 42 as shown in Table 10, more preferably, the AAV variant comprises a substituted sequence corresponding to the position amino acids 585 to 597 of SEQ ID NO:1 (AAV8), the sequence comprises a amino acids sequence selected from the groups consisting of SEQ ID NO:21 (AAV 8-Lib20), SEQ ID NO:25 (AAV 8-Lib25), SEQ ID NO:9 (AAV 8-Lib43), and SEQ ID NO:37 (AAV 8-Lib44).


In some embodiment, the AAV variant is AAV serotype 9. The present invention provides an AAV library comprising a multitude of adeno-associated virus (AAV) variants, the AAV variants comprises a variant AAV capsid protein comprising a substitution at one or more of amino acid residues N583, H584, Q585, S586, A587, Q588, A589, Q590, A591, Q592, T593, G594, W595, V596, corresponding to amino acid sequence of the native AAV 9 (SEQ ID NO:43), the substitution of amino acid residues is selected from N583Y, H584N, H584Q, H584K, H584L, H584F, Q585N, S586N, S586Q, S586A, S586D, S586G, A587T, A587Q, A587G, A587S, A587N, Q588A, Q588S, Q588D, Q588T, Q588N, A589S, A 589T, A589R, A589E, A589G, Q590A, Q590D, Q590G, Q590R, Q590T, A591P, A591T, Q592T, Q592A, Q592I, Q592S, Q592D, T593A, T593I, T593V, T593S, T593Y, G594Q, G594S, G594A, G594E, W595A, W595L, W595D, W595S, W595N, W595V, W 595T, W595M, V596D.


In one embodiment, the present invention provides library comprising a multitude of adeno-associated virus (AAV) variants, the AAV variants comprises a variant AAV capsid protein comprising one or more amino acid substitutions, the capsid protein comprise a substituted amino acid sequence corresponding to VR VIII region of the native AAV9 capsid protein. The capsid protein comprises a substituted amino acid sequence of Formula I at the amino acids corresponding to amino acid position 583 to 596 of the native AAV 9 (SEQ ID NO:43): X1X2X3X4X5X6X7X8X9X10X11X12X13X14, wherein

    • X1 is selected from Asn and Tyr,
    • X2 is selected from Leu, Asn, Gln, Lys, His, and Phe,
    • X3 is selected from Gln and Asn,
    • X4 is selected from Gln, Asn, Ser, Ala, Asp, and Gly,
    • X5 is selected from Gln, Thr, Ala, Gly, Ser, and Asn,
    • X6 is selected from Asn, Ala, Ser, Asp, Thr, and Gln,
    • X7 is selected from Thr, Ser, Ala, Arg, Glu, and Gly,
    • X8 is selected from Ala, Gln, Asp, Gly, Arg, and Thr,
    • X9 is selected from Pro, Ala, and Thr,
    • X10 is selected from Gln, Thr, Ala, Ile, Ser, and Asp,
    • X11 is selected from Ile, Ala, Thr, Val, Thr, Ser, and Tyr
    • X12 is selected from Gly, Gln, Ser, Ala, and Glu,
    • X13 is selected from Thr, Ala, Leu, Asp, Ser, Asn, Val, Trp, and Met,
    • X14 is selected from Val, and Asp,
    • the sequence doesn't comprise a amino acids sequence of SEQ ID NO:33 (native AAV9 VR VIII).


In one embodiment, VR VIII region is the position amino acids 583 to 595 of SEQ ID NO:43 (AAV9), as compared to a wild-type AAV9 capsid proteins; the capsid protein comprise a substituted amino acid sequence of Formula II at the amino acids corresponding to amino acid position 585 to 597 of the native AAV 9 (SEQ ID NO:43): X1X2X3X4X5X6X7X8X9X10X11X12X13, wherein

    • X1 is Asn,
    • X2 is Leu,
    • X3 is Gln,
    • X4 is Asn, or Ser,
    • X5 is selected from Ala, Ser, and Gly,
    • X6 is Asn,
    • X7 is Thr
    • X8 is selected from Ala, Gln, and Gly,
    • X9 is Pro, or Ala,
    • X10 is selected from Gln, Thr, and Ala,
    • X11 is Thr,
    • X12 is selected from Gly, Gln, Ala, and Glu,
    • X13 is selected from Thr, Asn, and Asp.


In the invention, the NCBI Reference Sequence of WT AAV9 capsid protein is AAS99264.1 (GenBank: AHF53541.1), as shown in SEQ ID NO:43.









(Amino Acid Sequence of WT AAV9 capsid)


SEQ ID NO: 4


MAADGYLPDWLEDNLSEGIREWWALKPGAPQPKANQQHQDNARGLVLPGY





KYLGPGNGLDKGEPVNAADAAALEHDKAYDQQLKAGDNPYLKYNHADAEF





QERLKEDTSFGGNLGRAVFQAKKRLLEPLGLVEEAAKTAPGKKRPVEQSP





QEPDSSAGIGKSGAQPAKKRLNFGQTGDTESVPDPQPIGEPPAAPSGVGS





LTMASGGGAPVADNNEGADGVGSSSGNWHCDSQWLGDRVITTSTRTWALP





TYNNHLYKQISNSTSGGSSNDNAYFGYSTPWGYFDFNRFHCHFSPRDWQR





LINNNWGFRPKRLNFKLFNIQVKEVIDNNGVKTIANNLTSTVQVFTDSDY





QLPYVLGSAHEGCLPPFPADVFMIPQYGYLTLNDGSQAVGRSSFYCLEYF





PSQMLRTGNNFQFSYEFENVPFHSSYAHSQSLDRLMNPLIDQYLYYLSKT





INGSGQNQQTLKFSVAGPSNMAVQGRNYIPGPSYRQQRVSTTVTQNNNSE





FAWPGASSWALNGRNSLMNPGPAMASHKEGEDRFFPLSGSLIFGKQGTGR





DNVDADKVMITNEEEIKTTNPVATESYGQVATNHQSAQAQAQTGWVQNQG





ILPGMVWQDRDVYLQGPIWAKIPHTDGNFHPSPLMGGFGMKHPPPQILIK





NTPVPADPPTAFNKDKLNSFITQYSTGQVSVEIEWELQKENSKRWNPEIQ





YTSNYYKSNNVEFAVNTEGVYSEPRPIGTRYLTRNL





The DNA sequence of WT AAV9 capsid is


atggctgccgatggttatcttccagattggctcgaggacaaccttagtga





aggaattcgcgagtggtgggctttgaaacctggagcccctcaacccaagg





caaatcaacaacatcaagacaacgctcgaggtcttgtgcttccgggttac





aaataccttggacccggcaacggactcgacaagggggagccggtcaacgc





agcagacgcggcggccctcgagcacgacaaggcctacgaccagcagctca





aggccggagacaacccgtacctcaagtacaaccacgccgacgccgagttc





caggagcggctcaaagaagatacgtcttttgggggcaacctcgggcgagc





agtcttccaggccaaaaagaggcttcttgaacctcttggtctggttgagg





aagcggctaagacggctcctggaaagaagaggcctgtagagcagtctcct





caggaaccggactcctccgcgggtattggcaaatcgggtgcacagcccgc





taaaaagagactcaatttcggtcagactggcgacacagagtcagtcccag





accctcaaccaatcggagaacctcccgcagccccctcaggtgtgggatct





cttacaatggcttcaggtggtggcgcaccagtggcagacaataacgaagg





tgccgatggagtgggtagttcctcgggaaattggcattgcgattcccaat





ggctgggggacagagtcatcaccaccagcacccgaacctgggccctgccc





acctacaacaatcacctctacaagcaaatctccaacagcacatctggagg





atcttcaaatgacaacgcctacttcggctacagcaccccctgggggtatt





ttgacttcaacagattccactgccacttctcaccacgtgactggcagcga





ctcatcaacaacaactggggattccggcctaagcgactcaacttcaagct





cttcaacattcaggtcaaagaggttacggacaacaatggagtcaagacca





tcgccaataaccttaccagcacggtccaggtcttcacggactcagactat





cagctcccgtacgtgctcgggtcggctcacgagggctgcctcccgccgtt





cccagcggacgttttcatgattcctcagtacgggtatctgacgcttaatg





atggaagccaggccgtgggtcgttcgtccttttactgcctggaatatttc





ccgtcgcaaatgctaagaacgggtaacaacttccagttcagctacgagtt





tgagaacgtacctttccatagcagctacgctcacagccaaagcctggacc





gactaatgaatccactcatcgaccaatacttgtactatctctcaaagact





attaacggttctggacagaatcaacaaacgctaaaattcagtgtggccgg





acccagcaacatggctgtccagggaagaaactacatacctggacccagct





accgacaacaacgtgtctcaaccactgtgactcaaaacaacaacagcgaa





tttgctggcctggagcttcttcttgggctctcaatggacgtaatagcttg





atgaatcctggacctgctatggccagccacaaagaaggagaggaccgttt





ctttcctttgtctggatctttaatttttggcaaacaaggaactggaagag





acaacgtggatgcggacaaagtcatgataaccaacgaagaagaaattaaa





actactaacccggtagcaacggagtcctatggacaagtggccacaaacca





ccagagtgcccaagcacaggcgcagaccggctgggttcaaaaccaaggaa





tacttccgggtatggtttggcaggacagagatgtgtacctgcaaggaccc





atttgggccaaaattcctcacaggacggcaactttcacccttctccgctg





atgggagggtttggaatgaagcacccgcctcctcagatcctcatcaaaaa





cacacctgtacctgcggatcctccaacggccttcaacaaggacaagctga





actctttcatcacccagtattctactggccaagtcagcgtggagatcgag





tgggagctgcagaaggaaaacagcaagcgctggaacccggagatccagta





cacttccaactattacaagtctaataatgttgaatttgctgttaatactg





aaggtgtatatagtgaaccccgccccattggcaccagatacctgactcgt





aatctgtaa






In one specific embodiment, the sequence comprises a amino acids sequence selected from the groups consisting of SEQ ID NO:3-42 as shown in Table 8, preferably, the AAV variant comprises a substituted sequence corresponding to the position amino acids 583 to 595 of SEQ ID NO:43 (AAV9), the sequence comprises a amino acids sequence selected from the groups consisting of SEQ ID NO:29 (AAV 9-Lib31), SEQ ID NO:14 (AAV 9-Lib 33), SEQ ID NO:9 (AAV 9-Lib43), and SEQ ID NO:11 (AAV 9-Lib46).


In another aspect, the present invention provides a library of polynucleotides encoding the above AAV variants of the AAV library or vectors comprising the above polynucleotides.


The present invention provides a library of cloning cells comprising the above AAV variants of the AAV library according to the present invention and/or comprising polynucleotides encoding the same


In another aspect, the present invention also provides a method of generating an AAV library, comprising:

    • a) generating variant capsid protein genes encoding variant capsid proteins comprising substituted sequences corresponding to VR VIII region of SEQ ID NO:1 (AAV8) or SEQ ID NO:43 (AAV9);
    • b) cloning said variant capsid protein genes into AAV vectors, wherein said AAV vectors are replication competent AAV vectors.


In one specific embodiment, VR VIII region is the position amino acids 585 to 597 or 598 of SEQ ID NO:1 (AAV8) or the position amino acids 583 to 595 or 596 of SEQ ID NO:43 (AAV9).


In one specific embodiment, the method further comprises:

    • 1) screening said AAV vector library from b) for variant AAV capsid proteins for increased transduction or tropism in human tissue or cells as compared to a non-variant parent capsid protein; and
    • 2) selecting said variant AAV capsid vector from c).


In another aspect, the present invention also provides use of an AAV library according to present invention, a method according to present invention, a library of polynucleotides according to present invention, and/or a library of cloning cells according to present invention for identifying an AAV variant infecting a target cell or tissue of interest.





BRIEF DESCRIPTION OF THE DRAWINGS


FIG. 1 shows the outline of in vivo screen strategy.



FIG. 2 shows the screen results. A) The week 1 screen result for liver. B) The week 1 screen result for brain. C) The week 4 screen result for various tissues. The result of starting library was marked in blue line.



FIG. 3 shows the effect of AAV8-VR VIII variants. A) Luciferase expression in HEK293T cells transduced with AAV8 and AAV8-VR VIII variants. MOI =10,000, n=3. B) In vivo luciferase expression in C57BL/6J mice 3 days after 1×10{circumflex over ( )}10 vg of control AAV8 and AAV8-VR VIII variants following intravenous injection. Negative control, PBS injected animals. The same results were observed in two independent biological repeats. C) Luciferase quantification of AAV8 and AAV8-VR VIII variants in C57BL/6J animals or PBS control at day 3, 7 and 14. n=6 Data are reported as mean±SEM. D) Luciferase quantification of AAV8 and AAV8-VR VIII variants in C57BL/6J animals or PBS control at day 3. E) Luciferase quantification of AAV8 and AAV8-VR VIII variants in C57BL/6J animals or PBS control at day 7. F) Luciferase quantification of AAV8 and AAV8-VR VIII variants in C57BL/6J animals or PBS control at day 14.The same results were observed in two independent biological repeats.



FIG. 4 shows at week 2 post injection, lung, liver, spleen, heart, kidney, lymph node, right quadriceps (LQ), left quadriceps (LQ) muscle and brain were harvested to detect the vector genome copy number in each tissue, n=6. The absolute GCNs in different tissues were plotted together for AAV8 (A), AAV8-Lib20 (B), AAV8-Lib25 (C), AAV8-Lib43 (D), AAV8-Lib44 (E), AAV8-Lib45 (F). The same results were observed in two independent biological repeats.



FIG. 5 shows the liver GCNs among different AAV8 VR VIII variants. Data are reported as mean±SEM



FIG. 6 shows at week 2 post injection, we determined the serum alanine transaminase (ALT) level. No significant change was noticed between control (PBS and AAV8) and AAV8-VR VIII variants.



FIG. 7 shows the effect of AAV9-VR VIII variants. A) In vivo luciferase expression in C57BL/6J mice 7 days after 1×10{circumflex over ( )}11 vg of control AAV9 and AAV9-VR VIII variants following intravenous injection. Negative control, PBS injected animals. B) Luciferase quantification of AAV9 and AAV9-VR VIII variants in C57BL/6J animals or PBS control. Data are reported as mean±SEM C) Luciferase expression and quantification (D) of AAV9 and AAV9-VR VIII variants in the head of C57BL/6J animals or PBS control. n=6 Data are reported as mean±SEM E) The head/body ratio of AAV9 and AAV9-VR VIII variants. For all the above experiments, the same results were observed in two independent biological repeats.



FIG. 8 shows luciferase expression in HEK293T cells transduced with AAV9 and AAV9-VR VIII variants. MOI=10,000, n=3.



FIG. 9 shows at week 2 post injection, tissues were harvested to detect the vector genome copy number, n=6. The absolute GCNs in each tissues were plotted for liver (A), brain (B), heart (C), and Lung (D). The same results were observed in two independent biological repeats.



FIG. 10 shows ALT level following AAV9 VR VIII variants-mediated gene delivery.



FIG. 11 shows the effect of AAV2-VR VIII variants. A) Luciferase expression in HEK293T cells transduced with AAV2 and AAV2-VR VIII variants. MOI=10,000, n=3. B) In vivo luciferase expression in C57BL/6J mice 3 days after 1×10{circumflex over ( )}10vg of control AAV2 and AAV2-VR VIII variants following intravenous injection. Negative control, PBS injected animals. The same results were observed in two independent biological repeats. C) Luciferase quantification of AAV2 and AAV2-VR VIII variants in C57BL/6J animals or PBS control at day 3, 7 and 14. n=6 Data are reported as mean±SEM.



FIG. 12 shows the effect of AAV2-VR VIII variants. A) In vivo luciferase expression in C57BL/6J mice 7 days after 1×10{circumflex over ( )}10 vg of control AAV2 and AAV2-VR VIII variants following intravenous injection. Negative control, PBS injected animals. B) Luciferase quantification of AAV2 and AAV8-VR VIII variants in C57BL/6J animals or PBS control at day 7. C) In vivo luciferase expression in C57BL/6J mice 14 days after 1×10{circumflex over ( )}10 vg of control AAV2 and AAV2-VR VIII variants following intravenous injection. Negative control, PBS injected animals. D) Luciferase quantification of AAV8 and AAV8-VR VIII variants in C57BL/6J animals or PBS control at day 14. The same results were observed in two independent biological repeats.



FIG. 13 shows hFIX expression in monkey plasma.





DETAILED DESCRIPTION

The following description of the disclosure is merely intended to illustrate various embodiments of the disclosure. As such, the specific modifications discussed are not to be construed as limitations on the scope of the disclosure. It will be apparent to one skilled in the art that various equivalents, changes, and modifications may be made without departing from the scope of the disclosure, and it is understood that such equivalent embodiments are to be included herein. All references cited herein, including publications, patents and patent applications are incorporated herein by reference in their entirety.


The articles “a”, “an”, and “the” are used herein to refer to one or to more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “a polypeptide complex” means one polypeptide complex or more than one polypeptide complex.


As used herein, the term “about” or “approximately” refers to a quantity, level, value, number, frequency, percentage, dimension, size, amount, weight or length that varies by as much as 30, 25, 20, 25, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1%to a reference quantity, level, value, number, frequency, percentage, dimension, size, amount, weight or length. In particular embodiments, the terms “about” or “approximately” when preceding a numerical value indicates the value plus or minus a range of 15%, 10%, 5%, or 1%.


Throughout this disclosure, unless the context requires otherwise, the words “comprise”, “comprises” and “comprising” will be understood to imply the inclusion of a stated step or element or group of steps or elements but not the exclusion of any other step or element or group of steps or elements. By “consisting of” is meant including, and limited to, whatever follows the phrase “consisting of”. Thus, the phrase “consisting of” indicates that the listed elements are required or mandatory, and that no other elements may be present. By “consisting essentially of” is meant including any elements listed after the phrase, and limited to other elements that do not interfere with or contribute to the activity or action specified in the disclosure for the listed elements. Thus, the phrase “consisting essentially of” indicates that the listed elements are required or mandatory, but that other elements are optional and may or may not be present depending upon whether or not they affect the activity or action of the listed elements.


Pharmaceutical Composition

The present disclosure also provides a pharmaceutical composition comprising the polypeptide complex or the bispecific polypeptide complex provided herein and a pharmaceutically acceptable carrier.


The term “pharmaceutically acceptable” indicates that the designated carrier, vehicle, diluent, excipient (s) , and/or salt is generally chemically and/or physically compatible with the other ingredients comprising the formulation, and physiologically compatible with the recipient thereof.


A “pharmaceutically acceptable carrier” refers to an ingredient in a pharmaceutical formulation, other than an active ingredient, which is bioactivity acceptable and nontoxic to a subject. Pharmaceutical acceptable carriers for use in the pharmaceutical compositions disclosed herein may include, for example, pharmaceutically acceptable liquid, gel, or solid carriers, aqueous vehicles, nonaqueous vehicles, antimicrobial agents, isotonic agents, buffers, antioxidants, anesthetics, suspending/dispending agents, sequestering or chelating agents, diluents, adjuvants, excipients, or non-toxic auxiliary substances, other components known in the art, or various combinations thereof.


Method of Treatment

Therapeutic methods are also provided, comprising: administering a therapeutically effective amount of the polypeptide complex or the bispecific polypeptide complex provided herein to a subject in need thereof, thereby treating or preventing a condition or a disorder. In certain embodiments, the subject has been identified as having a disorder or condition likely to respond to the polypeptide complex or the bispecific polypeptide complex provided herein.


As used herein, the term “subject” includes any human or nonhuman animal. The term “nonhuman animal” includes all vertebrates, e.g., mammals and non-mammals, such as nonhuman primates, sheep, dogs, cats, horses, cows, chickens, amphibians, reptiles, etc. Except when noted, the terms “patient” or “subject” are used interchangeably.


The terms “treatment” and “therapeutic method” refer to both therapeutic treatment and prophylactic/preventative measures. Those in need of treatment may include individuals already having a particular medical disorder as well as those who may ultimately acquire the disorder.


In certain embodiments, the conditions and disorders include tumors and cancers, for example, non-small cell lung cancer, small cell lung cancer, renal cell cancer, colorectal cancer, ovarian cancer, breast cancer, pancreatic cancer, gastric carcinoma, bladder cancer, esophageal cancer, mesothelioma, melanoma, head and neck cancer, thyroid cancer, sarcoma, prostate cancer, glioblastoma, cervical cancer, thymic carcinoma, leukemia, lymphomas, myelomas, mycoses fungoids, merkel cell cancer, and other hematologic malignancies, such as classical Hodgkin lymphoma (CHL) , primary mediastinal large B-cell lymphoma, T-cell/histiocyte-rich B-cell lymphoma, EBV-positive and -negative PTLD, and EBV-associated diffuse large B-cell lymphoma (DLBCL) , plasmablastic lymphoma, extranodal NK/T-cell lymphoma, nasopharyngeal carcinoma, and HHV8-associated primary effusion lymphoma, Hodgkin's lymphoma, neoplasm of the central nervous system (CNS) , such as primary CNS lymphoma, spinal axis tumor, brain stem glioma.


EXAMPLES
Example 1
The Equipments and Regents









TABLE 1







The equipment used in the invention









Equipments
Product number
Supplier





SpectraMax ® M5/M5e
SpectraMax ®
Molecular


Multimode
M5/M5e
Devices


Plate Reader




Diagnostica Stago STart
ST art
Diagnostica


4 Hemostasis Analyzer

Stago


EnVision 2105
2105-0010
PerkinElmer


multimode plate reader




Ice machine
ST150
Sciencetool


CYRO Vessel
CY50935-70
Thermo Fisher


Locator 4 PLUS

Scientific


   4° C. refrigerator
HYC390F
Haier


−20° C. refrigerator
DW-40L348
Haier


−80° C. refrigerator
8960086V
Thermo Fisher




Scientific


Biosafety cabinet
BSC-II-A2
Sujing


Incubator
HERAcell 240i
Thermo Fisher




Scientific


Countess ™ II
AMQAX1000
Thermo Fisher


cell counter

Scientific


Inverted Microscope
ECLIPS T52
Nikon


Refrigerated centrifuge
5424R
Eppendorf


Centrifuge
5810R
Eppendorf


Ultracentrifuge
Optima XPN-100
Beckman Coulter


Basic Power Supply
PowerPac Basic
Bio-Rad


Amersham Imager 680
Amersham Imager
GE Healthcare


blot and gel imager
680QC



NanoDrop One
NanoDrop One/Onec
Invitrogen


Microvolume UV-Vis
UV-Vis



Spectrophotometers




Applied Biosystems
QuantStudio ™ 7
Applied


QuantStudio ™ 7

Biosystems


Flex Real-Time




PCR System




ProFlex ™ 3 × 32-
ProFlex ™ 3 × 32-
Thermo Fisher


well PCR
well PCR
Scientific


System
System-4484073



Tanon 2500/2500R
2500 R
Tanon


Gel Imaging System




Milli-Q ® Direct 8 Water
Direct 8
EMD Millipore


Purification System
















TABLE 2







The regents and supplies used in the study









Reagents & Supplies












Cell culture
DMEM, High Glucose
Gibco 11965118



HEK293T
ATCC CRL-3216 ™



Trypsin-EDTA (0.25%), phenol red
Invitrogen 25200072



DPBS
Corning 21-031-CV



FBS
Corning 35-081-CV



DMSO
Sigma-Aldrich D2650



Antibiotic-Antimycotic, 100X
Gibco 15240062



Countess ™ Cell Counting Chamber Slides
Invitrogen C10312



Corning ® 150 mm TC-treated Culture
Corning 430599



Dish




1.5 mL MaxyClear Snaplock
Axygen Met-150-C



Microcentrifuge Tube



Construction of AAV
NdeI
NEB R0111S


plasmid
XbaI
NEB R0145S



NEBuilder HiFi DNA
NEB E2621L



Assembly Master Mix




Ampicillin Sodium(100 mg/ml)
TIANGEN RT501



Endura Competent Cells
Lucigen 60241-2



0.2 mL Polypropylene PCR Tube Strips,
Axygen PCR-0208-C



8 Tubes/Strip




8-Strip PCR Tube Caps for 0.2 mL PCR
Axygen PCR-02CP-C



Tube Strips, Clear PP



AAV VR VIII variants
PEI 25K
Polysciences 23966-1


packaging, mixing for in
EndoFree Plasmid Maxi Kit
QIAGEN 12362


vivo selection &
Benzonase
Novagen 70664


Recombinant AAV
OptiPrep ™ Density Gradient Medium
Sigma-Aldrich D1556


packaging
Power SYBR ™ Green PCR Master Mix
Applied Biosystems 4367659



Fisherbrand ™ Cell Lifters
Fisher Scientific 08100240



Quick-Seal Polypropylene Tube
Beckman Coulter 342414



APOLLO 20 mL 150 KDa Concentrators
Orbital Biosciences AP2015010



HiTrap ® Q High Performance
GE Healthcare 17-1154-01


In vivo Selection for
C57BL/6J mice
Shanghai SLAC Laboratory


liver-targeting variants

Animal Co.



DNesay Blood&Tissue kit
QIAGEN 69506


NGS to quantify the
Zymoclean ™ Gel DNA Recovery Kit
Zymo Research D4002


AAV genome reads in
Agarose
Biowest 111860


tissues
Marker II
TIANGEN MD102



Gel Loading Dye, Purple (6X)
NEB B7024S


Titration of particles by
AAV8 Titration ELISA
PROGEN-PRAAV8


ELISA
Recombinant Adeno-associated virus 8
ATCC VR-1816


In vivo rAAV-luciferase
XenoLight D-Luciferin-K+ Salt
PerkinElmer 122799-10


transduction and
Bioluminescent Substrate



detection
ALT ActivityAssay Kit
Sigma-Aldrich MAK052-1KT


In vivo rAAV-hFIX
F9 KO mice
Shanghai Model Oranisms


transduction




Tissule, plasma and
DPBS
Corning


serum collection

21-031-CV/Hyclone-5H30028.03



3.8% sodium citrate
HIMEDIA-R014



10% Neutral buffered formalin
INNOCHEM-A28231


Detection if hFIX
VisuLize Factor IX Antigen Kit
Affinity Biologicals FIX-AG


expression
Rox Factor IX
Rossix 900020


In vivo viral genome
Power SYBR ™ Green PCR Master Mix
Applied Biosystems 4367659


copy number
DEPC-Treated water
Invitrogen AM9916



DNesay Blood&Tissue kit
QIAGEN 69506



Hard-Shell ® 384-Well PCR Plates
Bio-Rad H5P3801



Axygen ® 60 μm CyclerSeal Sealing Film
Axygen PCR-TS



for Storage and PCR Application




Multiplate ™ 96-Well PCR Plates, low
Bio-Rad MLP-9601



profile



In vitro Infectivity
Bright-Glo ™ Luciferase Assay System
Promega E2620



96 Well Clear Round Bottom TC-Treated
Corning 3799



Microplate



Sodium dodecyl
NuPAGE ™ 4-12% Bis-Tris Protein Gels,
Invitrogen NP0321BOX


sulfate-polyacrylamide
1.0 mm, 10-well




NuPAGE ™ Sample Reducing Agent
Invitrogen NP0009



(10X)




Fast Silver Stain Kit
Beyotime P0017S



BenchMark ™ Protein Ladder
Invitrogen 10747012
















TABLE 3





The various oligos used in the study







Construction of AAV plasmids









pITR2-Rep2-Cap8-
Forward
5′-TAAGCCAACTAGTGGAACCGGTGCGGCCGCACGCGTGGAGTTTAAGCCC


library-ITR2-1

GAGTGAGCACGCAGGGTCTCCATTTTGAAGCGGGAGGTTTGAACGCGCAGCC




GCCATGCCGGGGTT-3′



Reverse
5′-GAAGATAACCATCGGCAGCCATTTAATTAAACCTGATTTAAATCATTTA




TTGTTCAAAG-3′


pITR2-Rep2-Cap8-
Forward
5′-CTTTGAACAATAAATGATTTAAATCAGGTTTAATTAAATGGCTGCCGAT


library-ITR2-2

GGTTAT CTTC-3′



Reverse
5′-TTCCAATTTGAGGAGCCGTGTTTTGCTGCTGCAACATATGGTTATCTGC




CACGATACCGTATT-3′


pITR2-Rep2-Cap8-
Forward
5′-ACACGGCTCCTCAAATTGGAATCTAGACTTGTCAACAGCCAGGGGGCCT


library-ITR2-3

TACCCGGTATGGTCTG-3′



Reverse
5′-GCCAACTCCATCACTAGGGGTTCCTGCGGCCGCTCGGTCCGCACGTGGT




TACCTACAAAATGCTAGCTTACAGATTACGGGTGAGGTAACG-3′


Cap8-library
Forward
5′-GCATCTTTGAACAATAAATGATTTAAATCAGGTATGGCTGCCGATG


region




pAAV-RC8
Forward
5′-TTGCTTGTTAATCAATAAACCG-3′


backbone
Reverse
5′-ACCTGATTTAAATCATTTATTGTTCAAAGATGC-3′


pAAV-RC9
Forward
5′-TTGCTTGTTAATCAATAAACCG-3′


backbone
Reverse
5′-ACCTGATTTAAATCATTTATTGTTCAAAGATGC-3′










Titering and Mixing of AAV Capsid Library









Rep gene
Forward
5′-GCAAGACCGGATGTTCAAAT-3′



Reverse
5′-CCTCAACCACGTGATCCTTT-3′










Titering of Recombinant AAV









CMV promoter
Forward
5′-TCCCATAGTAACGCCAATAGG-3′



Reverse
5′-CTTGGCATATGATACACTTGATG-3′



Forward
5′-TCCCATAGTAACGCCAATAGG-3′



Reverse
5′-CTTGGCATATGATACACTTGATG-3′










Next Generation Sequencing to quantify the AAV genome reads in tissues









VR VIII region
Forward
5′-CAAAATGCTGCCAGAGACAA-3′



Reverse
5′-GTCCGTGTGAGGAATCTTGG-3′










IN vivo viral genome copy number









CMV promoter
Forward
5′-TCCCATAGTAACGCCAATAGG-3′



Reverse
5′-CTTGGCATATGATACACTTGATG-3′
















TABLE 4







The primers used for amplifying pAAV-RC9-library fragment1









target
primers
sequences





Cap9-lib2-1
Cap9-F
GCATCTTTGAACAATAAATGATTTAAATCAGGTATGGCTGCCGATGG




TTATCT



Cap9-lib2-R
AGTTTGTGTCTGGGGTGCAGTATTAGCCGATTGTAAGTTTGTGGCCA




CTTGTCCATAGG





Cap9-lib7-1
Cap9-F
GCATCTTTGAACAATAAATGATTTAAATCAGGTATGGCTGCCGATGG




TTATCT



Cap9-lib7-R
GGTCCCTGTTTGAGGAGCGGTGTTTGCCGATTGCAGGTTTGTGGCCA




CTTGTCCATAGG





Cap9-lib31-1
Cap9-F
GCATCTTTGAACAATAAATGATTTAAATCAGGTATGGCTGCCGATGG




TTATCT



Cap9-lib31-R
ATTTTCTGTAGTTGGACCAGTATTTGAGTTTTGCAAATTTGTGGCCA




CTTGTCCATAGG





Cap9-lib33-1
Cap9-F
GCATCTTTGAACAATAAATGATTTAAATCAGGTATGGCTGCCGATGG




TTATCT



Cap9-lib33-R
AGTTCCGGTCGCAGGGGCTGTGTTGCTGCTCTGGAGATTTGTGGCCA




CTTGTCCATAGG





Cap9-lib43-1
Cap9-F
GCATCTTTGAACAATAAATGATTTAAATCAGGTATGGCTGCCGATGG




TTATCT



Cap9-lib43-R
GGTCCCCGTTTGAGGAGCGGTGTTTGCCGACTGTAGGTTTGTGGCCA




CTTGTCCATAGG





Cap9-lib11-1
Cap9-F
GCATCTTTGAACAATAAATGATTTAAATCAGGTATGGCTGCCGATGG




TTATCT



Cap9-lib11-R
AGTTCCTGTAGTTGGACCAGTGTTTGAGTTTTGCAAATTTGTGGCCA




CTTGTCCATAGG





Cap9-lib46-1
Cap9-F
GCATCTTTGAACAATAAATGATTTAAATCAGGTATGGCTGCCGATGG




TTATCT



Cap9-lib46-R
ATCTGCGGTAGCTGCTTGTGTGTTGCCGCTCTGGAGGTTTGTGGCCA




CTTGTCCATAGG
















TABLE 5







The primers used for amplifying pAAV-RC9-library fragment2









target
primers
sequences





Cap9-lib2-2
Cap9-lib2-F
AACTTACAATCGGCTAATACTGCACCCCAGACACAAACTGTTCAAAACC




AAGGAATACTTC



Cap9-R
GTTTATTGATTAACAAGCAATTACAGATTACGAGTCAGGT





Cap9-lib7-2
Cap9-lib7-F
AACCTGCAATCGGCAAACACCGCTCCTCAAACAGGGACCGTTCAAAACC




AAGGAATACTT



Cap9-R
GTTTATTGATTAACAAGCAATTACAGATTACGAGTCAGGT





Cap9-lib31-2
Cap9-lib31-F
AATTTGCAAAACTCAAATACTGGTCCAACTACAGAAAATGTTCAAAACC




AAGGAATACTTC



Cap9-R
GTTTATTGATTAACAAGCAATTACAGATTACGAGTCAGGT





Cap9-lib33-2
Cap9-lib33-F
AATCTCCAGAGCAGCAACACAGCCCCTGCGACCGGAACTGTTCAAAACC




AAGGAATACTT



Cap9-R
GTTTATTGATTAACAAGCAATTACAGATTACGAGTCAGGT





Cap9-lib43-2
Cap9-lib43-F
AACCTACAGTCGGCAAACACCGCTCCTCAAACGGGGACCGTTCAAAACC




AAGGAATACTT



Cap9-R
GTTTATTGATTAACAAGCAATTACAGATTACGAGTCAGGT





Cap9-lib11-2
Lib-LP-F
GCATCTTTGAACAATAAATGATTTAAATCAGGTATGGCTGCCGATGGTT




ATCT



Cap9-R
AGTTCCTGTAGTTGGACCAGTGTTTGAGTTTTGCAAATTTGTGGCCACT




TGTCCATAGG





Cap9-lib46-2
Lib-LP-F
GCATCTTTGAACAATAAATGATTTAAATCAGGTATGGCTGCCGATGGTT




ATCT



Cap9-R
ATCTGCGGTAGCTGCTTGTGTGTTGCCGCTCTGGAGGTTTGTGGCCACT




TGTCCATAGG









Example 2
Methods
Cell Culture

HEK293T cells were purchased from ATCC (ATCC, Manassas, Va.). HEK293T cells were maintained in complete medium containing DMEM (Gibco, Grand Island, N.Y.), 10% FBS (Corning, Manassas, Va.), 1% Anti-Anti (Gibco, Grand Island, N.Y.). HEK293T cells were grown in adherent culture using 15 cm dish (Corning, Corning, Calif.) in a humidified atmosphere at 37° C. in 5% CO2 and were sub-cultured after treatment with trypsin-EDTA (Gibco, Grand Island, N.Y.) for 2-5 min in the incubator, washed and re-suspended in the new complete medium.


Construction of AAV Plasmids

Plasmid pAAV-RC8 contains the Rep encoding sequences from AAV2 and Cap encoding sequences from AAV8. We generated a fragment that contains 5′ MluI and AAV's native promoter, upstream of the Rep2 gene in the pAAV-RC8 plasmid, by using the









forward primer:


5′-TAAGCCAACTAGTGGAACCGGTGCGGCCGCACGCGTGGAGTTTAAGC





CCGAGTGAGCACGCAGGGTCTCCATTTTGAAGCGGGAGGTTTGAACGCGC





AGCCGCCATGCCGGGGTT-3′,


and





reverse primer:


5′-GAAGATAACCATCGGCAGCCATTTAATTAAACCTGATTTAAATCATT





TATTGTTCAAAG-3′.






To substitute VR VIII sequence of wild type AAV8, we introduced NdeI and XbaI restriction sites into 1756 bp and 1790 bp of the type 8 capsule (Cap8) gene, so the Cap8 region was generated by high-fidelity PCR amplification of two DNA fragments from plasmid pAAV-RC8.


One fragment was produced by using the









forward primer:


5′-CTTTGAACAATAAATGATTTAAATCAGGTTTAATTAAATGGCTGCC





GATGGTTATCTTC-3′,


and





reverse primer:


5′-TTCCAATTTGAGGAGCCGTGTTTTGCTGCTGCAACATATGGTTATC





TGCCACGATACCGTATT-3′;





the other fragment was produced by using the


forward primer:


5′-ACACGGCTCCTCAAATTGGAATCTAGACTGTCAACAGCCAGGGGGC





CTTACCCGGTATGGTCTG-3′,


and





reverse primer:


5′-GCCAACTCCATCACTAGGGGTTCCTGCGGCCGCTCGGTCCGCACGT





GGTTACCTACAAAATGCTAGCTTACAGATTACGGGTGAGGTAACG-3′.






Plasmid pssAAV-CMV-GFP-mut was digested by NotI (NEB, Ipswich, Mass.). The three fragments and linearized vector (pssAAV-CMV-GFP-mut) were assembled together with the NEB HiFi Builder (NEB, Ipswich, Mass.). The assembled product with the correct orientation and sequence was called pITR2-Rep2-Cap8-ITR2.


We then synthesized these 52 VR VIII oligo sequences with flanking 20nt overlapping sequences the same as Cap8 gene (Genewiz). These 52 sequences were used to substitute the VR VIII of AAV8 capsid backbone, individually, which were further subcloned into an all-in-one construct containing the modified capsid sequences with rep and inverted terminated repeats (ITRs) from AAV2 (FIG. 1A). Plasmid pITR2-Rep2-Cap8-ITR2 was digested with the enzyme NdeI (NEB, Ipswich, Mass.) and XbaI (NEB, Ipswich, Mass.) for linearization to generate a vector backbone. To substitute the wild type AAV8 VR VIII region, each VR VIII oligo was assembled with linearized pITR2-Rep2-Cap8-mut-ITR2 vector individually. The assembled product with the correct orientation and sequence was called pITR2-Rep2-Cap8-library-ITR2. Therefore, we have generated 52 different pITR2-Rep2-Cap8-library-ITR2 plasmids.


To generate recombinant pAAV-RC8-library plasmids, the whole Cap8-library fragment, 2.2 kb, from selected pITR2-Rep2-Cap8-library-ITR2 plasmids and backbone from pAAV-RC8, 5.2 kb, were assembled together using the NEB HiFi Builder (NEB, Ipswich, Mass.). Briefly, the whole Cap8-library region was produced by high-fidelity PCR amplification of plasmid pITR2-Rep2-Cap8-library-ITR2 using the forward primer 5′-GCATCTTTGAACAATAAATGATTTAAATCAGGTATGGCTGCCGATGGTTATCT-3′ and reverse primer 5′-GTTTATTGATTAACAAGCAATTACAGATTACGGGTGAGGT-3′. The vector backbone was produced by high-fidelity PCR amplification of plasmid pAAV-RC8 using the forward primer 5′-TTGCTTGTTAATCAATAAACCG-3′ and reverse primer 5′-ACCTGATTTAAATCATTTATTGTTCAAAGATGC-3′. The assembled product with the correct orientation and sequence was called pAAV-RC8-library.


Plasmid pAAV-RC9 contains the Rep encoding sequences from AAV2 and Cap encoding sequences from AAV9, synthesized by Genewiz. The whole Cap9-library region was produced by high-fidelity PCR amplification of two DNA fragments from plasmid pAAV-RC9. One fragment was produced by using the primer sets in the Table 4, the other fragment was produced by using the primer sets in the Table 5. The linear vector backbone of pAAV-RC9 was also produced by high-fidelity PCR amplification of plasmid pAAV-RC9 using the forward primer of 5′-TTGCTTGTTAATCAATAAACCG-3′ and reverse primer of 5′-ACCTGATTTAAATCATTTATTGTTCAAAGATGC-3′. The two DNA fragments and linearized vector (pAAV-RC9) were assembled together using NEB HiFi Builder (NEB, Ipswich, Mass.). The product with the correct orientation and sequence was called pAAV-RC9-library.


AAV Capsid Library Packaging

The packaging and purification of AAV capsid library were performed as previously described with some modifications. Briefly, HEK293T cells were co-transfected with 23.7 μg of individual pITR2-Rep2-Cap8-library-ITR2 plasmid and 38.7 μg of pHelper (Cell Biolabs) for separate packaging. Polyethyleneimine (PEI, linear, MW 25000, Polysciences, Inc., Warrington, Pa.) was used as transfection reagent. Cells were harvested 72 hrs post-transfection using cell lifter (Fisher Scientific, China), subjected to 3 rounds of freeze-thaw to recover the AAV variants inside the cells. The cell lysates were then digested with Benzonase (EMD Millipore, Denmark, Germany) and subjected to tittering by SYBR Green qPCR (Applied Biosystems, Woolston Warrington, UK) using primers specific to the Rep gene (forward: 5′-GCAAGACCGGATGTTCAAAT-3′, reverse: 5′-CCTCAACCACGTGATCCTTT-3′). 5×109 vg of each AAV variants were then mixed together. The mixture was then purified on iodixanol gradient (Sigma, St. Louis, Mo.) in Quick-Seal Polypropylene Tube (Beckman Coulter, Brea, Calif.) followed by ion exchange chromatography using HiTrap Q HP (GE Healthcare, Piscataway, N.J.). The elution was concentrated by centrifugation using centrifugal spin concentrators with 150K molecular-weight cutoff (MWCO) (Orbital biosciences, Topsfield, Mass.). Following purification, the mixture containing 52 AAV VR VIII variants was quantified again by qPCR using the primer sets for Rep gene and diluted into two parts. The first part contains three independent aliquots acting as control viral mixture before selection. The second part was used for tail vein injection into C57BL/6J mice, at 2.5×1011 vg per animal, for in vivo selection.


When packaging rAAV-luciferase and rAAV-hFIX vectors, HEK293T cells were co-transfected with: i) pAAV-RC8 or selected pAAV-RC8-library and pAAV-RC9-library plasmids; ii) pAAV-CMV-Luciferase or pAAV-TTR-hFIX, respectively; iii) pHelper in equimolar amounts for each packaging. Plasmids were prepared using EndoFree Plasmid Kit (Qiagen, Hilder, Germany). The transfection, viral harvesting and purification steps were the same as the packaging of AAV VR VIII variants as mentioned above. The genome titer of the rAAV-luciferase vectors were quantified by qPCR using primers specific to the CMV promoter (forward: 5′-TCCCATAGTAACGCCAATAGG -3′, reverse: 5′-CTTGGCATATGATACACTTGATG -3′). The genome titer of the rAAV-hFIX vectors were quantified by qPCR using primers specific to the TTR promoter (forward: 5′-TCCCATAGTAACGCCAATAGG -3′, reverse: 5′-CTTGGCATATGATACACTTGATG-3′). The physical titer of rAAV8-and rAAV9-luciferase vectors were evaluated as described below (data not shown). The purity of rAAV were evaluated by SDS-PAGE silver staining, vector with ˜90% purity were used in our study (data not shown).


In Vivo Selection for Liver-Targeting Variants

All animal work was performed in accordance with institutional guidelines under the protocols approved by the institutional animal care and use committee of WuXi AppTec (Shanghai). The C57BL/6J mice (Shanghai SLAC Laboratory Animal Co., Ltd.), male, 6 to 8-week-old, were tail vein injected with mixture of AAV VR VIII variants as described above. At week 1, 2 and 4 post-injection, the animals were euthanized by cervical dislocation after being anesthetized with isoflurane. For week 1 and 2, liver and brain were harvested, and for week 4, lung, liver, spleen, heart, kidney, lymph node, quadriceps muscle and brain were also harvested. Then the total DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN) according to the manufacturer's protocol and then analyzed by next generation sequencing to compare the AAV read counts after selection vs before selection.









TABLE 7







The list of AAV8 VR VIII variants selected for further in vitro and in vivo


validation. The variant name their VR VIII sequence in DNA and AA were


showed. The mutations in reference to the VR VIII of AAV8 were marked in bold.












Protein_seq





(585-597, VP1



Variant name
Coding_dna (1753-1791, VP1 numbering)
numbering)
SEQ ID NO













WT AAV8
AACTTGCAGCAGCAAAACACGGCTCCTCAAATTGGAAC
NLQQQNTAPQIGT
 2





AAV8-Lib20
AACCTGCAATCGTCTACGGCCGGACCCCAGACACAGAC
NLQSSTAGPQTQ
21





AAV8-Lib25
AACCTCCAGAGCGGCAACACACGAGCAGCTACCTCAG
NLQSGNTRAATS
25





AAV8-Lib43
AACCTACAGTCGGCAAACACCGCTCCTCAAACGGGGAC
NLQSANTAPQTG
 9





AAV8-Lib44
AATTTGCAAAACTCAAATACTGCTCCGAGTACTGGAAC
NLQNSNTAPSTGT
37





AAV8-Lib45
AATTTCCAGAGCAGCAGCACAGACCCTGCGACCGGAG
NFQSSSTDPATGD
38




















TABLE 9







The list of AAV9 variants selected for further in vitro and in vivo


validation. The variant name their VR VIII sequence in DNA and AA were


showed. The mutations in reference to the VR VIII of AAV9 were marked in bold.












Protein_seq (583-595,
SEQ


Variant name
Coding_dna (1752-1791, VP1 numbering)
VP1 numbering)
ID NO





WT AAV9
AACCACCAGAGTGCCCAAGCACAGGCGCAGACCGGCTGG
NHQSAQAQAQTGW
33





AAV9-Lib2
AACTTACAATCGGCTAATACTGCACCCCAGACACAAACT
NLQSANTAPQTQT
 4





AAV9-Libll
AATTTGCAAAACTCAAACACTGGTCCAACTACAGGAACT
NLQNSNTGPTTGT
13





AAV9-Lib31
AATTTGCAAAACTCAAATACTGGTCCAACTACAGAAAAT
NLQNSNTGPTTEN
29





AAV9-Lib33
AATCTCCAGAGCAGCAACACAGCCCCTGCGACCGGAACT
NLQSSNTAPATGT
14





AAV9-Lib43
AACCTACAGTCGGCAAACACCGCTCCTCAAACGGGGACC
NLQSANTAPQTGT
 9





AAV9-Lib46
AACCTCCAGAGCGGCAACACACAAGCAGCTACCGCAGAT
NLQSGNTQAATAD
11









Next Generation Sequencing to Quantify the AAV Genome Reads in Tissues

The DNA from control viral mixture before injection and the total DNA isolated from various tissues were subjected to PCR to amplify the VR VIII region using the primer set (forward: 5′-CAAAATGCTGCCAGAGACAA-3′ and reverse: 5′-GTCCGTGTGAGGAATCTTGG-3′). The PCR products at the correct size were gel purified (Zymo Research, Irvine, Calif.) and then quantified by nanodrop. These products were analyzed by next generation sequencing with Illumina Hiseq X conducted at the WuXi NextCODE. During the analysis, the reads were separated by each VR VIII DNA sequence with no mismatch allowed. Then, we obtained the absolute read count of individual VR VIII in each experimental condition. Then, we converted the data into relative read count to normalize the difference for different time point and different tissues.


Titration of AAV Particles by ELISA

The AAV particle concentration was determined by the Progen AAV8 Titration ELISA kit (Progen Biotechnik GMBH, Heidelberg, Germany), against a standard curve prepared in the ELISA kit. Briefly, the recombinant adeno-associated virus 8 reference standard stock (rAAV8-RSS, ATCC, VR-1816) and samples were diluted with ready-to-use sample buffer so that they can be measured within the linear range of the ELISA (7.81×106-5.00×108 capsids/mL). The rAAV8-RSS was diluted in the range of 1:2000 to 1:16000, whereas samples were diluted between 1:2000 and 1:256000. Pipette 100 μL of ready-to-use sample buffer (blank), serial dilutions of standard, and samples (both diluted in ready-to-use sample buffer) into the wells of the microtiter strips. Seal strips with adhesion foil provided and incubate for 1 h at 37° C. Next, the plate was emptied and washed with 200 μL ready-to-use sample buffer 3 times. Pipette 100 μL biotin conjugate into the wells and seal strips with adhesion foil. After a 1-hour incubation at 37° C., the plates were emptied and washed 3 times. 100 μL streptavidin conjugate was then added to the wells and incubated for 1 hour at 37° C. Repeat washing step as described above, and pipette 100 μL substrate into the wells. Incubate the plate for 15 minutes at room temperature, and stop color reaction by adding 100 μL of stop solution into each well. Measure intensity of color reaction with a photometer at 450 nm wavelength within 30 minutes.


In Vitro Infectivity

HEK293T cells were seeded in 96-well cell-culture plates (Corning, Wujiang, J S) 16 hrs before transduction. Cells were mock infected or infected with rAAV-VR VIII variants individually, MOI=10,000, in serum- and antibiotic-free DMEM for 2 hrs. 48 hrs post infection, the cells were lysed to detect luciferase expression using the Bright-Glo™ Luciferase Assay System (Promega, Madison, Wis.) according to the manufacturer's instructions.


Sodium Dodecyl Sulfate-Polyacrylamide

For sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis, samples were denatured in NuPage Reducing Agent and NuPAGE LDS Sample Buffer (both from Invitrogen, Cartsbad, Calif.) at 100° C. for 10 min before being loaded onto NuPAGE 4-12% Bis-Tris minigels (Invitrogen, Cartsbad, Calif.). After electrophoresis, gels were silver-stained, using a Fast Silver Stain Kit (Beyotime, Shanghai, China). View gels using a white light box and a suitable imaging system.


In Vivo rAAV-Luciferase and Serum ALT Detection


The C57BL/6J mice, male, 6 to 8-week-old, were injected with appropriate amount of rAAV-luciferase vectors by tail vein injection. Bioluminescence were detected at day 3, week 1 and week 2 after viral injection. Before each detection, the mice will receive the 15 mg/ml D-Luciferin (PerkinElmer) by intraperitoneal injection. 10 mins after D-Luciferin injection, the mice will receive anesthesia using isoflurane. Xenogen Lumina II small animal in vivo imaging system (PerkinElmer) was used to select the region of interest (ROI), quantify and analyze the signal presented as photons/second/cm2/steridian (p/sec/cm2/sr). After the bioluminescence detection at week 2, the animals will be euthanized using 10% CO2 followed by serum and tissue collection for serum alanine aminotransferase (ALT) detection and genome copy number detection. The ALT levels was determined by Alanine Aminotransferase Activity Assay Kit (SIGMA) according to the manufacturer's protocol.


In Vivo rAAV-hFIX Transduction


The potency of rAAV-hFIX gene transfer efficiency was initially assessed in 6 to 8-week-old male wild-type C57BL/6J mice by assessing hFIX levels in plasma following tail vein injection of the vector. Next, the F9 KO mice in C57BL/6J background purchased from Shanghai Model Organisms, male, 6 to 8-week-old, were injected with appropriate amount of AAV vectors by tail vein injection to assess the efficacy.


Tissue, Plasma and Serum Collection

At appropriate time after viral injection, blood was collected by retroorbital bleeding. For terminal blood withdraw, immediately after CO2 euthanasia, cardiac puncture was performed to collect blood followed by perfusion using PBS to harvest livers. The largest liver lobe was fixed with 10% Neutral buffered formalin (NBF) for pathological examination. Two independent sampling of other liver lobes were collected for snap-frozen and maintained in −80° C. for genome copy number detection. For serum collection, blood is placed in 4° C. for 2 hrs. Then spin down the blood at 8000 rpm for 15 mins, and aspirate the supernatant. For plasma collection, blood was added into 3.8% sodium citrate at a ratio of 9:1. Then, spin down the mixture at 8000 rpm for 5 mins, and aspirate the supernatant. The serum and plasma were maintained in −80° C.


Detection of hFIX Expression and Activity


The hFIX expression level was determined by an enzyme-linked immunosorbent assay (ELISA) (Affinity Biologicals, Ancaster, ON, Canada) according to the manufacturer's protocol. Briefly, a flat-bottomed, 96-well plate was coated with goat antibody against human factor IX. Standards were made by using serial dilutions of calibrator plasma (0.0313-1 IU/mL). Mouse plasma was diluted 1:200 in sample diluent buffer, and 100 μL samples and standards were added to the wells. After a 1-hour incubation at room temperature, the plates were emptied and washed with 300 μL diluted wash buffer 3 times. The plates were then incubated for 30 minutes at r temperature with 100 μL horseradish peroxidase (HRP)-conjugated secondary antibody solution. After a final wash step, the HRP activity was measured with Tetramethylbenzidine (TMB) substrate. The color reaction was stopped after 10 minutes using stop solution and read spectrophotometrically at 450 nm within 30 minutes. The reference curve is a log-log plot of the absorbance values versus the factor IX concentration, and the factor IX content in plasma samples can be read from the reference curve.


The hFIX activity in mice was determined in a chromogenic assay using the ROX factor IX activity assay kit (Rossix, Mo{umlaut over ( )}lndal, Sweden) according to the manufacture's protocol. Briefly, standard dilutions were prepared using normal human plasma in diluent buffer, range from 25% to 200% activity (100% activity is defined as 1 IU/mL factor IX in plasma). The experimental plasma samples were diluted 1:320 in diluent buffer, and 25 μL samples and standards were added to low binding 96 well microplates. 25 μL Reagent A (containing lyophilized human factor VIII, human factor X, bovine factor V and a fibrin polymerization inhibitor) was added to the wells and incubated for 4 minutes at 37° C. And then 150 μL Reagent B (containing lyophilized human factor XIa, human factor II, calcium chloride and phospholipids) was added to the wells. After 8 minutes at 37° C., activated factor X generation was terminated by the addition of 50 μL factor Xa Substrate (Z-D-Arg-Gly-Arg-pNA), and the absorbance was read at 405 nm. Plot the maximal absorbance change/minute (ΔA405 max/min) vs. factor IX activity in a Log-Log graph, and the factor IX activity of the samples can be calculated using the reference curve.


In Vivo Viral Genome Copy Number

Absolute qPCR using SYBR Green (Applied Biosystems, Woolston Warrington, UK) was used to quantify AAV viral genome copy number. Total DNA was extracted from various tissues using DNeasy Blood & Tissue Kit (QIAGEN, Hilden, Germany) according to the manufacturer's protocol. Total DNA concentration was determined using Nanodrop, and 40ng of DNA from each sample was used as the template for qPCR. qPCR was performed on all tissue samples and control, done in triplicate, using primers specific for the CMV promoter (forward: TCCCATAGTAACGCCAATAGG, reverse: CTTGGCATATGATACACTTGATG). Linearized pssAAV-CMV-luci-mut plasmid at 2.89×101, 2.89×102, 2.89×103, 2.89×104, 2.89×105, 2.89×106, 2.89×107 copy numbers (0.0002, 0.002, 0.02, 0.2, 2, 20, 200 pg) were used to generate a standard curve to calculate the copy numbers.


Example 3
In Vivo Selection

52 different VR VIII sequences (Table 6). These 52 sequences were used to substitute the VR VIII of AAV8 capsid backbone, individually, which were further subcloned into an all-in-one construct containing the modified capsid sequences with rep and inverted terminated repeats (ITRs) from AAV2. These constructs were used to package wild-type-like AAV particles, individually, then mixed together at equal viral genome, followed by purification. The purified AAV variant library was divided into two parts. One part was used for NGS detection (n=3) as the starting library baseline. Another part was subjected to systemic delivery for in vivo selection to isolate liver and brain-targeting AAV variants (FIG. 1). Notably, the design contained all the available unique VR VIII sequences including that of WT AAV8, or AAV8-Lib40, in our screen (Table 6). We used AAV8-Lib40 as our internal control during the screening and selection process.


At week 1 post administration, liver and brain were harvested. Compared with the starting library and AAV8-Lib40, we were able to identify a few variants enriched in liver (FIG. 2A) and brain (FIG. 2B). At week 4 post administration, lung, liver, spleen, heart, kidney, lymph node, quadriceps (QA) muscle and brain were also harvested to evaluate biodistribution. We were able to identify variants that preferably target liver or brain than other tissues (FIG. 2C, Table 10).









TABLE 10







Variants that showed increased liver targeting,


normalized to WT AAV8 to baseline as 100%.











Protein_seq





(585-597/8,
SEQ
Ratio (relative


Variants
VP1 numbering)
ID No.
wtAAV8)













AAV8-Lib01
NNQNTNTAPTAGT
 3
106.14%





AAV8-Lib04
NNQAANTQAQTGL
 6
227.97%





AAV8-Lib05
NLQSGNTQAATSD
 7
181.93%





AAV8-Lib07
NLQSANTAPQTGT
 9
230.06%





AAV8-Lib08
NLQQTNSAPIVGA
10
116.07%





AAV8-Lib09
NLQSGNTQAATAD
11
112.02%





AAV8-Libll
NLQNSNTGPTTGT
13
119.50%





AAV8-Lib12
NLQSSNTAPATGT
14
253.36%





AAV8-Lib13
NNQAANTQAQTGL
 6
180.94%





AAV8-Lib15
NNQSANTQAQTGL
16
257.83%





AAV8-Lib19
NNQNATTAPITGN
20
239.08%





AAV8-Lib20
NLQSSTAGPQTQT
21
181.06%





AAV8-Lib21
NLQQQNTAPIVGA
22
150.83%





AAV8-Lib23
NLQQTNSAPIVGA
10
110.46%





AAV8-Lib25
NLQSGNTRAATSD
25
129.13%





AAV8-Lib33
NLQSSNTAPATGT
14
100.38%





AAV8-Lib35
NLQQQNTAPQIGT
 2
131.97%





AAV8-Lib36
NLQQTNTGPIVGN
32
121.99%





AAV8-Lib37
NLQQTNTGPIVGN
32
131.34%





AAV8-Lib38
NHQSAQAQAQTGW
33
121.67%





AAV8-Lib40
NLQQQNTAPQIGT
 2
100.00%





AAV8-Lib43
NLQSANTAPQTGT
 9
142.69%





AAV8-Lib44
NLQNSNTAPSTGT
37
258.75%





AAV8-Lib46
NLQSGNTQAATAD
11
111.35%





AAV8-Lib47
NFQNNTTAADTEM
39
124.68%





AAV8-Lib48
NLQSGNTQAATSD
 7
176.81%





AAV8-Lib49
NLQAANTAAQTQV
24
112.13%





AAV8-Lib52
NLQQQNAAPIVGA
42
128.43%









While before the purification, we were able to titer all the AAV VR VIII variants individually for mixing equal amount and purification, we failed to detect AAV8-Lib26 by NGS both in our starting library and screens (FIG. 2A-C). This implied that the mutations in AAV8-Lib26 may not comply with the current AAV purification methods. Apart from this, we concluded that our capsid library design and screen strategy yielded highly viable AAV virions that facilitated the enrichment of liver- and brain-targeted variants.


To further validate the gene delivery capability, the selected VR VIII sequences (Table 7) were subcloned into recombinant AAV capsid plasmid for the packaging of luciferase reporter gene. AAV8-Lib25 and AAV8-Lib43 demonstrated significantly higher transgene expression in vitro (FIG. 3A). Importantly, we found most of novel AAV variants showed highly significant increase in in vivo transduction (FIG. 3B-3E). As negative control, AAV8-Lib45, whose VR VIII was downregulated during our screen, showed significantly decreased transduction both in vitro (FIG. 3A) and in vivo (FIGS. 3B and 3C). These results, to an extent, validated our screen process and results.


Furthermore, when we systemically characterized their biodistribution, we confirmed that these variants maintained a liver targeting profile as indicated by dominant GCNs in the liver than other tissues (FIG. 4A-E). Importantly, the liver genome copy numbers were significantly higher for AAV8 VR VIII variants than AAV8 (FIG. 5) further confirming the improved targeting capability. AAV8-Lib45, on the other hand, showed significantly lower liver GCNs further confirming our screen strategy (FIG. 5).


As a gene therapy vector, it is of most importance to have a good safety profile. To this end, we detected serum alanine transaminase (ALT) level, an important maker for liver toxicity. The ALT level was maintained below baseline for all of the groups (FIG. 6). These results indicate that AAV8 VRIIII variants could serve as alternative gene delivery tool to the liver.


As we have identified promising VR VIII sequences for gene delivery to the brain, we hypothesized that substituting WT VR VIII of AAV9 with brain-enriched VR VIII sequences (FIG. 2B) would generate variants with higher CNS-targeting capability. To test it, the AAV9-VR VIII capsid (Table 9) were used to package the genetic payload carrying luciferase reporter gene for evaluating transduction efficiency. We found that AAV9-Lib46 showed significantly higher transgene expression than WT AAV9 in vivo (FIGS. 7A and 7B). Interestingly, AAV9-Lib31, AAV9-Lib33, and in particular, AAV9-Lib43 showed a peripheral tissue-detargeting while maintained comparable CNS gene delivery (FIG. 7A). To this end, we specifically compare and qualify the luciferase expression in the head (FIGS. 7C and 7D) and found a dramatic shift for the head/body ratio of transgene expression (FIG. 7G).


Then, we tested the in vitro transduction of our leading candidates AAV9-Lib43 and AAV9-Lib46. Following infection HEK293T cells, AAV9-Lib43 showed significantly decreased transgene expression (FIG. 8) and AAV9-Lib46 showed significantly increased transgene expression (FIG. 8). These data were consistent with their overall body expression in vivo (FIGS. 7A and 7B).


Next, we profiled the biodistribution of AAV9 and AAV9 VR VIII variants. As is well known that AAV9 has a tropism for liver, heart and CNS, we observed significantly decreased GCNs in the liver for AAV9-Lib31, AAV9-Lib33, and AAV9-Lib43 and higher GCNs for AAV9-Lib46 (FIG. 9A), consistent with the transgene expression results (FIG. 8A). AAV9-Lib43 and AAV9-Lib46 demonstrated significantly increased GCNs in the brain (FIG. 9B). Though not significant, we also observed elevated GCNs in heart and lung (FIGS. 9C and 9D). Furthermore, no ALT elevation were detected following AAV9 VR VIII variants-mediated gene delivery (FIG. 10). These results indicate that AAV9 VRIIII variants could serve as alternative gene delivery tool to the CNS following systemic gene delivery.


Example 4
AAV2 VR VIII Variants

5 sequences listed in Table 11 were used to substitute the VR VIII of AAV2 capsid backbone (corresponding to amino acid position 582-594 of WT AAV2 YP_680426.1 (GenBank: NC_001401.2), individually, which were further subcloned into an all-in-one construct containing the modified capsid sequences with rep and inverted terminated repeats (ITRs) from AAV2. These constructs were used to package wild-type-like AAV particles, individually, then mixed together at equal viral genome, followed by purification. The purified AAV variant library was divided into two parts. One part was used for NGS detection (n=3) as the starting library baseline. Another part was subjected to systemic delivery for in vivo selection to isolate liver and brain-targeting AAV variants.


To further validate the gene delivery capability, the selected VR VIII sequences (Table 11) were subcloned into recombinant AAV2 capsid plasmid for the packaging of luciferase reporter gene. AAV2-Lib20, AAV2-Lib25, AAV2-Lib43, AAV2-Lib44, AAV2-Lib45 demonstrated significantly lower transgene expression in vitro (FIG. 11A). Importantly, we found most of novel AAV variants showed highly significant decrease in in vivo transduction (FIG. 11B-11C and FIG. 12A-D).









TABLE 11







The list of AAV2 VR VIII variants selected for further in


vitro and in vivo validation. The variant name their VR VIII


sequence in DNA and AA were showed. The mutations in reference


to the VR VIII of AAV2 were marked in bold.









Variant

Protein_seq (585-597,


name
Coding_dna (1753-1791, VP1 numbering)
VP1 numbering)





WT AAV8
AACCTCCAGAGAGGCAACAGACAAGCAGCTACCGCAGAT
NLQRGNRQAATAD





AAV2-Lib20
AACCTGCAATCGTCTACGGCCGGACCCCAGACACAGACT
NLQSSTAGPQTQT





AAV2-Lib25
AACCTCCAGAGCGGCAACACACGAGCAGCTACCTCAGAT
NLQSGNTRAATSD





AAV2-Lib43
AACCTACAGTCGGCAAACACCGCTCCTCAAACGGGGACC
NLQSANTAPQTGT





AAV2-Lib44
AATTTGCAAAACTCAAATACTGCTCCGAGTACTGGAACT
NLQNSNTAPSTGT





AAV2-Lib45
AATTTCCAGAGCAGCAGCACAGACCCTGCGACCGGAGAT
NFQSSSTDPATGD









Example 5
Delivering a Nucleic Acid Vector to a Cell and/Tissue Using rAAV Used to Package a Genetic Payload that Comprise a Heterologous Nucleic Acid Region Comprising a Sequence Encoding a Protein or Polypeptide of Interest

The protein or polypeptide of interest is a protein or polypeptide describe in Table 12-14.


AAV8-hFIX, AAV8-Lib25-hFIX and AAV8-Lib43-hFIX were injected into 3-4 yeas old male cynomolgus monkeys with the dose of 5E12 vg/kg, monkeys enrolled in these experiments were all tested with neutralization antibody titer<1:50 against AAV8. Blood samples were harvested before dosage and at Day3, week1, week2 and week3, hFIX expression were detected in plasma by ELISA. The result shows that all of AAV8, AAV-Lib25 and AAV8-Lib43 can express hFIX efficiently in monkeys, AAV8-Lib25 express higher hFIX than AAV8 and AAV8-Lib43 (FIG. 13).









TABLE 12







Exemplary Proteins and polypeptides of interest (Liver Disease)










Non-limiting




Exemplary diseases,
Non-limiting


Protein or
disorders,
NCBI


Polypeptide
or phenotypes
Protein IDs





Cystathionine-beta-
Homocystinuria
NP_000062.1,


synthase (CBS)

NP_001171479.1,




NP_001171480.1


Factor IX (FIX)
Hemophilia B
NP_000124.1


Factor VIII (F8)
Haemophilia A
NP_000123.1,




NP_063916.1


Glucose-6-phosphatase
Glycogen Storage
NP_001257326.1


catalytic subunit (G6PC)
Disease Type I
AAI30479.1



(GSD1)
AAI36370.1


Glucose 6-phosphatase
GSD-Ia
NP_000142.2,


(G6Pase)

NP_001257326.1


Glucuronidase,
MPSVII-Sly
NP_000172.2,


beta (GUSB)

NP_001271219.1


Hemochromatosis
Hemochromatosis
NP_000401.1,


(HFE)

NP_620572.1,




NP_620573.1,




NP_620575.1,




NP_620576.1,




NP_620577.1,




NP_620578.1,




NP_620579.1,




NP_620580.1


Iduronate 2-sulfatase
MPSII-Hunter
NP_000193.1,


(IDS)

NP_001160022.1,




NP_006114.1


Iduronidase, alpha-1
MPSI-Hurler
NP_000194.2,


(IDUA)

AAA51698.1


Low density lipoprotein
Phenylketonuria
NP_000518.1,


receptor (LDLR)
(PKU)
NP_001182727.1,




NP_001182728.1,




NP_001182729.1,




NP_001182732.1,




AAP36025.1


Myophosphorylase
McArdle disease
NP_001158188.1,


(PYGM)
(glycogen storage
NP_005600.1



disease type V, GSD5)



N-acetylglucosam-
Sanfilippo syndrome
NP_000254.2


inidase, alpha
(MPSIIIB)



(NAGLU)




N-sulfoglucosamine
Mucopolysaccharidosis
NP_000190.1


sulfohydrolase (SGSH)
type
NP_001339851.1



IIIA (MPS IIIA)
NP 001339850.1




AAH47318.1


Ornithine
OTC deficiency
NP_000522.3,


carbamoyltransferase

AAA59975.1


(OTC)




Phenylalanine
Hypercholesterolaemia
NP_000268.1


hydroxylase
or Phenylketonuria



(PAH)
(PKU)



UDP
Crigler-Najjar
NP_000454.1


glucuronosyltransferase
syndrome



1 family, polypeptide A1




(UGT1A1)
















TABLE 11







Exemplary Proteins and polypeptides of interest (CNS Disease)











Non-limiting NCBI



Non-limiting Exemplary diseases,
Protein IDs or Patent


Protein or Polypeptide
disorders, or phenotypes
SEQ ID NOs





Acid alpha-glucosidase (GAA)
Pompe disease
NP_000143.2,




NP_001073271.1,




NP_001073272.1


ApaLI
Mitochondrial heteroplasmy,
YP_007161330.1



myoclonic epilepsy with




ragged red fibers (MERRF)




or mitochondrial




encephalomyopathy, lactic acidosis,




and stroke-like episodes




(MELAS)



Aromatic L-amino acid
Parkinson’s disease
NP_000781.1,


decarboxylase (AADC)

NP_001076440.1,




NP_001229815.1,




NP_001229816.1,




NP_001229817.1,




NP_001229818.1,




NP_001229819.1


Aspartoacylase (ASPA)
Canavan’s disease
NP_000040.1,




NP_001121557.1


Battenin
Ceroid lipofuscinosis
NP_000077.1



neuronal 3 (CLN3)
NP_001035897.1




NP_001273033.1




NP_001273034.1




NP_001273038.1




NP_001273039.1




AAH04433.1


Ceroid lipofuscinosis neuronal 2 (CLN2)
Late infantile neuronal
NP_000382.3,



ceroidlipofuscinosis
AAB80725.1



or Batten’s disease



Cluster of Differentiation 86
Malignant melanoma
NP_001193853.1,


(CD86 or B7-2)

NP_001193854.1,




NP_008820.3,




NP_787058.4,




NP_795711.1


Cystathionine-beta-synthase (CBS)
Homocystinuria
NP_000062.1,




NP_001171479.1,




NP_001171480.1


Dystrophin or Minidystrophin
Muscular dystrophy
NP_000100.3,




NP_003997.1,




NP_004000.1,




NP_004001.1,




NP_004002.3,




NP_004003.2,




NP_004004.1,




NP_004005.1,




NP_004006.1,




NP_004007.1,




NP_004008.1,




NP_004009.1,




NP_004010.1,




NP_004011.2,




NP_004012.2,




NP_004013.1,




NP_004014.2


Frataxin (FXN)
Friedreich ataxia (FA)
NP_000135.2




NP_852090.1




AAH23633.1




AAH48097.1


Glial cell-derived
Parkinson’s disease
NP_000505.1,


neurotrophic factor (GDNF)

NP_001177397.1,




NP_001177398.1,




NP_001265027.1,




NP_954701.1


Glutamate decarboxylase 1(GAD1)
Parkinson’s disease
NP_000808.2,




NP_038473.2


Glutamate decarboxylase 2 (GAD2)
Parkinson's disease
NP_000809.1,




NP_001127838.1


Hexosaminidase A, α polypeptide, also called
Tay-Sachs
NP_000511.2


beta-Hexosaminidase alpha (HEXA)




Hexosaminidase B, β polypeptide, also called
Tay-Sachs
NP_000512.1,


beta-Hexosaminidase beta (HEXB)

NP_001278933.1


Interleukin 12 (IL-12)
Malignant melanoma
NP_000873.2,




NP_002178.2


Methyl CpG binding protein 2 (MECP2)
Rett syndrome
NP_001104262.1,




NP_004983.1


Myotubularin 1 (MTM1)
X-linked myotubular myopathy
NP_000243.1


NADH ubiquinone oxidoreductase subunit 4
Leber hereditary optic
YP_003024035.1


(ND4)




Nerve growth factor (NGF)
Alzheimer’s disease
NP_002497.2


neuropeptide Y (NPY)
Parkinson’s disease, epilepsy
NP_000896.1


Neurturin (NRTN)
Parkinson’s disease
NP_004549.1


Palmitoyl-protein thioesterase 1 (PPT1)
Ceroid lipofuscinosis neuronal 1
NP_000301.1



(CLN1)
AAH08426.1


Sarcoglycan alpha, beta, gamma,
Muscular dystrophy
SGCA


delta, epsilon, or zeta

NP_000014.1,


(SGCA, SGCB, SGCG,

NP_001129169.1


SGCD, SGCE, or SGCZ)

SGCB




NP_000223.1




SGCG




NP_000222.1




SGCD




NP_000328.2,




NP_001121681.1,




NP_758447.1




SGCE




NP_001092870.1,




NP_001092871.1,




NP_003910.1




SGCZ




NP_631906.2


Tumor necrosis factor receptor fused to an
Arthritis, Rheumatoid arthritis
SEQ ID NO. 1 of


antibody Fc (TNFR:Fc)

WO2013025079


Ubiquitin-protein ligase E3A (UBE3A)
Angelman Syndrome (AS)
NP_570853.1




NP_000453.2




NP_570854.1




NP_001341434.1




AAH02582.2


β-galactosidase 1 (GLB1)
GM1 gangliosidosis
NP_000395.3




AAB81350.1
















TABLE 12







Exemplary Proteins and polypeptides of interest (Other Disease)










Non-limiting




Exemplary diseases,
Non-limiting NCBI



disorders,
Protein IDs or Patent


Protein or Polypeptide
or phenotypes
SEQ ID NOs





Adenine nucleotide
progressive external
NP_001142.2


translocator (ANT-1)
ophthalmoplegia



Alpha-1-antitrypsin
Hereditary
NP_000286.3,


(AAT)
emphysema or
NP_001002235.1,



Alpha-1-antitrypsin
NP_001002236.1,



deficiency
NP_001121172.1,




NP_001121173.1,




NP_001121174.1,




NP_001121175.1,




NP_001121176.1,




NP_001121177.1,




NP_001121178.1,




NP_001121179.1,




AAA51546.1,




AAB59375.1


Aquaporin 1 (AQP1)
Radiation Induced
NP_932766.1



Xerostomia (RIX)
NP_001126220.1




AAH22486.1


ATPase copper
Menkes syndrome
NP_000043.4


transporting

NP_001269153.1


alpha (ATP7A)




ATPase,
Chronic heart failure
NP_001672.1,


Ca++ transporting,

NP_733765.1


cardiac muscle,




slow twitch 2




(SERCA2)




C1 esterase
Hereditary
NP_000053.2


inhibitor (C1EI)
Angioedema (HAE)
AAH11171.1




AAB59387.1




AAA35613.1


Cyclic nucleotide
Achromatopsia
NP_001073347.1


gated channel alpha 3
(ACHM)
AF272900.1


(CNGA3)

AAH96300.1




AAI50602.1


Cyclic nucleotide
Achromatopsia
NP_061971.3


gated channel
(ACHM)
AAF86274.1


beta 3 (CNGB3)




Cystic fibrosis
Cystic fibrosis
NP_000483.3


transmembrane




conductance




regulator (CFTR)




Galactosidase,
Fabry disease
NP_000160.1


alpha (AGA)




Glucocerebrosidase
Gaucher disease
NP_000148.2,


(GC)

NP_001005741.1,




NP_001005742.1,




NP_001165282.1,




NP_001165283.1


Granulocyte-
Prostate cancer
NP_000749.2


macrophage




colonystimulating




factory (GM-CSF)




HIV-1 gag-proΔrt
HIV infection
SEQ ID NOs. 1-5 of


(tgAAC09)

WO2006073496


Lipoprotein
LPL deficiency
NP_000228.1


lipase (LPL)




Medium-chain
Medium-chain
NP_000007.1,


acyl-CoA
acyl-CoA
NP_001120800.1,


dehydrogenase
dehydrogenase
NP_001272971.1,


(MCAD)
(MCAD) deficiency
NP_001272972.1,




NP_001272973.1


Myosin 7A (MYO7A)
Usher syndrome 1B
NP_000251.3,




NP_001120651.2,




NP_001120652.1


Poly(A) binding
Oculopharyngeal
NP_000321.1


protein nuclear 1
Muscular Dystrophy



(PABPN1)
(OPMD)



Propionyl CoA
Propionic acidaemias
NP_000273.2,


carboxylase,

NP_001121164.1,


alpha polypeptide

NP_001171475.1


(PCCA)




Rab escort
Choroideremia (CHM)
NP_001138886.1


protein-1 (REP-1)

NP_001307888.1




CAA55011.1


Retinal pigment
Leber
NP_000320.1


epithelium-specific
congenital amaurosis



protein




65kDa (RPE65)




Retinoschisin 1 (RS1)
X-Linked Retinitis
NP_000321.1



Pigmentosa (XLRP)



Short-chain acyl-CoA
Short-chain acyl-CoA
NP_000008.1


dehydrogenase
dehydrogenase (SCAD)




(SCAD) deficiency



Very long-acyl-CoA
Very long-chain
NP_000009.1,


dehydrogenase
acyl-CoA
NP_001029031.1,


(VLCAD)
dehydrogenase
NP_001257376.1,



(VLCAD) deficiency
NP_001257377.1









The embodiments of the present invention have been described above, but the present invention is not limited thereto, and those skilled in the art can understand that modifications and changes can be made within the scope of the purport of the present invention. The manner of modifications and changes should fall within the scope of protection of the present invention.

Claims
  • 1. An AAV library comprising a multitude of AAV variants, wherein each AAV variant comprise a variant of native AAV8 or AAV9 capsid protein comprising a substituted amino acid sequence relative to native AAV 8 or AAV9 capsid protein, the substituted amino acid sequence is located at VR VIII region of the native AAV 8 or AAV9 capsid protein, the native AAV 8 is with an amino acid sequence of SEQ ID NO:1, the native AAV 9 is with an amino acid sequence of SEQ ID NO:43.
  • 2. The AAV library of claim 1, wherein the substituted amino acid sequence is located at amino acid position 585 to 597 or 585 to 598 of SEQ ID NO:1; or at the amino acids corresponding to amino acid position 583 to 595 or 583 to 596 of SEQ ID NO:43.
  • 3. (canceled)
  • 4. The library of claim 2, wherein the substituted sequence located the position amino acids 585 to 598 of SEQ ID NO:1 is: X1X2X3X4X5X6X7X8X9X10X11X12X13X14, wherein  Formula I:X1 is Asn, or Tyr,X2 is Leu, or Asn, or Gln, or Lys, or His, or Phe,X3 is Gln, or Asn,X4 is Gln, or Asn, or Ser, or Ala, or Asp, or Gly,X5 is Gln, or Thr, or Ala, or Gly, or Ser, or Asn,X6 is Asn, or Ala, or Ser, or Asp, or Thr, or Gln,X7 is Thr, or Ser, or Ala, or Arg, or Glu, or Gly,X8 is Ala, or Gln, or Asp, or Gly, or Arg, or Thr,X9 is Pro, or Ala, or Thr,X10 is Gln, or Thr, or Ala, or Ile, or Ser, or Asp,X11 is Ile, or Ala, or Thr, or Val, or Thr, or Ser, or TyrX12 is Gly, or Gln, or Ser, or Ala, or Glu,X13 is Thr, or Ala, or Leu, or Asp, or Ser, or Asn, or Val, or Trp, or Met,X14 is Val, or Asp,the sequence doesn't comprise an amino acids sequence of SEQ ID NO:2.
  • 5. The library of claim 4, wherein the substituted sequence is selected from SEQ ID NO: 3-42.
  • 6. (canceled)
  • 7. The AAV library of claim 2, wherein the substituted sequence located at the position amino acids 583 to 596 of SEQ ID NO:43 is: X1X2X3X4X5X6X7X8X9X10X11X12X13X14, wherein  Formula I:X1 is Asn, or Tyr,X2 is Leu, or Asn, or Gln, or Lys, or His, or Phe,X3 is Gln, or Asn,X4 is Gln, or Asn, or Ser, or Ala, or Asp, or Gly,X5 is Gln, or Thr, or Ala, or Gly, or Ser, or Asn,X6 is Asn, or Ala, or Ser, or Asp, or Thr, or Gln,X7 is Thr, or Ser, or Ala, or Arg, or Glu, or Gly,X8 is Ala, or Gln, or Asp, or Gly, or Arg, or Thr,X9 is Pro, or Ala, or Thr,X10 is Gln, or Thr, or Ala, or Ile, or Ser,X11 is Ile, or Ala, or Thr, or Val, or Thr, or Ser, or TyrX12 is Gly, or Gln, or Ser, or Ala, or Glu,X13 is Thr, or Ala, or Leu, or Asp, or Ser, or Asn, or Val, or Trp, or Met,X14 is Val, or Asp,the sequence doesn't comprise an amino acids sequence of SEQ ID NO:33.
  • 8. The library of claim 7, wherein the substituted sequence is selected from SEQ ID NO: 3-42.
  • 9. A library of polynucleotides encoding the AAV variants of the AAV library according to claim 1.
  • 10. A library of vectors comprising the polynucleotides encoding the AAV variants of the AAV library according to claim 1.
  • 11. A library of cloning cells comprising the AAV variants of the AAV library according to claim 1 and/or comprising polynucleotides encoding the same.
  • 12. A method of generating an AAV library, comprising: a) generating variant capsid protein genes encoding variant of native AAV8 or AAV9 capsid proteins, the variant comprises a substituted sequence relative to native AAV 8 or AAV9 capsid protein, the substituted amino acid sequence is located at VR VIII region of SEQ ID NO:1 (AAV8) or SEQ ID NO:43 (AAV9);b) cloning said variant capsid protein genes into AAV vectors, wherein said AAV vectors are replication competent AAV vectors.
  • 13. The method of claim 12, wherein VR VIII region is the position amino acids 585 to 597 or 598 of SEQ ID NO:1 (AAV8) or the position amino acids 583 to 595 or 596 of SEQ ID NO:43 (AAV9).
  • 14. The method of claim 13, further comprising: 1) screening said AAV vector library from b) for variant AAV capsid proteins for increased transduction or tropism in human tissue or cells as compared to a non-variant parent capsid protein; and2) selecting said variant AAV capsid vector from c).
  • 15. Use of an AAV library according to claim 1, a method according to any one of claim 12, a library of polynucleotides according to claim 8, a library of vectors according to claim 10 and/or a library of cloning cells according to claim 9 for identifying an AAV variant infecting a target cell or tissue of interest.
Priority Claims (1)
Number Date Country Kind
PCT/CN2019/111527 Oct 2019 CN national
CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of and priority to PCT Application No. PCT/CN2019/111527, filed Oct. 16, 2019, the entire contents of which are incorporated by reference herein for all purposes.

PCT Information
Filing Document Filing Date Country Kind
PCT/CN2020/121098 10/15/2020 WO