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  • C12N2750/14011—Parvoviridae
  • C12N2750/14111—Dependovirus, e.g. adenoassociated viruses
  • C12N2750/14141—Use of virus, viral particle or viral elements as a vector
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  • C12Y305/04—Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5) in cyclic amidines (3.5.4)
  • C12Y305/04004—Adenosine deaminase (3.5.4.4)

Definitions

• Adeno-associated viruses have been used to deliver genes encoding many therapeutic proteins in animal models of human disease 3,4 , in clinical trials 5 , and in FDA- approved drugs 6,7 .
• AAV has become a popular in vivo delivery method due to its clinical validation, its ability to target a variety of clinically relevant tissues, and its relatively well- understood and favorable safety profile.
• nucleic acid molecules in some aspects, described herein are nucleic acid molecules, compositions, recombinant AAV (rAAV) particles, kits, and methods for delivering a complete base editor (or “nucleobase editor”) to cells, e.g., via a single AAV vector (or genome).
• rAAV recombinant AAV
• the disclosure provides compositions, methods, and uses for delivery of size-minimized adenine base editors and cytosine base editors in a single AAV vector, wherein the adenine base editor and associated regulatory elements have a length shorter than the packaging capacity of AAV, of ⁇ 4.9 kilobases (kb).
• BEs Base editors 8,9
• BEs can efficiently install targeted mutations in a variety of therapeutically relevant cell types in vitro and in animal models of human genetic diseases 1,10 .
• BEs can also efficiently install targeted mutations in a variety of therapeutically relevant tissues in subjects, such as human subjects, including liver tissues.
• base editing does not require double-strand DNA breaks and therefore generates minimal unwanted indel byproducts, chromosomal translocations 11 , chromosomal aneuploidy 12 , large deletions 13,14 , p53 activation 15,16 , or chromothripsis 17 .
• Base editors can correct point mutations that cause various genetic diseases, but their delivery to subjects in vivo is complicated by their large size (about 5.2 kb), which typically exceeds the maximum packaging capacity of an adeno-associated virus (AAV), which is ⁇ 4.9 kb between the inverted terminal repeats (ITRs) 18,19 .
• AAV adeno-associated virus
• packaging BEs containing the commonly used Streptococcus pyogenes Cas9 protein (SpCas9, which is about 4.2 kb in length) and a single- guide RNA (sgRNA) in a single vector has not been workable.
• SpCas9 Streptococcus pyogenes Cas9 protein
• sgRNA single- guide RNA
• this approach leaves little room for customized expression and control elements, such as nuclear localization sequences (NLSs).
• AAVs that deliver base editors must also include the guide RNA, promoters driving base editor and sgRNA expression, and cis regulatory elements.
• each “split” portion of the base editor transgene is fused to a small, trans-splicing intein 27 , or each portion is expressed as mRNAs that undergoes trans-splicing 28 .
• each of the two AAV vectors is packaged in a separate AAV viral particle (or virion).
• Dual AAV approaches rely on the incorporation of trans-splicing inteins that mediate reconstitution of the full-length BE from the split portions in the cell following delivery and transduction of the AAV particles. Because two AAV particles are required to deliver a single base editor, two successful and relatively simultaneous transductions of the target cell are necessary.
• Adenine base editors are a particularly useful class of editing agents because they install A•T-to-G•C conversions that correct approximately half of all known pathogenic SNPs 9 .
• PACE Phage-assisted continuous evolution
• ABE7.10 which contains the TadA7.10 deaminase, can perform clean and efficient A•T-to-G•C conversion in DNA with very low levels of undesired by-products, such as small insertions or deletions (indels), in cultured cells, adult mice, plants, and other organisms. Additional details about the TadA- 8e and TadA710 deaminase can be found in PCT Publication No WO 2021/158921 published August 12, 2021; PCT Publication No. WO 2018/027078, published on February 8, 2018, PCT Patent Publication No.
• CBEs cytosine base editors
• Current CBEs contain a uracil glycosylase inhibitor domain, which is about 84 bp in length. Although not very large, these additional 84 base pairs render delivery of CBEs in a single AAV vector more difficult than ABEs.
• Ran and colleagues engineered a size-minimized S.
• aureus Cas9 for delivery in a single AAV vector in vivo to install double-strand breaks into target genomic DNA.
• Ran AAV cassette contained a U6 promoter-driven sgRNA and a cytomegalovirus (CMV) promoter- or thyroxine-binding globulin (TBG) promoter-driven SaCas9 transgene.
• CMV cytomegalovirus
• TSG thyroxine-binding globulin
• This disclosure provides size-minimized AAV vectors that have lengths of less than about 4.90 kb between the ITRs.
• This single-AAV base editing platform offers similar or improved editing efficiencies compared to dual-AAV ABE8e in a variety of tissues across multiple doses when delivered systemically into mice.
• Exemplary AAV vectors of the disclosure do not incorporate, or rely on the use of, trans-splicing inteins for successful delivery.
• the AAV vectors of the disclosure are based, at least in part, on genetic engineering advances that generated vectors containing size-minimized components necessary for efficient expression in target cells and editing of target bases in vivo.
• Exemplary target cells include muscle cells, neurons, liver cells, neuromuscular cells, and cardiac cells.
• the disclosed AAV vectors are smaller than the vectors disclosed in U.S. Patent Publication No.2018/0127780, published May 10, 2018, and PCT Publication No. WO 2020/236982, published November 26, 2020, and thus are adapted for incorporation into a single AAV particle.
• the disclosed AAV vectors are based in part on the discovery that a post-transcriptional response element, such as WPRE, in the transcriptional terminator (or polyadenylation signal) is not necessary for successful expression of the base editor in target tissues in vivo.
• the disclosed AAV vectors thus contain shorter (or size-minimized) terminators.
• the disclosed AAV vectors further contain other size-minimized regulatory elements, such as short promoters.
• the disclosed AAV vectors are also based in part on the discovery that a guide RNA compatible with any of the disclosed Cas proteins can be encoded at the 3 ⁇ end of the vector and maintain a total ITR-to-ITR length of less than 4.9 kb, less than 4.8 kb, less than 4.7 kb, less than 4.6 kb, or less than 4.5 kb.
• a base editor and its guide can be efficiently packaged in a single rAAV particle for delivery in vivo.
• the guide RNA may be encoded in the vector in an orientation (3 ⁇ to 5 ⁇ ) reverse of that of the base editor (i.e., 5 ⁇ to 3 ⁇ ) and the promoter driving expression of the base editor transgene (and its origin of replication).
• the disclosure also provides size-minimized base editors. These base editors were developed to enable efficient in vivo base editing mediated by single AAV particle.
• the disclosed AAV-encoded base editors that may comprise size-minimized Cas proteins. These Cas9 proteins are about 1000-1050 amino acids in length, which is about 350 amino acids shorter than a SpCas9 protein
• These size-minimized Cas proteins include but are not limited to S. aureus Cas9 (SaCas9), Nme2Cas9, C.
• the disclosed AAV nucleic acid molecules do not comprise an intein, such as a trans-splicing intein (e.g., do not comprise a trans-splicing intein derived from Nostoc punctiforme, or Npu).
• the disclosed AAV nucleic acid molecules comprise a transcriptional terminator that does not comprise a post-transcriptional response element.
• the disclosed AAV nucleic acid molecules do not comprise an intein or a post-transcriptional response element.
• the nucleic acid molecules comprise a first nucleic acid segment comprising: (i) a 5 ⁇ inverted terminal repeat (ITR); (ii) a first nucleic acid segment comprising sequence encoding a base editor operably linked to a first promoter, wherein the base editor comprises a nucleic acid programmable DNA binding protein (napDNAbp) domain and a deaminase domain; and a polyadenylation (polyA) signal; (iii) a second nucleic acid segment encoding a guide RNA (gRNA) operably linked to a second promoter; and (iv) a 3 ⁇ ITR.
• ITR inverted terminal repeat
• rAAV vectors having size-minimized regulatory elements that allow for packaging of a large transgenes.
• rAAV nucleic acid molecules that comprise, in 5 ⁇ to 3 ⁇ order: (i) a 5 ⁇ inverted terminal repeat (ITR); (ii) a first nucleic acid segment comprising a transgene operably linked to a first promoter, wherein the first promoter has a length of less than 300 nucleotides; and a transcriptional terminator that does not contain a posttranscriptional response element; (iii) a second nucleic acid segment operably linked to a second promoter, wherein the direction of transcription of the second nucleic acid segment is reversed relative to the direction of transcription of the first nucleic acid segment; and (iv) a 3 ⁇ ITR.
• ITR inverted terminal repeat
• the length the length between the 5 ⁇ ITR and the 3 ⁇ ITR is less than about 4.90 kb. In some embodiments, the length the length between the 5 ⁇ ITR and the 3 ⁇ ITR is less than about 4.85 kb, less than about 4.80 kb, less than about 4.75 kb, less than about 4.725 kb, less than about 4.70 kb, or less than 4.65 kb.
• the first nucleic acid segment encodes a base editor
• the second nucleic acid segment encodes a gRNA.
• the first nucleic acid segment encodes a protein that is not a base editor.
• any of the disclosed base editors may comprise (i) a napDNAbp domain; and (ii) a deaminase domain.
• the disclosed base editors may comprise a wild-type napDNAbp domain (e.g., wild-type SaKKH-Cas9).
• the disclosed base editors may comprise a napDNAbp domain that has nickase activity (e.g., SaKKH-Cas9 nickase, or “SaKKH”).
• the napDNAbp domain is a Cas9 nickase domain.
• the napDNAbp domain is SaKKH-Cas9 nickase.
• the napDNAbp domain may be selected from an S.
• the disclosed single-AAV encoded base editors can potentially target the vast majority of adenines across the genome, or the vast majority of cytosines across the genome.
• the napDNAbp domain is an SaCas9 domain, SaCas9 nickase domain, SaKKH domain, or SaKKH nickase domain.
• the AAV-encoded ABEs of the disclosure contain an adenosine deaminase domain containing a single deaminase, i.e. a deaminase monomer (such as a TadA-8e monomer), rather than an adenosine deaminase dimer (i.e., two adenosine deaminases).
• a deaminase monomer such as a TadA-8e monomer
• a deaminase dimer i.e., two adenosine deaminases.
• Use of a deaminase monomer facilitates generation of size-minimized base editos.
• the TadA monomers are about 166 amino acids in length.
• Any of the disclosed adenine base editors may comprise an adenosine deaminase domain that is a variant of E.
• the adenosine deaminase is selected from a TadA-8e, a TadA-8e(V106W), a TadA9, a TadA20, and a TadA7.10 deaminase.
• any of the base editors of the disclosure comprises an adenosine deaminase fused to the N-terminus of a napDNAbp domain, such as a Cas9 nickase.
• the adenosine deaminase is TadA-8e. [0023]
• the present disclosure provides size-minimized ABE8e variants.
• Each variant is compatible with single-AAV delivery, and three such variants collectively offer PAM compatibility sufficient to target 87% and edit 82% of adenines in the human genome.
• These three variants are Sauri-ABE8e, SaKKH-ABE8e, and SaABE8e.
• Each contain the TadA-8e adenosine deaminase and the nickase variant of SauriCas9, SaKKH- Cas9, and SaCas9, respectively.
• the present disclosure further provides ABE8e variants CjCas9-ABE8e and Nme2Cas9-ABE8e.
• the present disclosure further provides ABE variants SaKKH-ABE8e(V106W), SauriCas9-ABE8e(V106W), CjCas9-ABE8e(V106W), Nme2Cas9-ABE8e(V106W) and SaCas9-ABE8e(V106W); SaKKH-ABE9 SauriCas9- ABE9, CjCas9-ABE9, Nme2Cas9-ABE9, and SaCas9-ABE9; SaKKH-ABE20, SauriCas9- ABE20, CjCas9-ABE20, Nme2Cas9-ABE20, and SaCas9-ABE20; and SaKKH-ABE7.10, SauriCas9-ABE7.10, CjCas9-ABE7.10, Nme2Cas9-ABE7.10, and SaCas9-ABE7.10.
• the wild-type, or the nickase variant, of SauriCas9, SaKKH- Cas9, SaCas9, CjCas9, and Nme2Cas9, respectively may be used.
• the present disclosure further provides size-minimized CBE variants, and in particular size-minimized BE3.9 variants. Examples of these variants include CjCas9-BE3.9, CjCas9-FERNY-BE3.9, and CjCas9-evoFERNY-BE3.9.
• the base editor further comprises a uracil glycosylase inhibitor (UGI) domain.
• UMI uracil glycosylase inhibitor
• an exemplary cytidine deaminase e.g., a rAPOBEC1 deaminase
• the size of an exemplary cytidine deaminase (e.g., a rAPOBEC1 deaminase) of the disclosed CBEs is about 229 amino acids.
• single-AAV delivery of ABEs achieved editing of 66%, 33%, and 22% in liver, heart, and muscle tissues, respectively, at doses lower than or similar to those used in recent preclinical and clinical studies of AAV particles targeting these tissues (see, e.g., Clinical Trial Nos. NCT02122952 (SMA treatment) and NCT03375164 (DMD treatment)).
• SMA treatment Clinical Trial Nos.
• DMD treatment NCT03375164
• PCSK9 Liver protein Proprotein Convertase Subtilisin/Kexin Type 9
• PCSK9 Liver protein Proprotein Convertase Subtilisin/Kexin Type 9
• LDL-R low-density lipoprotein receptor
• Angiopoetin-like 3 protein Angptl3
• LPL lipoprotein lipase
• single-AAV BEs offer several potential advantages over dual AAV approaches for clinical use: clinical-scale production of a single vector rather than two; increased potency, especially at lower doses; and reduced complexity from a simpler construct that obviates the need to use a trans-splicing intein.
• in vivo editing approaches compatible with single-AAV delivery may be more readily applied to large animal models and human therapeutics where systemic delivery is commonly used.
• Development of smaller promoters that provide sufficient expression of base editors allow further minimization of the elements of single-AAV ABEs, which should facilitate clinical translation by increasing the proportion of full-length packaged AAV genomes.
• the disclosed cells may comprise any of the disclosed nucleic acid molecules, rAAV vectors, or rAAV particles described herein.
• kits comprising any of the disclosed rAAV particles and instructions for delivery to a cell (such as a host cell) are provided.
• Still other aspects of the present disclosure provide methods comprising contacting a target nucleic acid molecule with any of the compositions described herein.
• the target nucleic acid molecule is in a cell, such as a eukaryotic cell (e.g., a mammalian cell).
• the target nucleic acid molecule is genomic DNA.
• the genomic DNA is in a cell or tissue of a subject, such as a human subject.
• compositions comprising administering to a subject in need there of a therapeutically effective amount of any of the compositions (or rAAV particles) described herein.
• the subject has a disease or disorder (e.g. a genetic disease).
• the disease or condition is cardioavascular disease.
• the compositions are administered to the liver tissue cardiac tissue or skeletal muscle tissue of the subject.
• FIG.1A shows an AAV construct evaluated in vivo. sgRNA targeting a Pcsk9 gene having the W8 mutation was delivered with EGFP in one AAV that was co- injected with either one or two additional AAVs encoding either an intact or intein-split SaABE8e, respectively.
• a total of two AAVs were used to deliver the intact SaABE8e and sgRNA, and three AAVs were used to deliver the intein-split SaABE8e.
• Black boxes represent ITRs, EFS promoter is EF1 ⁇ short, W3 is truncated WPRE, bGH is bovine growth hormone polyadenylation signal, the purple box is the U6 promoter-driven sgRNA cassette in the orientation indicated by the arrow, NpuN & NpuC split inteins from Nostoc punctiforme are shown in brown, and protein coding regions are indicated for EGFP and SaABE8e.
• FIG. 1B shows in vivo editing efficiency from injection of AAV encoding intein-split and intact SaABE8e.
• the total dose of base editor AAV administered to each mouse is shown.
• FIG.1C shows a comparison of in vivo editing efficiency from injection of AAV9 encoding intact SaABE8e in five different AAV architectures when administered at the dose shown.
• editor AAV dose was either 4x10 11 vector genomes (vg) or 4x10 10 vg and sgRNA EGFP
• AAV dose was either 4x10 11 vg or 4x10 10 vg for a 1:1 ratio of base editor AAV to sgRNA AAV.
• the sizes of the delivered editor AAV constructs are shown in the legend.
• FIGs.2A-2C Development and characterization of a single AAV SaABE8e.
• FIG. 2A shows a schematic of the single AAV SaABE8e genome (5,064 bp including ITRs). Arrow indicates direction of the U6 sgRNA cassette.
• FIG.2B shows a comparison of dual to single SaABE8e.
• Base editor AAVs were administered at the dose indicated in the legend (dual AAVs were delivered with the dose indicated of editor AAV and sgRNA AAV, while single AAVs were delivered at the dose indicated) to C57BL/6J mice aged 6- to 8-week-old weighing 20-25 grams via retroorbital injection, and tissues were harvested three weeks post injection and analyzed by high-throughput DNA sequencing (HTS).
• FIGs.3A-3D Characterization of Nme2ABE8e (FIG.3A), CjABE8e (FIG.3B), and SauriABE8e (FIG.3C) in HEK293T cells. Editing of each target adenine within the protospacer is shown. Target sites are indicated, with sequences of each target protospacer and PAM listed in Table 1.
• FIG.3D shows the percent of genomic adenines in the hg38 human reference genome targetable by size-minimized ABEs independently and collectively. A schematic showing a representative portion of the genome targetable by size- minimized ABEs is shown, with targetable PAMs denoted with colored lines and targetable adenines denoted with colored dots.
• FIGs.4A-4D Characterization of Nme2ABE8e (FIG.4A), CjABE8e (FIG.4B), and SauriABE8e (FIG.4C) in HEK293T cells. Base editing activity windows from 8-9 genomic target sites for each size-minimized ABE are shown. Positions that were not present in any tested site are shaded gray.
• FIG.4D shows the percent of genomic adenines in the hg38 human reference genome targetable by size-minimized ABEs either independently or collectively.
• FIGs.5A-5K Assessment of genome edting and plasma lipids when targeting PCSK9, Pcsk9, and Angptl3 with single-AAV in vivo.
• FIG.5A shows a strategy for assessing base editing and plasma analytes in AAV treated mice, and was created using BioRender.
• Human PCSK9 editing was performed using humanized PCSK9 mice, while mouse Pcsk9 and Angptl3 editing was performed at the endogenous mouse loci of wild-type C57BL/6J mice.
• AAV was administered by retroorbital injection at 6-8 weeks of age at a dose of 1x10 11 vg/mouse.
• FIG.5C shows dose-dependent base editing for dual SpABE8e and single SaKKH-ABE8e at mouse Pcsk9 exon 1 splice donor.
• the total AAV dose administered is indicated below each set of bars in vg/mouse.
• the total AAV dose administered is indicated below each set of bars in vg/mouse.
• FIG.5D shows direct comparison of editing efficiencies of dual-AAV8 intein-split SaKKH-ABE8e and single-AAV8 SaKKH-ABE8e targeting the Pcsk9 exon 1 donor site in bulk liver at two doses.
• FIG.5E shows plasma PCSK9 protein in humanized mice treated with 1x10 11 vg single-AAV8 SaKKH-ABE8e.
• FIG.5H shows plasma total cholesterol in humanized mice treated with 1x10 11 vg single-AAV8 SaKKH-ABE8e.
• FIG.5K shows C57BL/6J in mice treated with 1x10 11 vg single-AAV8 SaKKH-ABE8e or non- targeting control.
• non- targeting control is dual AAV8 SpABE7.10 with sgRNA targeting mouse Dnmt1, an unrelated site in the mouse genome, administered at the same timepoint, route, and dose.
• FIG.6 shows the validation of SaABE targets in mouse Neuro-2A and 3T3 cells.
• FIG.8A shows the SaABE8e activity window at Pcsk9 W8R in liver.
• SaABE8e maintains a wide editing window in vivo, consistent with observations in cultured cells.
• FIGs.10A and 10B show editing in Neuro-2A cells with SauriABE8e at the Pcks9 exon 1 splice donor target.
• FIG.10A shows targeting of mouse Pcsk9 exon 1 splice donor with SauriABE8e and SaKKH-ABE8e in mouse Neuro-2A cells.
• the target adenine is A 9 with respect to the Sauri protospacer, A5 with respect to SaKKH protospacer.
• FIG.10B shows a comparison of SaCas9 guide RNA scaffolds 33,74 on editing activity at the mouse Pcsk9 exon 1 splice donor.
• FIGs.11A and 11B In vivo editing of control AAVs for lipid modification experiments.6- to 8-week-old C57BL/6J mice were injected by retroorbital injection and whole liver was analyzed by HTS after four weeks.
• FIG.11A shows editing at Dnmt1 A41A (silent edit) with dual SpABE7.10 at a dose of 1x10 11 vg dual AAV8.
• FIG.11B shows installation of the Pcsk9 W8R substitution using single SaKKH-ABE8e at a dose of 1x10 11 vg single AAV8.
• FIGs.12A-12D Dose response of single-AAV8 SaKKH-ABE8e and dual-AAV8 SpABE8e (with Pcsk9 exon 1 splice donor site-targeting sgRNA) on plasma Pcsk9 and total cholesterol.
• FIG.12A shows circulating Pcsk9 protein and FIG.12B shows total cholesterol from plasma taken weekly, normalized to baseline.
• FIG.12C shows irculating Pcsk9 protein and FIG.12D shows total cholesterol from plasma taken weekly, raw (unnormalized).
• FIGs.13A-13E Raw (unnormalized) levels of plasma analytes of either single- AAV ABE or nontargeting control dual-AAV ABE mice, for human PCSK9 and mouse Angptl3 targets.
• FIG.13A shows ELISA of human PCSK9 in plasma from humanized mice.
• FIG.13B shows total plasma cholesterol in humanized PCSK9 mice.
• FIG.13C shows ELISA of mouse Angptl3 in plasma from C57BL/6J mice.
• FIG.13D shows total plasma cholesterol in C57BL/6J mice.
• FIG.14 is a schematic showing a construct for a single AAV vector expressing a cytosine base editor, which includes a uracil glycosylase domain. The Cas9 domain of the cytosine base editor is a CjCas9.
• FIG.15 shows a base editor-matched comparison of guide-dependent on-target editing between single-AAV SaKKH-ABE8e and dual-AAV SaKKH-ABE8e at the Pcsk9 exon 1 splice donor site.
• FIGs.16A-16C shows guide-dependent off-target DNA editing analyses in vivo and in culture between single-AAV8 SaKKH and each half of an AAV8 intein-split SaKKH- ABE8e.
• FIG.16A shows in vivo editing in liver tissue from single-AAV ABE treated mice.
• the top three predicted off target (“OT”) sites for SaKKH-ABE8e targeting Pcsk9 exon 1 splice donor were sequenced from liver tissue.
• FIG.16B shows the editing observed at OT2 is dose-dependent.
• OT off-target;
• NT non-targeting dose-matched dual AAV8 ABE7.10 targeting Dnmt1, an unrelated gene.
• FIG.16C shows editing in cell culture. On-and off-target sites were sequenced after plasmid transfection of N2A cells with sgRNA targeting Pcsk9 exon 1 donor site and full-length or intein-split SpABE8e.
• FIG.18 shows a comparison of the editing windows of exemplary single AAV- encoded ABEs in the liver. [0051] FIGs.19A-19B.
• FIG.20 shows the quantification of AAV genomes from tissue encoding SaABE8e dual AAV (SaABE8e with intact editor on one genome and sgRNA and EGFP on a second genome) or single AAV (SaABE8e and guide RNA all-in-one), both installing Pcsk9 W8R packaged in AAV9.
• FIG.21 shows the alkaline gel electrophoresis of packaged AAV genomes.
• FIG.22A-22D show the off-target mRNA editing.
• RNA was extracted from mouse livers treated with single-AAV8 SaKKH-ABE8e and untreated mouse livers, reverse transcribed, and cDNA amplicons from Aars, Canx, Ctnnb, and Usp38 mRNA were analyzed by HTS. Dots represent individual adenines across the sequenced amplicon (n 3 mice).
• rAAV recombinant AAV
• rAAV vectors comprise size-minimized base editors and regulatory components that enable the vector to have a length within the 4.7kb-4.9kb packaging capacity of rAAV particles.
• rAAV particles that contain any of the disclosed rAAV vectors and a capsid protein are also provided, as well as compositions and cells comprising same. Methods of administering such compositions, and cells, to a subject are further provided. Further provided are base editors and compositions and cells comprising these base editors.
• AAV vectors or AAV genomes
• ITR inverted terminal repeat
• AAV viral particles which are used to transduce a host cell (e.g., mammalian cell, human cell).
• AAV has been used to deliver genes encoding many therapeutic proteins in animal models of human disease, in clinical trials and in FDA- approved drugs.
• a suite of available AAV serotypes provide access to a variety of clinically relevant cell types in mice, nonhuman primates, and humans.
• the disclosure provides rAAV vectors having size-minimized regulatory elements that allow for packaging of a larger transgene than the vectors of the prior art.
• the transgene encodes a base editor, such as an adenine base editor.
• the transgene is not a base editor.
• the base editor contains a napDNAbp domain that is a compact protein, such as an S. aureus Cas9 (SaCas9), an N. meningitidis 2 Cas9 (Nme2Cas9), a C. jejuni Cas9 (CjCas9), or an S. auricularis (SauriCas9) domain, or a variant thereof.
• rAAV vectors that contain a first nucleic acid segment comprising: (i) a 5 ⁇ ITR; (ii) a first nucleic acid segment comprising sequence encoding a base editor operably linked to a first promoter wherein the base editor comprises a nucleic acid programmable DNA binding protein (napDNAbp) domain and a deaminase domain; and a polyadenylation (polyA) signal; (iii) a second nucleic acid segment encoding a guide RNA (gRNA) operably linked to a second promoter; and (iv) a 3 ⁇ ITR, wherein the length between the 5 ⁇ ITR and the 3 ⁇ ITR is less than about 4.90 kb.
• gRNA guide RNA
• the rAAV vectors consist essentially of components (i)-(iv).
• the nucleic acid vector is the genome of an adeno-associated virus packaged in a rAAV particle.
• the first and/or the second nucleic acid segment is operably linked to a first promoter.
• the first promoter is a constitutive promoter.
• the first promoter is an inducible promoter.
• the first promoter is a short promoter.
• the first promoter has a length of less than 325 nucleotides, less than 300 nucleotides, less than 285 nucleotides, less than 270 nucleotides, less than 265 nucleotides, or less than 250 nucleotides. This short length ensures optimal packaging capacity for the base editor and additional regulatory elements. In some embodiments, the first promoter has a length of between 200 and 250 nucleotides, 225 and 255 nucleotides, 250 and 275 nucleotides, 275 and 300 nucleotides, or 300 and 325 nucleotides. In certain embodiments, the first promoter has a length of 280 nucleotides.
• the first promoter has a length of 229 nucleotides, 253 nucleotides, or 324 nucleotides.
• the first promoter is a tissue-specific promoter.
• the first promoter may be a cardiac tissue-specific promoter, a muscle tissue-specific promoter, or a neuronal tissue-specific promoter.
• the first promoter may be active in a tissue other than liver, muscle, and neurons, such as ocular tissue.
• the first promoter is active in neuromuscular tissue.
• the first promoter is an EF-1 ⁇ (short) (“EFS”) promoter, which is the intron-less form of EF-1 ⁇ .
• the first promoter is an MeCP2 promoter, which is active in neuronal tissues.
• the first promoter is a P3 promoter, which is active in liver tissues.
• the first promoter is a U1a promoter, which is active in liver tissues. Additional details about the MeCP2 promoter, P3 promoter, and U1a promoter is found in Gray et al., Human Gene Therapy.Sep 2011.1143-1153; Viecelli et al., Hepatology, 60: 1035-1043 (2014); and Ibraheim et al., Genome Biol.19, 137 (2016), respectively, each of which is incorporated herein by reference.
• the first nucleic acid segment comprises a transcriptional terminator.
• the first nucleic acid segment does not contain a posttranscriptional response element (e.g., W3).
• the transcriptional terminator is a polyA signal selected from a bovine growth hormone (bGH) signal, human growth hormone (hGH) signal, or SV40 signal.
• the terminator is a bGH polyA signal.
• the terminator is a SV40 late polyA signal.
• the first nucleic acid segment comprises a minimal minute virus of mice (MVM) intron.
• the MVM is positioned 5 ⁇ of the promoter and 3 ⁇ of the transgene.
• the second nucleic acid segment comprises a nucleotide sequence encoding a gRNA operably linked to a second promoter.
• the second promoter is a constitutive promoter.
• the second promoter is an inducible promoter.
• the second promoter is a U6 promoter, such as a human U6 promoter.
• the direction of transcription of the second nucleic acid segment is reversed relative to the direction of transcription of the first nucleic acid segment.
• the disclosed rAAV vectors which contain a first nucleic acid segment that contains a promoter and terminator and a second nucleic acid segment that may encode a guide RNA—have packaging capacities between the 5 ⁇ ITR and the 3 ⁇ ITR of lengths that fit a transgene encoding one or more of the disclosed base editors.
• the disclosed AAV vectors may contain a length between the 5 ⁇ ITR and the 3 ⁇ ITR of between 4.7 kb and 4.9 kb.
• the disclosed AAV vectors may contain a length between the 5 ⁇ ITR and the 3 ⁇ ITR of between 4.7 kb and 5.1 kb.
• the disclosed AAV vectors may contain a length between the 5 ⁇ ITR and the 3 ⁇ ITR of between 4.6 kb and 4.9 kb, or between 4.6 kb and 4.8 kb.
• the length between the 5 ⁇ ITR and the 3 ⁇ ITR is about 4.60 kb, about 4.65 kb, about 4.70 kb, about 4.725 kb, about 4.75 kb, about 4.80 kb, about 4.825 kb, about 4.85 kb, about 4.90 kb, or about 4.95 kb.
• the length the length between the 5 ⁇ ITR and the 3 ⁇ ITR is less than about 4.90 kb.
• the length between the 5 ⁇ ITR and the 3 ⁇ ITR is about 4.80 kb. In some embodiments, the length between the ITRs is 4.804 kb (4804 bp). In some embodiments, the length between the ITRs is 4.828 kb. In some embodiments, the length between the ITRs is 4.722 kb.
• the disclosure provides rAAV vectors containing size-minimized adenine base editors, and rAAV vectors containing size-minimized cytosine base editors. Exemplary AAV vectors of the disclosure are shown in FIGs.2A and 14.
• rAAV vectors that comprise: (i) a 5 ⁇ ITR; (ii) a first nucleic acid segment comprising sequence encoding a SaKKH-ABE8e, a SauriCas9- ABE8e, a CjCas9-ABE8e base editor, or a Nme2Cas9 base editor operably linked to a first promoter, wherein the first promoter is selected from the EFS, MeCP2, P3, and U1A promoters; and a bGH polyadenylation (polyA) signal; (iii) a second nucleic acid segment encoding a guide RNA (gRNA) operably linked to a U6 promoter, wherein the direction of transcription of the second nucleic acid segment is reversed relative to the direction of transcription of the nucleic acid molecule; and (iv) a 3 ⁇ ITR.
• gRNA guide RNA
• the rAAV vectors contain a first nucleic acid segment comprising: (i) a 5 ⁇ ITR; (ii) a first nucleic acid segment comprising sequence encoding a Sauri-ABE8e base editor operably linked to an EFS promoter; and a polyadenylation (polyA) signal; (iii) a second nucleic acid segment encoding a guide RNA (gRNA) operably linked to a U6 promoter, wherein the direction of transcription of the second nucleic acid segment is reversed relative to the direction of transcription of the nucleic acid molecule; and (iv) a 3 ⁇ ITR.
• gRNA guide RNA
• the length between the 5 ⁇ ITR and the 3 ⁇ ITR is less than about 4.90 kb.
• the poly(A) signal is a bGH poly(A) signal.
• the rAAV vectors comprise, from 5 ⁇ to 3 ⁇ : (i) a 5 ⁇ ITR; (ii) a first nucleic acid segment comprising sequence encoding a SaKKH-ABE8e base editor operably linked to an EFS promoter; and a bGH polyadenylation (polyA) signal; (iii) a second nucleic acid segment encoding a guide RNA (gRNA) operably linked to a U6 promoter, wherein the direction of transcription of the second nucleic acid segment is reversed relative to the direction of transcription of the nucleic acid molecule; and (iv) a 3 ⁇ ITR.
• gRNA guide RNA
• the rAAV vectors contain a first nucleic acid segment comprising: (i) a 5 ⁇ ITR; (ii) a first nucleic acid segment comprising sequence encoding a Sauri-ABE8e base editor operably linked to an EFS promoter; and a bGH polyadenylation (polyA) signal; (iii) a second nucleic acid segment encoding a guide RNA (gRNA) operably linked to a U6 promoter, wherein the direction of transcription of the second nucleic acid segment is reversed relative to the direction of transcription of the nucleic acid molecule; and (iv) a 3 ⁇ ITR.
• the base editor is SauriCas9-ABE8e.
• the base editor is CjCas9-ABE8e.
• the rAAV vectors encode a CBE and comprise, from 5 ⁇ to 3 ⁇ : (i) a 5 ⁇ ITR; (ii) a first nucleic acid segment comprising sequence encoding a CjCas9- FERNY-BE3.9 or CjCas9-evoFERNY-BE3 base editor operably linked to a first promoter that is an EFS promoter; and a polyadenylation (polyA) signal; (iii) a second nucleic acid segment encoding a guide RNA (gRNA) operably linked to a U6 promoter, wherein the direction of transcription of the second nucleic acid segment is reversed relative to the direction of transcription of the nucleic acid molecule; and (iv) a 3 ⁇ ITR.
• gRNA guide RNA
• the rAAV vectors encode a CBE and comprise, from 5 ⁇ to 3 ⁇ : (i) a 5 ⁇ ITR; (ii) a first nucleic acid segment comprising sequence encoding a CjCas9-FERNY-BE3.9 or CjCas9-evoFERNY-BE3 base editor operably linked to a first promoter, wherein the first promoter is selected from the EFS, MeCP2, P3, and U1A promoters; and a polyadenylation (polyA) signal; (iii) a second nucleic acid segment encoding a guide RNA (gRNA) operably linked to a U6 promoter, wherein the direction of transcription of the second nucleic acid segment is reversed relative to the direction of transcription of the nucleic acid molecule; and (iv) a 3 ⁇ ITR.
• gRNA guide RNA
• the poly(A) signal is a bGH poly(A) signal. In some embodiments, the poly(A) signal is a SV40 poly(A) signal.
• any of the disclosed rAAV vectors are encapsidated in an AAV8 capsid. In some embodiments, the disclosed rAAV vectors are encapsidated in an AAV9 capsid.
• Further provided herein are empirical testing of regulatory elements in the disclosed AAV vectors for high expression levels of the encoded base editor. Definitions [0074] As used herein and in the claims, the singular forms “a,” “an,” and “the” include the singular and the plural unless the context clearly indicates otherwise.
• an agent includes a single agent and a plurality of such agents.
• An “adeno-associated virus” or “AAV” is a virus which infects humans and some other primate species.
• the wild-type AAV genome is a single-stranded deoxyribonucleic acid (ssDNA), either positive- or negative-sensed.
• the genome comprises two inverted terminal repeats (ITRs), one at each end of the DNA strand, and two open reading frames (ORFs): rep and cap between the ITRs.
• the rep ORF comprises four overlapping genes encoding Rep proteins required for the AAV life cycle.
• the cap ORF comprises overlapping genes encoding capsid proteins: VP1, VP2 and VP3, which interact together to form the viral capsid.
• VP1, VP2 and VP3 are translated from one mRNA transcript, which can be spliced in two different manners: either a longer or shorter intron can be excised resulting in the formation of two isoforms of mRNAs: a ⁇ 2.3 kb- and a ⁇ 2.6 kb-long mRNA isoform.
• the capsid forms a supramolecular assembly of approximately 60 individual capsid protein subunits into a non-enveloped, T-1 icosahedral lattice capable of protecting the AAV genome.
• rAAV particles may comprise a nucleic acid vector (e.g., a recombinant genome), which may comprise at a minimum: (a) one or more heterologous nucleic acid regions (or transgenes) comprising a sequence encoding a protein or polypeptide of interest (e.g., a base editor) or an RNA of interest (e.g., a gRNA); and (b) one or more regions comprising inverted terminal repeat (ITR) sequences (e.g., wild-type ITR sequences or engineered ITR sequences) flanking the one or more nucleic acid regions (e.g., heterologous nucleic acid regions).
• ITR inverted terminal repeat
• the nucleic acid vector is between 4 kb and 5 kb in size (e.g., 4.2 to 4.7 kb in size). In some embodiments, the nucleic acid vector is circular. In some embodiments, the nucleic acid vector is single-stranded. In some embodiments, the nucleic acid vector is double-stranded. In some embodiments, a double-stranded nucleic acid vector may be, for example, a self-complimentary vector that contains a region of the nucleic acid vector that is complementary to another region of the nucleic acid vector, initiating the formation of the double-strandedness of the nucleic acid vector.
• adenosine deaminase or “adenosine deaminase domain” refers to a protein or enzyme that catalyzes a deamination reaction of an adenosine (or adenine).
• the terms are used interchangeably.
• the disclosure provides base editors comprising one or more adenosine deaminase domains.
• an adenosine deaminase domain may comprise a heterodimer of a first adenosine deaminase and a second deaminase domain, connected by a linker.
• Adenosine deaminases may be may be enzymes that convert adenine (A) to inosine (I) in DNA or RNA. Such adenosine deaminase can lead to an A:T to G:C base pair conversion.
• the deaminase is a variant of a naturally-occurring deaminase from an organism. In some embodiments, the deaminase does not occur in nature.
• the deaminase is at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75% at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to a naturally-occurring deaminase.
• the adenosine deaminase is derived from a bacterium, such as, E. coli, S. aureus, S. typhi, S. putrefaciens, H. influenzae, or C. crescentus.
• the adenosine deaminase is a TadA deaminase.
• the TadA deaminase is an E. coli TadA deaminase (ecTadA).
• the TadA deaminase is a truncated E. coli TadA deaminase.
• the truncated ecTadA may be missing one or more N-terminal amino acids relative to a full-length ecTadA.
• the truncated ecTadA may be missing 1, 2, 3, 4, 5 ,6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 6, 17, 18, 19, or 20 N-terminal amino acid residues relative to the full length ecTadA. In some embodiments, the truncated ecTadA may be missing 1, 2, 3, 4, 5 ,6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 6, 17, 18, 19, or 20 C-terminal amino acid residues relative to the full length ecTadA. In some embodiments, the ecTadA deaminase does not comprise an N-terminal methionine. Reference is made to U.S.
• the “antisense” strand of a segment within double-stranded DNA is the template strand, and which is considered to run in the 3' to 5' orientation.
• the “sense” strand is the segment within double-stranded DNA that runs from 5' to 3', and which is complementary to the antisense strand of DNA, or template strand, which runs from 3' to 5'.
• the sense strand is the strand of DNA that has the same sequence as the mRNA, which takes the antisense strand as its template during transcription, and eventually undergoes (typically, not always) translation into a protein.
• the antisense strand is thus responsible for the RNA that is later translated to protein, while the sense strand possesses a nearly identical makeup to that of the mRNA. Note that for each segment of dsDNA, there will possibly be two sets of sense and antisense, depending on which direction one reads (since sense and antisense is relative to perspective). It is ultimately the gene product, or mRNA, that dictates which strand of one segment of dsDNA is referred to as sense or antisense.
• Base editing refers to genome editing technology that involves the conversion of a specific nucleic acid base into another at a targeted genomic locus. In certain embodiments, this can be achieved without requiring double-stranded DNA breaks (DSB), or single stranded breaks (i.e., nicking).
• DSB double-stranded DNA breaks
• nicking single stranded breaks
• CRISPR-based systems begin with the introduction of a DSB at a locus of interest
• CRISPR- based systems begin with the introduction of a DSB at a locus of interest
• cellular DNA repair enzymes mend the break, commonly resulting in random insertions or deletions (indels) of bases at the site of the DSB.
• base editor refers to an agent comprising a polypeptide that is capable of making a modification to a base (e.g., A, T, C, G, or U) within a nucleic acid sequence (e.g., DNA or RNA) that converts one base to another (e.g., A to G, A to C, A to T, C to T, C to G, C to A, G to A, G to C, G to T, T to A, T to C, T to G).
• the base editor is capable of deaminating a base within a nucleic acid such as a base within a DNA molecule.
• the base editor is capable of deaminating an adenine (A) in DNA.
• Such base editors may include a nucleic acid programmable DNA binding protein (napDNAbp) fused to an adenosine deaminase.
• Some base editors include CRISPR-mediated fusion proteins that are utilized in the base editing methods described herein.
• the base editor comprises a nuclease-inactive Cas9 (dCas9) fused to a deaminase which binds a nucleic acid in a guide RNA-programmed manner via the formation of an R-loop, but does not cleave the nucleic acid.
• dCas9 nuclease-inactive Cas9
• the dCas9 domain of the fusion protein may include a D10A and a H840A mutation (which renders Cas9 capable of cleaving only one strand of a nucleic acid duplex), as described in PCT/US2016/058344, which published as WO 2017/070632 on April 27, 2017 and is incorporated herein by reference in its entirety.
• the DNA cleavage domain of S. pyogenes Cas9 includes two subdomains, the HNH nuclease subdomain and the RuvC1 subdomain.
• the HNH subdomain cleaves the strand complementary to the gRNA (the “targeted strand”, or the strand in which editing or deamination occurs), whereas the RuvC1 subdomain cleaves the non-complementary strand containing the PAM sequence (the “non- edited strand”).
• the RuvC1 mutant D10A generates a nick in the targeted strand
• the HNH mutant H840A generates a nick on the non-edited strand (see Jinek et al., Science, 337:816-821(2012); Qi et al., Cell.28;152(5):1173-83 (2013), each of which are incorporated herein by reference).
• a base editor is a macromolecule or macromolecular complex that results primarily (e.g., more than 80%, more than 85%, more than 90%, more than 95%, more than 99%, more than 99.9%, or 100%) in the conversion of a nucleobase in a polynucleic acid sequence into another nucleobase (i.e., a transition or transversion) using a combination of 1) a nucleotide-, nucleoside-, or nucleobase-modifying enzyme and 2) a nucleic acid binding protein that can be programmed to bind to a specific nucleic acid sequence.
• the base editor comprises a DNA binding domain (e.g., a programmable DNA binding domain such as a dCas9 or nCas9) that directs it to a target sequence.
• the base editor comprises a nucleobase modifying enzyme fused to a programmable DNA binding domain (e.g., a dCas9 or nCas9).
• a “nucleobase modifying enzyme” is an enzyme that can modify a nucleobase and convert one nucleobase to another (e.g., a deaminase such as a adenosine deaminase).
• Base editors that carry out certain types of base conversions (e.g., adenosine (A) to guanine (G), C to G) are contemplated.
• a base editor converts an A to G.
• the base editor comprises an adenosine deaminase.
• An “adenosine deaminase” is an enzyme involved in purine metabolism. It is needed for the breakdown of adenosine from food and for the turnover of nucleic acids in tissues. Its primary function in humans is the development and maintenance of the immune system.
• adenosine deaminase catalyzes hydrolytic deamination of adenosine (forming inosine, which base pairs as G) in the context of DNA.
• adenosine deaminases that act on DNA.
• known adenosine deaminase enzymes only act on RNA (tRNA or mRNA).
• tRNA or mRNA Evolved deoxyadenosine deaminase enzymes that accept DNA substrates and deaminate dA to deoxyinosine have been described, e.g., in PCT Application PCT/US2017/045381, filed August 3, 2017, which published as WO 2018/027078, and PCT Application No.
• a base editor converts a C to a T.
• the base editor comprises a cytidine deaminase.
• cytosine deaminase refers to an enzyme that catalyzes the chemical reaction “cytosine + H2O uracil + NH 3 ” or “5-methyl-cytosine + H 2 O ⁇ thymine + NH 3 .”
• cytosine deaminase refers to an enzyme that catalyzes the chemical reaction “cytosine + H2O uracil + NH 3 ” or “5-methyl-cytosine + H 2 O ⁇ thymine + NH 3 .”
• cytosine deaminase or “cytidine deaminase” refers to an enzyme that catalyzes the chemical reaction “cytosine + H2O uracil + NH 3 ” or “5-methyl-cytosine + H 2 O ⁇ thymine + NH 3 .”
• a nucleotide change, or mutation may in turn lead to an amino acid change in the protein, which may affect the protein’s function,
• the cytosine base editor comprises a dCas9 or nCas9 fused to a cytidine deaminase.
• the cytidine deaminase domain is fused to the N-terminus of the dCas9 or nCas9.
• the base editor further comprises a domain that inhibits uracil glycosylase, and/or a nuclear localization signal.
• WO 2021/108717 published June 3, 2021, the contents of each of which are incorporated herein by reference in their entireties.
• Exemplary adenine and cytosine base editors are also described in Rees & Liu, Base editing: precision chemistry on the genome and transcriptome of living cells, Nat. Rev. Genet. 2018;19(12):770-788; as well as U.S. Patent Publication No.2018/0073012, published March 15, 2018, which issued as U.S. Patent No.10,113,163, on October 30, 2018; U.S. Patent Publication No.2017/0121693, published May 4, 2017, which issued as U.S. Patent No. 10,167,457 on January 1, 2019; PCT Publication No.
• Cas9 or “Cas9 nuclease” refers to an RNA-guided nuclease comprising a Cas9 domain, or a fragment thereof (e.g., a protein comprising an active or inactive DNA cleavage domain of Cas9, and/or the gRNA binding domain of Cas9).
• a “Cas9 domain” as used herein, is a protein fragment comprising an active or inactive cleavage domain of Cas9 and/or the gRNA binding domain of Cas9.
• a “Cas9 protein” is a full length Cas9 protein.
• a Cas9 nuclease is also referred to sometimes as a casn1 nuclease or a CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat)-associated nuclease.
• CRISPR is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements, and conjugative plasmids).
• CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids.
• CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA).
• crRNA CRISPR RNA
• type II CRISPR systems correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and a Cas9 domain.
• the tracrRNA serves as a guide for ribonuclease 3-aided processing of pre-crRNA.
• Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the spacer
• the target strand not complementary to crRNA is first cut endonucleolytically, then trimmed 3′-5′ exonucleolytically.
• RNA-binding and cleavage typically requires protein and both RNAs.
• single guide RNAs (“sgRNA”, or simply “gRNA”) can be engineered so as to incorporate aspects of both the crRNA and tracrRNA into a single RNA species.
• sgRNA single guide RNAs
• Cas9 recognizes a short motif in the CRISPR repeat sequences (the PAM or protospacer adjacent motif) to help distinguish self versus non-self.
• Cas9 nuclease sequences and structures are well known to those of skill in the art (see, e.g., “Complete genome sequence of an M1 strain of Streptococcus pyogenes.” Ferretti et al., J.J., McShan W.M., Ajdic D.J., Savic D.J., Savic G., Lyon K., Primeaux C., Sezate S., Suvorov A.N., Kenton S., Lai H.S., Lin S.P., Qian Y., Jia H.G., Najar F.Z., Ren Q., Zhu H., Song L., White J., Yuan X., Clifton S.W., Roe B.A., McLaughlin R.E., Proc.
• Cas9 orthologs have been described in various species, including, but not limited to, S. pyogenes and S. thermophilus (e.g., StCas9 or St1Cas9).
• Cas9 nucleases and sequences include Cas9 sequences from the organisms and loci disclosed in Chylinski, Rhun, and Charpentier, “The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems” (2013) RNA Biology 10:5, 726- 737; the entire contents of which are incorporated herein by reference.
• a Cas9 nuclease comprises one or more mutations that partially impair or inactivate the DNA cleavage domain.
• a nuclease-inactivated Cas9 domain may interchangeably be referred to as a “dCas9” protein (for nuclease-“dead” Cas9).
• Methods for generating a Cas9 domain (or a fragment thereof) having an inactive DNA cleavage domain are known (see, e.g., Jinek et al., Science.337:816-821(2012); Qi et al., “Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression” (2013) Cell.28;152(5):1173-83, the entire contents of each of which are incorporated herein by reference).
• the DNA cleavage domain of Cas9 is known to include two subdomains the HNH nuclease subdomain and the RuvC1 subdomain.
• the HNH subdomain cleaves the strand complementary to the gRNA, whereas the RuvC1 subdomain cleaves the non-complementary strand. Mutations within these subdomains can silence the nuclease activity of Cas9.
• the mutations D10A and H840A completely inactivate the nuclease activity of S. pyogenes Cas9 (Jinek et al., Science.337:816-821(2012); Qi et al., Cell.28;152(5):1173-83 (2013)).
• proteins comprising fragments of Cas9 are provided.
• a protein comprises one of two Cas9 domains: (1) the gRNA binding domain of Cas9; or (2) the DNA cleavage domain of Cas9.
• proteins comprising Cas9 or fragments thereof are referred to as “Cas9 variants.”
• a Cas9 variant shares homology to Cas9, or a fragment thereof.
• a Cas9 variant is at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, at least about 99.8% identical, or at least about 99.9% identical to wild type Cas9 (e.g., SpCas9 of SEQ ID NO: 74).
• wild type Cas9 e.g., SpCas9 of SEQ ID NO: 74.
• the Cas9 variant may have 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, or more amino acid changes compared to wild type Cas9 (e.g., SpCas9 of SEQ ID NO: 74).
• wild type Cas9 e.g., SpCas9 of SEQ ID NO: 74.
• the Cas9 variant comprises a fragment of Cas9 (e.g., a gRNA binding domain or a DNA-cleavage domain), such that the fragment is at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to the corresponding fragment of wild type Cas9 (e.g., SpCas9 of SEQ ID NO: 74).
• a fragment of Cas9 e.g., a gRNA binding domain or a DNA-cleavage domain
• the fragment is at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% identical, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% of the amino acid length of a corresponding wild type Cas9 (e.g., SpCas9 of SEQ ID NO: 74).
• a corresponding wild type Cas9 e.g., SpCas9 of SEQ ID NO: 74.
• nCas9 or “Cas9 nickase” refers to a Cas9 or a variant thereof, which cleaves or nicks only one of the strands of a target cut site thereby introducing a nick in a double strand DNA molecule rather than creating a double strand break.
• This can be achieved by introducing appropriate mutations in a wild-type Cas9 which inactivates one of the two endonuclease activities of the Cas9
• Any suitable mutation which inactivates one Cas9 endonuclease activity but leaves the other intact is contemplated, such as one of D10A or H840A mutations in the wild-type S.
• CRISPR is a family of DNA sequences (i.e., CRISPR clusters) in bacteria and archaea that represent snippets of prior infections by a virus that have invaded the prokaryote.
• CRISPR-associated proteins including Cas9 and homologs thereof
• CRISPR-associated RNA a prokaryotic immune defense system.
• CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA).
• crRNA CRISPR RNA
• tracrRNA trans-encoded small RNA
• rnc endogenous ribonuclease 3
• the tracrRNA serves as a guide for ribonuclease 3-aided processing of pre-crRNA. Subsequently, Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the RNA. Specifically, the target strand not complementary to crRNA is first cut endonucleolytically, then trimmed 3 ⁇ -5′ exonucleolytically. In nature, DNA-binding and cleavage typically requires protein and both RNAs. However, single guide RNAs (“sgRNA”, or simply “gRNA”) can be engineered so as to incorporate aspects of both the crRNA and tracrRNA into a single RNA species–the guide RNA.
• sgRNA single guide RNAs
• Cas9 recognizes a short motif in the CRISPR repeat sequences (the PAM or protospacer adjacent motif) to help distinguish self versus non-self.
• Cas9 orthologs have been described in various species, including, but not limited to, S. pyogenes and S. thermophilus. Additional suitable Cas9 nucleases and sequences will be apparent to those of skill in the art based on this disclosure, and such Cas9 nucleases and sequences include Cas9 sequences from the organisms and loci disclosed in Chylinski, Rhun, and Charpentier, “The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems” (2013) RNA Biology 10:5, 726-737; the entire contents of which are incorporated herein by reference.
• deaminase or “deaminase domain” refers to a protein or enzyme that catalyzes a deamination reaction.
• the deaminase is an adenosine (or adenine) deaminase, which catalyzes the hydrolytic deamination of adenine or adenosine.
• the adenosine deaminase catalyzes the hydrolytic deamination of adenine or adenosine in deoxyribonucleic acid (DNA) to inosine.
• the deaminase is a cytidine (or cytosine) deaminase, which catalyzes the hydrolytic deamination of cytidine to uracil.
• the deaminases described herein may be from any organism, such as a bacterium.
• the deaminase or deaminase domain is a variant of a naturally- occurring deaminase from an organism. In some embodiments, the deaminase or deaminase domain does not occur in nature.
• the deaminase or deaminase domain is at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75% at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to a naturally-occurring deaminase.
• the term “DNA binding protein” or “DNA binding protein domain” refers to any protein that localizes to and binds a specific target DNA nucleotide sequence (e.g. a gene locus of a genome). This term embraces RNA-programmable proteins, which associate (e.g.
• RNA-programmable proteins are CRISPR-Cas9 proteins as well as Cas9 equivalents homologs orthologs or paralogs whether naturally occurring or non-naturally occurring (e.g. engineered or modified), and may include a Cas9 equivalent from any type of CRISPR system (e.g.
• Cpf1 (a type-V CRISPR-Cas systems) (now known as Cas12a), C2c1 (a type V CRISPR-Cas system), C2c2 (a type VI CRISPR-Cas system), C2c3 (a type V CRISPR-Cas system), dCas9, GeoCas9, CjCas9, Nme2Cas9, SaCas9, SaKKH-Cas9, SauriCas9, Cas12b, Cas12c, Cas12d, Cas12g, Cas12h, Cas12i, Cas13d, Cas14, Argonaute, and nCas9.
• DNA editing efficiency refers to the number or proportion of intended base pairs that are edited. For example, if a base editor edits 10% of the base pairs that it is intended to target (e.g., within a cell or within a population of cells), then the base editor can be described as being 10% efficient. Some aspects of editing efficiency embrace the modification (e.g.
• off-target editing frequency refers to the number or proportion of unintended base pairs, e.g., DNA base pairs, that are edited.
• On-target and off-target editing frequencies may be measured by the methods and assays described herein, further in view of techniques known in the art, including high-throughput sequencing reads.
• high-throughput sequencing involves the hybridization of nucleic acid primers (e.g., DNA primers) with complementarity to nucleic acid (e.g., DNA) regions just upstream or downstream of the target sequence or off-target sequence of interest.
• nucleic acid primers with sufficient complementarity to regions upstream or downstream of the target sequence and Cas9-independent off-target sequences of interest may be designed using techniques known in the art, such as the PhusionU PCR kit (Life Technologies), Phusion HS II kit (Life Technologies), and Illumina MiSeq kit
• the number of off-target DNA edits may be measured by techniques known in the art, including high-throughput screening of sequencing reads, EndoV-Seq, GUIDE-Seq, CIRCLE-Seq, and Cas-OFFinder.
• nucleic acid primers with sufficient complementarity to regions upstream or downstream of the Cas9-dependent off-target site may likewise be designed using techniques and kits known in the art. These kits make use of polymerase chain reaction (PCR) amplification, which produces amplicons as intermediate products.
• the target and off-target sequences may comprise genomic loci that further comprise protospacers and PAMs. Accordingly, the term “amplicons,” as used herein, may refer to nucleic acid molecules that constitute the aggregates of genomic loci, protospacers and PAMs.
• High-throughput sequencing techniques used herein may further include Sanger sequencing and Illumina-based next-generation genome sequencing (NGS).
• on-target editing refers to the introduction of intended modifications (e.g., deaminations) to nucleotides (e.g., adenine) in a target sequence, such as using the base editors described herein.
• off-target DNA editing refers to the introduction of unintended modifications (e.g. deaminations) to nucleotides (e.g. adenine) in a sequence outside the canonical base editor binding window (i.e., from one protospacer position to another, typically 2 to 8 nucleotides long).
• Off-target DNA editing can result from weak or non-specific binding of the gRNA sequence to the target sequence.
• the term “bystander editing” refers to synonymous off-target point mutations at nucleobases that are near (proximate to) the target base and do not change the outcome of the intended mutation (e.g., the intended disruption of a splice acceptor site, incorporation of a premature stop codon, or reversal of a mutant codon).
• Bystander edits may encompass non- silent mutations in the relevant codon of the transcript that do not result in a different translated protein.
• the terms “purity” and “product purity” of a base editor refer to the mean the percentage of edited sequencing reads (reads in which the target nucleobase has been converted to a different base) in which the intended target conversion occurs (e.g., in which the target A, and only the target A, is converted to a G). See Komor et al., Sci Adv 3 (2017).
• the terms “upstream” and “downstream” are terms of relativety that define the linear position of at least two elements located in a nucleic acid molecule (whether single or double-stranded) that is orientated in a 5 ⁇ -to-3 ⁇ direction.
• a first element is upstream of a second element in a nucleic acid molecule where the first element is positioned somewhere that is 5 ⁇ to the second element.
• a SNP is upstream of a Cas9-induced nick site if the SNP is on the 5 ⁇ side of the nick site.
• a first element is downstream of a second element in a nucleic acid molecule where the first element is positioned somewhere that is 3 ⁇ to the second element.
• a SNP is downstream of a Cas9-induced nick site if the SNP is on the 3 ⁇ side of the nick site.
• the nucleic acid molecule can be a DNA (double or single stranded).
• RNA double or single stranded
• RNA hybrid of DNA and RNA.
• the analysis is the same for single strand nucleic acid molecule and a double strand molecule since the terms upstream and downstream are in reference to only a single strand of a nucleic acid molecule, except that one needs to select which strand of the double stranded molecule is being considered.
• the strand of a double stranded DNA which can be used to determine the positional relativity of at least two elements is the “sense” or “coding” strand.
• a “sense” strand is the segment within double- stranded DNA that runs from 5 ⁇ to 3 ⁇ , and which is complementary to the antisense strand of DNA, or template strand, which runs from 3 ⁇ to 5 ⁇ .
• a SNP nucleobase is “downstream” of a promoter sequence in a genomic DNA (which is double-stranded) if the SNP nucleobase is on the 3 ⁇ side of the promoter on the sense or coding strand.
• an effective amount of a base editor may refer to the amount of the editor that is sufficient to edit a target site nucleotide sequence, e.g., a genome.
• an effective amount of a base editor described herein, e.g., of a base editor comprising a nickase Cas9 domain and a guide RNA may refer to the amount of the base editor that is sufficient to induce editing of a target site specifically bound and edited by the base editor.
• an agent e.g., a base editor, a nuclease, a hybrid protein, a protein dimer, a complex of a protein (or protein dimer) and a polynucleotide, or a polynucleotide
• an agent e.g., a base editor, a nuclease, a hybrid protein, a protein dimer, a complex of a protein (or protein dimer) and a polynucleotide, or a polynucleotide
• the term “functional equivalent” refers to a second biomolecule that is equivalent in function, but not necessarily equivalent in structure to a first biomolecule.
• a “Cas9 equivalent” refers to a protein that has the same or substantially the same functions as Cas9, but not necessarily the same amino acid sequence.
• the specification refers throughout to “a protein X or a functional equivalent thereof ”
• a “functional equivalent” of protein X embraces any homolog, paralog, fragment, naturally occurring, engineered, circular permutant, mutated, or synthetic version of protein X which bears an equivalent function.
• fusion protein refers to a hybrid polypeptide which comprises protein domains from at least two different proteins.
• One protein may be located at the amino-terminal (N-terminal) portion of the fusion protein or at the carboxy-terminal (C- terminal) protein thus forming an “amino-terminal fusion protein” or a “carboxy-terminal fusion protein,” respectively.
• a protein may comprise different domains, for example, a nucleic acid binding domain (e.g., the gRNA binding domain of Cas9 that directs the binding of the protein to a target site) and a nucleic acid cleavage domain or a catalytic domain of a nucleic-acid editing protein.
• Another example includes a Cas9 or equivalent thereof fused to an adenosine deaminae.
• any of the proteins described herein may be produced by any method known in the art.
• the proteins described herein may be produced via recombinant protein expression and purification, which is especially suited for fusion proteins comprising a peptide linker.
• Methods for recombinant protein expression and purification are well known, and include those described by Green and Sambrook, Molecular Cloning: A Laboratory Manual (4 th ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (2012)), the entire contents of which are incorporated herein by reference.
• guide nucleic acid or “napDNAbp-programming nucleic acid molecule” or equivalently “guide sequence” refers to one or more nucleic acid molecules which associate with and direct or otherwise program a napDNAbp protein to localize to a specific target nucleotide sequence (e.g., a gene locus of a genome) that is complementary to the one or more nucleic acid molecules (or a portion or region thereof) associated with the protein, thereby causing the napDNAbp protein to bind to the nucleotide sequence at the specific target site.
• a specific target nucleotide sequence e.g., a gene locus of a genome
• a non-limiting example is a guide RNA of a Cas protein of a CRISPR- Cas genome editing system.
• guide nucleic acids can be all RNA, all DNA, or a chimeric of RNA and DNA.
• the guide nucleic acids may also include nucleotide analogs.
• Guide nucleic acids can be expressed as transcription products or can be synthesized.
• a “guide RNA”, or “gRNA” refers to a synthetic fusion of the endogenous bacterial crRNA and tracrRNA that provides both targeting specificity and a scaffold and/or binding ability for Cas9 nuclease to a target DNA. This synthetic fusion does not exist in nature and is also commonly referred to as an sgRNA.
• guide RNA also embraces equivalent guide nucleic acid molecules that associate with Cas9 equivalents, homologs, orthologs, or paralogs, whether naturally occurring or non-naturally occurring (e.g., engineered or recombinant), and which otherwise program the Cas9 equivalent to localize to a specific target nucleotide sequence.
• the Cas9 equivalents may include other napDNAbp from any type of CRISPR system (e.g., type II, V, VI), including Cpf1 (a type-V CRISPR-Cas systems), C2c1 (a type V CRISPR-Cas system), C2c2 (a type VI CRISPR-Cas system) and C2c3 (a type V CRISPR-Cas system).
• Cpf1 a type-V CRISPR-Cas systems
• C2c1 a type V CRISPR-Cas system
• C2c2 a type VI CRISPR-Cas system
• C2c3 a type V CRISPR-Cas system
• a guide RNA is a particular type of guide nucleic acid which is mostly commonly associated with a Cas protein of a CRISPR-Cas9 and which associates with Cas9, directing the Cas9 protein to a specific sequence in a DNA molecule that includes complementarity to the protospacer sequence for the guide RNA.
• guide RNAs associate with Cas9, directing (or programming) the Cas9 protein to a specific sequence in a DNA molecule that includes a sequence complementary to the protospacer sequence for the guide RNA.
• a “spacer sequence” is the sequence of the guide RNA ( ⁇ 20 nts in length) which has the same sequence (with the exception of uridine bases in place of thymine bases) as the protospacer of the PAM strand of the target (DNA) sequence, and which is complementary to the target strand (or non-PAM strand) of the target sequence.
• the “target sequence” refers to the ⁇ 20 nucleotides in the target DNA sequence that have complementarity to the protospacer sequence in the PAM strand.
• the target sequence is the sequence that anneals to or is targeted by the spacer sequence of the guide RNA.
• the spacer sequence of the guide RNA and the protospacer have the same sequence (except the spacer sequence is RNA, and the protospacer is DNA).
• the terms “guide RNA core,” “guide RNA scaffold sequence” and “backbone sequence” refer to the sequence within the gRNA that is responsible for Cas9 binding, it does not include the 20 bp spacer sequence that is used to guide Cas9 to target DNA.
• host cells are mammalian cells such as human cells
• methods of transducing and transfecting a host cell such as a human cell, e.g., a human cell in a subject, with one or more vectors provided herein, such as one or more viral (e.g., rAAV) vectors provided herein.
• a host cell such as a human cell, e.g., a human cell in a subject
• vectors such as one or more viral (e.g., rAAV) vectors provided herein.
• rAAV viral vectors provided herein.
• any of the base editors, guide RNAs, and or combinations thereof, described herein may be introduced into a host cell in any suitable way, either stably or transiently.
• a base editor may be transfected into the host cell.
• the host cell may be transduced or transfected with a nucleic acid construct that encodes a base editor.
• a host cell may be transduced (e.g., with a viral particle encoding a base editor) with a nucleic acid that encodes a base editor, or the translated base editor.
• a host cell may be transfected with a nucleic acid (e.g., a plasmid) that encodes a base editor or the translated base editor.
• a nucleic acid e.g., a plasmid
• Such transductions or transfections may be stable or transient.
• host cells expressing a base editor or containing a base editor may be transduced or transfected with one or more gRNA molecules, for example when the base editor comprises a Cas9 (e.g., nCas9) domain.
• a plasmid expressing a base editor may be introduced into host cells through electroporation, transient transfection (e.g., lipofection, such as with Lipofectamine 3000 ® ), stable genome integration (e.g., piggybac), viral transduction, or other methods known to those of skill in the art.
• transient transfection e.g., lipofection, such as with Lipofectamine 3000 ®
• stable genome integration e.g., piggybac
• viral transduction e.g., viral transient transfection, such as with Lipofectamine 3000 ®
• viral transduction e.g., lipofection, such as with Lipofectamine 3000 ®
• host cells for packaging of viral particles e.g., lipofection, such as with Lipofectamine 3000 ®
• a suitable host cell is a cell that may be infected by the viral vector, can replicate it, and can package it into viral particles that can infect fresh host cells.
• a cell can host a
• the host cell is a eukaryotic cell, for example, a yeast cell, an insect cell, or a mammalian cell.
• the type of host cell will, of course, depend on the vector employed, and suitable host cell/vector combinations will be readily apparent to those of skill in the art.
• An “intein” is a segment of a protein that is able to excise itself and join the remaining portions (the exteins) with a peptide bond in a process known as protein splicing.
• Inteins are also referred to as “protein introns.”
• the process of an intein excising itself and joining the remaining portions of the protein is herein termed “protein splicing” or “intein- mediated protein splicing.”
• an intein of a precursor protein comes from two genes.
• Such intein is referred to herein as a split intein
• the catalytic subunit ⁇ of DNA polymerase III is encoded by two separate genes, dnaE-n and dnaE-c.
• intein-N The intein encoded by the dnaE-n gene is herein referred as “intein-N.”
• intein-C The intein encoded by the dnaE-c gene is herein referred as “intein-C.”
• the nucleic acid molecules do not contain an intein.
• the nucleic acid molecules do not contain a trans- splicing intein.
• Other intein systems may also be used.
• a synthetic intein based on the dnaE intein, the Cfa-N and Cfa-C intein pair has been described (e.g., in Stevens et al., J Am Chem Soc.2016 Feb 24;138(7):2162-5, incorporated herein by reference).
• a synthetic intein based on the dnaE intein, the Nostoc punctiforme (Npu) intein pair has been described (see Zettler, J., Schutz, V. & Mootz, H. D., The naturally split Npu DnaE intein exhibits an extraordinarily high rate in the protein trans-splicing reaction.
• the intein is a fast-splicing gp41 intein, such as a gp41-8 intein.
• a fast-splicing gp41 intein such as a gp41-8 intein.
• Non-limiting examples of intein pairs that may be used in accordance with the present disclosure include: Cfa DnaE intein, Npu DnaE intein, gp41-8 intein, Ssp GyrB intein, Ssp DnaX intein, Ter DnaE3 intein, Ter ThyX intein, Rma DnaB intein and Cne Prp8 intein (e.g., as described in US Patent 8,394,604, incorporated herein by reference).
• the linker is positioned between, or flanked by, two groups, molecules, or other domains and connected to each one via a covalent bond, thus connecting the two.
• the linker is an amino acid or a plurality of amino acids (e.g. a peptide or protein).
• the linker is an organic molecule, group, polymer, or chemical domain. Chemical groups include, but are not limited to, disulfide, hydrazone, and azide domains.
• the linker is 5-100 amino acids in length, for example, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 30-35, 35-40, 40-45, 45-50, 50-60, 60-70, 70-80, 80-90, 90-100, 100-150, or 150-200 amino acids in length. Longer or shorter linkers are also contemplated.
• the linker is an XTEN linker, which is 32 amino acids in length. In some embodiments, the linker is a 32-amino acid linker.
• the linker is a 30- 31- 33- or 34-amino acid linker
• mutation refers to a substitution of a residue within a sequence, e.g. a nucleic acid or amino acid sequence, with another residue; a deletion or insertion of one or more residues within a sequence; or a substitution of a residue within a sequence of a genome in a subject to be corrected. Mutations are typically described herein by identifying the original residue followed by the position of the residue within the sequence and by the identity of the newly substituted residue.
• Mutations can include a variety of categories, such as single base polymorphisms, microduplication regions, indel, and inversions, and is not meant to be limiting in any way. Mutations can include “loss-of- function” mutations which are mutations that reduce or abolish a protein activity.
• loss-of-function mutations are recessive, because in a heterozygote the second chromosome copy carries an unmutated version of the gene coding for a fully functional protein whose presence compensates for the effect of the mutation.
• a loss-of- function mutation is dominant, one example being haploinsufficiency, where the organism is unable to tolerate the approximately 50% reduction in protein activity suffered by the heterozygote.
• This is the explanation for a few genetic diseases in humans, including Marfan syndrome, which results from a mutation in the gene for the connective tissue protein called fibrillin.
• Mutations also embrace “gain-of-function” mutations, which is one which confers an abnormal activity on a protein or cell that is otherwise not present in a normal condition.
• gain-of-function mutations are in regulatory sequences rather than in coding regions, and can therefore have a number of consequences. Because of their nature, gain-of-function mutations are usually dominant. Many loss-of-function mutations are recessive, such as autosomal recessive. Many of the USH2A mutations for which the presently disclosed base editing methods aim to correct are autosomal recessive.
• nucleic acid programmable DNA binding protein refers to any protein that may associate (e.g., form a complex) with one or more nucleic acid molecules (i.e., which may broadly be referred to as a “napDNAbp- programming nucleic acid molecule” and includes, for example, guide RNA in the case of Cas systems) which direct or otherwise program the protein to localize to a specific target nucleotide sequence (e.g., a gene locus of a genome) that is complementary to the one or more nucleic acid molecules (or a portion or region thereof) associated with the protein thereby causing the protein to bind to the nucleotide sequence at the specific target site.
• a specific target nucleotide sequence e.g., a gene locus of a genome
• napDNAbp embraces CRISPR-Cas9 proteins, as well as Cas9 equivalents, homologs, orthologs, or paralogs, whether naturally occurring or non-naturally occurring (e.g., engineered or modified), and may include a Cas9 equivalent from any type of CRISPR system (e.g., type II, V, VI), including Cpf1 (a type-V CRISPR-Cas systems), C2c1 (a type V CRISPR-Cas system), C2c2 (a type VI CRISPR-Cas system), C2c3 (a type V CRISPR-Cas system), dCas9, GeoCas9, CjCas9, Cas12a, Cas12b, Cas12c, Cas12d, Cas12g, Cas12h, Cas12i, Cas13d, Cas14, Argonaute, and nCas9.
• CRISPR-Cas9 any type of CRISPR system
• C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector,” Science 2016; 353 (6299), the contents of which are incorporated herein by reference.
• napDNAbp nucleic acid programmable DNA binding protein
• the invention embraces any such programmable protein, such as the Argonaute protein from Natronobacterium gregoryi (NgAgo) which may also be used for DNA-guided genome editing.
• NgAgo-guide DNA system does not require a PAM sequence or guide RNA molecules, which means genome editing can be performed simply by the expression of generic NgAgo protein and introduction of synthetic oligonucleotides on any genomic sequence. See Gao et al., DNA-guided genome editing using the Natronobacterium gregoryi Argonaute. Nature Biotechnology 2016; 34(7):768-73, which is incorporated herein by reference.
• the napDNAbp is a RNA-programmable nuclease, when in a complex with an RNA, may be referred to as a nuclease:RNA complex.
• the bound RNA(s) is referred to as a guide RNA (gRNA).
• gRNAs can exist as a complex of two or more RNAs, or as a single RNA molecule. gRNAs that exist as a single RNA molecule may be referred to as single-guide RNAs (sgRNAs), though “gRNA” is used interchangeably to refer to guide RNAs that exist as either single molecules or as a complex of two or more molecules. Typically, gRNAs that exist as single RNA species comprise two domains: (1) a domain that shares homology to a target nucleic acid (e.g., and directs binding of a Cas9 (or equivalent) complex to the target); and (2) a domain that binds a Cas9 protein.
• a target nucleic acid e.g., and directs binding of a Cas9 (or equivalent) complex to the target
• Cas9 or equivalent
• domain (2) corresponds to a sequence known as a tracrRNA, and comprises a stem-loop structure.
• domain (2) is homologous to a tracrRNA as depicted in Figure 1E of Jinek et al., Science 337:816-821(2012), the entire contents of which is incorporated herein by reference
• gRNAs eg those including domain 2
• U.S. Patent No.9,340,799 entitled “mRNA-Sensing Switchable gRNAs,” and PCT Application No.
• a gRNA comprises two or more of domains (1) and (2), and may be referred to as an “extended gRNA.”
• an extended gRNA will, e.g., bind two or more Cas9 proteins and bind a target nucleic acid at two or more distinct regions, as described herein.
• the gRNA comprises a nucleotide sequence that complements a target site, which mediates binding of the nuclease/RNA complex to said target site, providing the sequence specificity of the nuclease:RNA complex.
• the RNA-programmable nuclease is the (CRISPR-associated system) Cas9 endonuclease, for example Cas9 (Csn1) from Streptococcus pyogenes (see, e.g., “Complete genome sequence of an M1 strain of Streptococcus pyogenes.” Ferretti J.J. et al.., Proc. Natl. Acad. Sci. U.S.A.98:4658- 4663(2001); “CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III.” Deltcheva E.
• Cas9 Cas9
• the napDNAbp nucleases (e.g., Cas9) use RNA:DNA hybridization to target DNA cleavage sites, these proteins are able to be targeted, in principle, to any sequence specified by the guide RNA.
• napDNAbp nucleases such as Cas9
• site-specific cleavage e.g., to modify a genome
• CRISPR/Cas systems Science 339, 819-823 (2013)
• Mali P. et al. RNA-guided human genome engineering via Cas9.
• Science 339, 823-826 (2013) Hwang, W.Y. et al. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nature Biotechnology 31, 227-229 (2013)
• nickase refers to a napDNAbp (e.g., a Cas9) having only a single nuclease activity that cuts only one strand of a target DNA, rather than both strands.
• nickase type napDNAbp does not leave a double-strand break
• exemplary nickases include SpCas9 and SaCas9 nickases.
• An exemplary nickase comprises a sequence having at least 99%, or 100%, identity to the amino acid sequence of SEQ ID NO: 107.
• a nuclear localization signal or sequence is an amino acid sequence that tags, designates, or otherwise marks a protein for import into the cell nucleus by nuclear transport. Typically, this signal consists of one or more short sequences of positively charged lysines or arginines exposed on the protein surface. Different nuclear localized proteins may share the same NLS.
• NLS nuclear localization signal
• NES nuclear export signal
• a single nuclear localization signal can direct the entity with which it is associated to the nucleus of a cell.
• sequences may be of any size and composition, for example, more than 25, 25, 15, 12, 10, 8, 7, 6, 5, or 4 amino acids, but will preferably comprise at least a four to eight amino acid sequence known to function as a nuclear localization signal (NLS).
• NLS nuclear localization signal
• Nucleic acid molecules may be naturally occurring, for example, in the context of a genome, a transcript, an mRNA, tRNA, rRNA, siRNA, snRNA, a plasmid, cosmid, chromosome, chromatid, or other naturally occurring nucleic acid molecule.
• a nucleic acid molecule may be a non-naturally occurring molecule, e.g. a recombinant DNA or RNA, an artificial chromosome, an engineered genome, or fragment thereof, or a synthetic DNA, RNA, DNA/RNA hybrid, or including non-naturally occurring nucleotides or nucleosides.
• nucleic acid examples include nucleic acid analogs, e.g. analogs having other than a phosphodiester backbone.
• Nucleic acids may be purified from natural sources, produced using recombinant expression systems and optionally purified, chemically synthesized, etc. Where appropriate, e.g. in the case of chemically synthesized molecules, nucleic acids may comprise nucleoside analogs such as analogs having chemically modified bases or sugars, and backbone modifications. A nucleic acid sequence is presented in the 5′ to 3′ direction unless otherwise indicated.
• a nucleic acid is or comprises natural nucleosides (e.g.
• nucleoside analogs e.g.2-aminoadenosine, 2-thiothymidine, inosine, pyrrolo-pyrimidine, 3-methyl adenosine, 5-methylcytidine, 2-aminoadenosine, C5- bromouridine, C5-fluorouridine, C5-iodouridine, C5-propynyl-uridine, C5-propynyl-cytidine, C5-methylcytidine, 2-aminoadenosine, 7-deazaadenosine, 7-deazaguanosine, inosinedenosine, 8-oxoguanosine, O(6)-methylguanine, and 2-thiocytidine); chemically
• phage-assisted continuous evolution refers to continuous evolution that employs phage as viral vectors.
• PACE phage-assisted continuous evolution
• the general concept of PACE technology has been described, for example, in PCT Application No. PCT/US2009/056194, filed September 8, 2009, published as WO 2010/028347 on March 11, 2010; PCT Application No. PCT/US2011/066747, filed December 22, 2011, published as WO 2012/088381 on June 28, 2012; U.S. Application, U.S. Patent No.9,023,594, issued May 5, 2015, PCT Application No.
• promoter is art-recognized and refers to a nucleic acid molecule with a sequence recognized by the cellular transcription machinery and able to initiate transcription of a downstream gene.
• a promoter may be constitutively active, meaning that the promoter is always active in a given cellular context, or conditionally active, meaning that the promoter is only active in the presence of a specific condition.
• conditional promoter may only be active in the presence of a specific protein that connects a protein associated with a regulatory element in the promoter to the basic transcriptional machinery, or only in the absence of an inhibitory molecule.
• a subclass of conditionally active promoters is inducible promoters that require the presence of a small molecule “inducer” for activity. Examples of inducible promoters include, but are not limited to, arabinose-inducible promoters, Tet-on promoters, and tamoxifen-inducible promoters.
• the disclosure provides vectors with appropriate promoters for driving expression of the nucleic acid sequences encoding the base editors (or one or more individual components thereof).
• promoter refers to the sequence (e.g., a ⁇ 20 bp sequence) in DNA adjacent to the PAM (protospacer adjacent motif) sequence which shares the same sequence as the spacer sequence of the guide RNA, and which is complementary to the target sequence of the non-PAM strand.
• the spacer sequence of the guide RNA anneals to the target sequence located on the non-PAM strand.
• PAM protospacer adjacent motif
• protospacer as the ⁇ 20-nt target-specific guide sequence on the guide RNA itself, rather than referring to it as a “spacer” (and that the protospacer (DNA) and the spacer (RNA) have the same sequence).
• protospacer as used herein may be used interchangeably with the term “spacer.”
• spacer The context of the discription surrounding the appearance of either “protospacer” or “spacer” will help inform the reader as to whether the term is refence to the gRNA or the DNA sequence. Both usages of these terms are acceptable since the state of the art uses both terms in each of these ways.
• the term “protospacer adjacent sequence” or “PAM” refers to an approximately 2-6 base pair DNA sequence that is an important targeting component of a Cas9 nuclease. Typically, the PAM sequence is on either strand, and is downstream in the 5 ⁇ to 3 ⁇ direction of Cas9 cut site.
• the canonical PAM sequence i.e., the PAM sequence that is associated with the Cas9 nuclease of Streptococcus pyogenes or SpCas9
• N is any nucleobase followed by two guanine (“G”) nucleobases.
• any given Cas9 nuclease e.g., SpCas9
• the PAM sequence can be modified by introducing one or more mutations, including (a) D1135V, R1335Q, and T1337R “the VRQR variant”, which alters the PAM specificity to NGAN or NGNG, (b) D1135E, R1335Q, and T1337R “the EQR variant”, which alters the PAM specificity to NGAG, and (c) D1135V, G1218R, R1335E, and T1337R “the VRER variant”, which alters the PAM specificity to NGCG.
• Cas9 enzymes from different bacterial species can have varying PAM specificities.
• Cas9 from Staphylococcus aureus (SaCas9) recognizes NGRRT or NGRRN.
• Cas9 from Neisseria meningitis (NmeCas) recognizes NNNNGATT.
• a Cas9 from Staphylococcus auricularis (SauriCas9) recognizes NNGG and NNNGG.
• a Cas9 from Streptococcus thermophilis (StCas9) recognizes NNAGAAW.
• a Cas9 from Treponema denticola (TdCas) recognizes NAAAAC.
• TdCas Treponema denticola
• non-SpCas9s bind a variety of PAM sequences, which makes them useful when no suitable SpCas9 PAM sequence is present at the desired target cut site.
• non-SpCas9s may have other characteristics that make them more useful than SpCas9.
• Cas9 from Staphylococcus aureus is about 1 kilobase smaller than SpCas9, so it can be packaged into adeno-associated virus (AAV).
• AAV adeno-associated virus
• a protein, peptide, or polypeptide will be at least three amino acids long.
• a protein, peptide, or polypeptide may refer to an individual protein or a collection of proteins.
• One or more of the amino acids in a protein, peptide, or polypeptide may be modified, for example, by the addition of a chemical entity such as a carbohydrate group, a hydroxyl group, a phosphate group, a farnesyl group, an isofarnesyl group, a fatty acid group, a linker for conjugation, functionalization, or other modification, etc.
• a protein, peptide, or polypeptide may also be a single molecule or may be a multi-molecular complex.
• a protein, peptide, or polypeptide may be just a fragment of a naturally occurring protein or peptide.
• a protein, peptide, or polypeptide may be naturally occurring, recombinant, or synthetic, or any combination thereof. It should be appreciated that the disclosure provides any of the polypeptide sequences provided herein without an N-terminal methionine (M) residue.
• M N-terminal methionine
• the sense strand is the strand of DNA that has the same sequence as the mRNA, which takes the antisense strand as its template during transcription, and eventually undergoes (typically, not always) translation into a protein.
• the antisense strand is thus responsible for the RNA that is later translated to protein, while the sense strand possesses a nearly identical makeup to that of the mRNA. Note that for each segment of dsDNA, there will possibly be two sets of sense and antisense, depending on which direction one reads (since sense and antisense is relative to perspective). It is ultimately the gene product, or mRNA, that dictates which strand of one segment of dsDNA is referred to as sense or antisense.
• a “split Cas9 protein” or “split Cas9” refers to a Cas9 protein that is provided as an N-terminal portion (which is referred to herein interchangeably as an N-terminal half) and a C-terminal portion (which is referred to herein interchangeably as a C-terminal half) encoded by two separate nucleotide sequences.
• the polypeptides corresponding to the N-terminal portion and the C-terminal portion of the Cas9 protein may be combined (joined) to form a complete Cas9 protein.
• a Cas9 protein is known to consist of a bi-lobed structure linked by a disordered linker (e.g., as described in Nishimasu et al., Cell, Volume 156, Issue 5, pp.935– 949, 2014, incorporated herein by reference).
• the “split” occurs between the two lobes, generating two portions of a Cas9 protein, each containing one lobe.
• the subject is a human.
• the subject is a non-human mammal.
• the subject is a non-human primate.
• the subject is a rodent. In some embodiments, the subject is a sheep, a goat, cattle, a cat, or a dog. In some embodiments, the subject is a vertebrate, an amphibian, a reptile, a fish, an insect, a fly, or a nematode. In some embodiments, the subject is a research animal. In some embodiments, the subject is genetically engineered, e.g., a genetically engineered non-human subject. The subject may be of either sex and at any stage of development. In some embodiments, the subject is a domesticated animal. In some embodiments, the subject is a plant.
• target site refers to a sequence within a nucleic acid molecule that is edited by a base editor (BE) disclosed herein.
• BE base editor
• target site in the context of a single strand, also can refer to the “target strand” which anneals or binds to the spacer sequence of the guide RNA.
• the target site can refer, in certain embodiments, to a segment of double-stranded DNA that includes the protospacer (i.e., the strand of the target site that has the same nucleotide sequence as the spacer sequence of the guide RNA) on the PAM- strand (or non-target strand) and target strand, which is complementary to the protospacer and the spacer alike, and which anneals to the spacer of the guide RNA, thereby targeting or programming a Cas9 base editor to target the target site.
• a “transcriptional terminator” is a nucleic acid sequence that causes transcription to stop.
• a transcriptional terminator may be unidirectional or bidirectional.
• a transcriptional terminator sequence prevents transcriptional activation of downstream nucleic acid sequences by upstream promoters.
• a transcriptional terminator may be necessary in vivo to achieve desirable expression levels or to avoid transcription of certain sequences.
• a transcriptional terminator is considered to be “operably linked to” a nucleotide sequence when it is able to terminate the transcription of the sequence it is linked to. [00135] In eukaryotic systems, the terminator region may comprise specific DNA sequences that permit site-specific cleavage of the new transcript so as to expose a polyadenylation site.
• a terminator may comprise a signal for the cleavage of the RNA.
• the terminator signal promotes polyadenylation of the message.
• the terminator and/or polyadenylation site elements may serve to enhance output nucleic acid levels and/or to minimize read through between nucleic acids.
• the transcriptional terminator contains a posttranscriptional response element, a sequence that, when transcribed, creates a tertiary structure enhancing expression.
• the posttranscriptional response element is derived from woodchuck hepatitis virus (WHV), i.e., is a WPRE.
• WPRE woodchuck hepatitis virus
• the terminator contains the gamma subunit of a WPRE, or a W3, as first reported in Choi, J. H., et al. (2014), Mol. Brain 7: 17, incorporated herein by reference.
• the WPRE also has alpha and beta subunits.
• the posttranscriptional response element is inserted 5 ⁇ of the transcriptional terminator.
• the WPRE is a truncated WPRE sequence. In certain embodiments, the WPRE is a full-length WPRE.
• Terminators for use in accordance with the present disclosure include any terminator of transcription described herein or known to one of ordinary skill in the art. Examples of terminators include, without limitation, the termination sequences of genes such as, for example, the bovine growth hormone terminator, and viral termination sequences such as for example, the SV40 terminator and bGH terminator In some embodiments the termination signal may be a sequence that cannot be transcribed or translated, such as those resulting from a sequence truncation.
• transitions refer to the interchange of purine nucleobases (A ⁇ G) or the interchange of pyrimidine nucleobases (C ⁇ T). This class of interchanges involves nucleobases of similar shape.
• the compositions and methods disclosed herein are capable of inducing one or more transitions in a target DNA molecule.
• the compositions and methods disclosed herein are also capable of inducing both transitions and transversion in the same target DNA molecule. These changes involve A ⁇ G, G ⁇ A, C ⁇ T, or T ⁇ C.
• transitions In the context of a double-strand DNA with Watson-Crick paired nucleobases, transitions refer to the following base pair exchanges: A:T ⁇ G:C, G:G ⁇ A:T, C:G ⁇ T:A, or T:A ⁇ C:G.
• the compositions and methods disclosed herein are capable of inducing one or more transitions in a target DNA molecule.
• the compositions and methods disclosed herein are also capable of inducing both transitions and transversion in the same target DNA molecule, as well as other nucleotide changes, including deletions and insertions.
• “transversions” refer to the interchange of purine nucleobases for pyrimidine nucleobases, or in the reverse and thus, involve the interchange of nucleobases with dissimilar shape. These changes involve T ⁇ A, T ⁇ G, C ⁇ G, C ⁇ A, A ⁇ T, A ⁇ C, G ⁇ C, and G ⁇ T.
• transversions refer to the following base pair exchanges: T:A ⁇ A:T, T:A ⁇ G:C, C:G ⁇ G:C, C:G ⁇ A:T, A:T ⁇ T:A, A:T ⁇ C:G, G:C ⁇ C:G, and G:C ⁇ T:A.
• treatment refers to a clinical intervention aimed to reverse, alleviate, delay the onset of, or inhibit the progress of a disease or disorder, or one or more symptoms thereof, as described herein.
• treatment refers to a clinical intervention aimed to reverse, alleviate, delay the onset of, or inhibit the progress of a disease or disorder, or one or more symptoms thereof, as described herein.
• treatment may be administered after one or more symptoms have developed and/or after a disease has been diagnosed.
• treatment may be administered in the absence of symptoms, e.g., to prevent or delay onset of a symptom or inhibit onset or progression of a disease.
• treatment may be administered to a susceptible individual prior to the onset of symptoms (e.g., in light of a history of symptoms and/or in light of genetic or other susceptibility factors).
• upstream and downstream are terms of relativety that define the linear position of at least two elements located in a nucleic acid molecule (whether single or double-stranded) that is orientated in a 5 ⁇ -to-3 ⁇ direction.
• a first element is upstream of a second element in a nucleic acid molecule where the first element is positioned somewhere that is 5 ⁇ to the second element.
• a SNP is upstream of a Cas9-induced nick site if the SNP is on the 5 ⁇ side of the nick site.
• a first element is downstream of a second element in a nucleic acid molecule where the first element is positioned somewhere that is 3 ⁇ to the second element.
• a SNP is downstream of a Cas9-induced nick site if the SNP is on the 3 ⁇ side of the nick site.
• the nucleic acid molecule can be a DNA (double or single stranded). RNA (double or single stranded), or a hybrid of DNA and RNA.
• the analysis is the same for single strand nucleic acid molecule and a double strand molecule since the terms upstream and downstream are in reference to only a single strand of a nucleic acid molecule, except that one needs to select which strand of the double stranded molecule is being considered.
• the strand of a double stranded DNA which can be used to determine the positional relativity of at least two elements is the “sense” or “coding” strand.
• a “sense” strand is the segment within double-stranded DNA that runs from 5 ⁇ to 3 ⁇ , and which is complementary to the antisense strand of DNA, or template strand, which runs from 3 ⁇ to 5 ⁇ .
• a SNP nucleobase is “downstream” of a promoter sequence in a genomic DNA (which is double-stranded) if the SNP nucleobase is on the 3' side of the promoter on the sense or coding strand.
• variant refers to a protein having characteristics that deviate from what occurs in nature that retains at least one functional i.e. binding, interaction, or enzymatic ability and/or therapeutic property thereof.
• a “variant” is at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to the wild type protein.
• a variant of Cas9 may comprise a Cas9 that has one or more changes in amino acid residues as compared to a wild type Cas9 amino acid sequence.
• a variant of a deaminase may comprise a deaminase that has one or more changes in amino acid residues as compared to a wild type deaminase amino acid sequence, e.g. following ancestral sequence reconstruction of the deaminase.
• changes include chemical modifications, including substitutions of different amino acid residues truncations, covalent additions (e.g. of a tag), and any other mutations.
• the term also encompasses circular permutants, mutants, truncations, or domains of a reference sequence, and which display the same or substantially the same functional activity or activities as the reference sequence. This term also embraces fragments of a wild type protein.
• variants are overall very similar, and in many regions, identical to the amino acid sequence of the protein described herein.
• the variant proteins may comprise, or alternatively consist of, an amino acid sequence which is at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100%, identical to, for example, the amino acid sequence of a wild-type protein, or any protein provided herein.
• polypeptide having an amino acid sequence at least, for example, 95% “identical” to a query amino acid sequence it is intended that the amino acid sequence of the subject polypeptide is identical to the query sequence except that the subject polypeptide sequence may include up to five amino acid alterations per each 100 amino acids of the query amino acid sequence.
• up to 5% of the amino acid residues in the subject sequence may be inserted, deleted, or substituted with another amino acid.
• alterations of the reference sequence may occur at the amino- or carboxy-terminal positions of the reference amino acid sequence or anywhere between those terminal positions, interspersed either individually among residues in the reference sequence or in one or more contiguous groups within the reference sequence.
• whether any particular polypeptide is at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to, for instance, the amino acid sequence of a fusion protein can be determined conventionally using known computer programs.
• a preferred method for determining the best overall match between a query sequence (a sequence of the present invention) and a subject sequence can be determined using the FASTDB computer program based on the algorithm of Brutlag et al. (Comp. App. Biosci.6:237-245 (1990)).
• the query and subject sequences are either both nucleotide sequences or both amino acid sequences.
• the result of said global sequence alignment is expressed as percent identity.
• the percent identity is corrected by calculating the number of residues of the query sequence that are N- and C- terminal of the subject sequence, which are not matched/aligned with a corresponding subject residue, as a percent of the total bases of the query sequence. Whether a residue is matched/aligned is determined by results of the FASTDB sequence alignment. This percentage is then subtracted from the percent identity, calculated by the above FASTDB program using the specified parameters, to arrive at a final percent identity score. This final percent identity score is what is used for the purposes of the present invention.
• vector refers to a nucleic acid that can be modified to encode a gene of interest and that is able to enter into a host cell and replicate within the host cell, and then transfer a replicated form of the vector into another host cell.
• suitable vectors include viral vectors, such as AAV vectors or bacteriophages and filamentous phage, and conjugative plasmids.
• napDNAbp domains As used herein the term “wild type” is a term of the art understood by skilled persons and means the typical form of an organism, strain, gene or characteristic as it occurs in nature as distinguished from mutant or variant forms.
• napDNAbp domains [00149] The base editors described herein comprise a nucleic acid programmable DNA binding (napDNAbp) domain.
• the napDNAbp is associated with at least one guide nucleic acid (e.g., guide RNA), which localizes the napDNAbp to a DNA sequence that comprises a DNA strand (i.e., a target strand) that is complementary to the guide nucleic acid, or a portion thereof (e.g., the protospacer of a guide RNA).
• guide nucleic acid e.g., guide RNA
• the guide nucleic-acid “programs” the napDNAbp domain to localize and bind to a complementary sequence of the target strand.
• the napDNAbp can be a CRISPR (clustered regularly interspaced short palindromic repeat)-associated nuclease.
• CRISPR is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids).
• CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids.
• CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA).
• crRNA CRISPR RNA
• type II CRISPR systems correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and a Cas9 protein.
• the tracrRNA serves as a guide for ribonuclease 3-aided processing of pre-crRNA.
• Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the spacer.
• the target strand not complementary to crRNA is first cut endonucleolytically, then trimmed 3′-5′ exonucleolytically.
• RNA-binding and cleavage typically requires protein and both RNAs.
• single guide RNAs (“sgRNA”, or simply “gNRA”) can be engineered so as to incorporate aspects of both the crRNA and tracrRNA into a single RNA species. See, e.g., Jinek et al., Science 337:816-821(2012), the entire contents of which is hereby incorporated by reference.
• gRNA single guide RNAs
• the base editors may comprise the canonical SpCas9, or any ortholog Cas9 protein, or any variant Cas9 protein—including any naturally occurring variant, mutant, or otherwise engineered version of Cas9—that is known or which can be made or evolved through a directed evolutionary or otherwise mutagenic process.
• the napDNAbp has a nickase activity, i.e., only cleave one strand of the target DNA sequence.
• the napDNAbp has an inactive nuclease, e.g., are “dead” proteins.
• Cas9 proteins that may be used are those having a smaller molecular weight than the canonical SpCas9 (e.g., for easier delivery) or having modified or rearranged primary amino acid sequence (e.g., the circular permutant forms).
• the base editors described herein may also comprise Cas9 equivalents, including Cas12a/Cpf1 proteins.
• the napDNAbps used herein e.g., SpCas9, SaCas9, or SaCas9 variant or SpCas9 variant
• the disclosure contemplates any Cas9, Cas9 variant, or Cas9 equivalent which has at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.9% sequence identity to any of the Cas9 proteins disclosed herein.
• the napDNAbp domain comprises a nickase variant of a wild-type Cas9.
• the napDNAbp domain comprises any of the Cas9 nickases disclosed herein.
• the napDNAbp directs cleavage of one or both strands at the location of a target sequence, such as within the target sequence and/or within the complement of the target sequence. In some embodiments, the napDNAbp directs cleavage of one or both strands within about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 50, 100, 200, 500, or more base pairs from the first or last nucleotide of a target sequence. For example, an aspartate-to-alanine substitution (D10A) in the RuvC I catalytic domain of Cas9 from S.
• D10A aspartate-to-alanine substitution
• pyogenes converts Cas9 from a nuclease that cleaves both strands to a nickase (cleaves a single strand).
• Other examples of mutations that render Cas9 a nickase include, without limitation, H840A, N854A, and N863A in reference to the canonical SpCas9 sequence, or to equivalent amino acid positions in other Cas9 variants or Cas9 equivalents.
• Cas protein refers to a full-length Cas protein obtained from nature, a recombinant Cas protein having a sequences that differs from a naturally occurring Cas protein, or any fragment of a Cas protein that nevertheless retains all or a significant amount of the requisite basic functions needed for the disclosed methods, i.e., (i) possession of nucleic-acid programmable binding of the Cas protein to a target DNA, and (ii) ability to nick the target DNA sequence on one strand.
• the Cas proteins contemplated herein embrace CRISPR Cas9 proteins, as well as Cas9 equivalents, variants (e.g., Cas9 nickase (nCas9) or nuclease inactive Cas9 (dCas9)) homologs, orthologs, or paralogs, whether naturally occurring or non-naturally occurring (e.g., engineered or recombinant), and may include a Cas9 equivalent from any type of CRISPR system (e.g., type II, V, VI), including Cpf1 (a type-V CRISPR-Cas systems), C2c1 (a type V CRISPR-Cas system), C2c2 (a type VI CRISPR-Cas system) and C2c3 (a type V CRISPR-Cas system).
• CRISPR Cas9 proteins as well as Cas9 equivalents, variants (e.g., Cas9 nickase (nCas9) or nuclease inactive Ca
• Cas9 or “Cas9 domain” embraces any naturally occurring Cas9 from any organism, any naturally-occurring Cas9 equivalent or functional fragment thereof, any Cas9 homolog, ortholog, or paralog from any organism, and any mutant or variant of a Cas9, naturally-occurring or engineered.
• Cas9 is not meant to be particularly limiting and may be referred to as a “Cas9 or equivalent.” Exemplary Cas9 proteins are further described herein and/or are described in the art and are incorporated herein by reference. The present disclosure is unlimited with regard to the particular napDNAbp that is employed in the base editors of the disclosure.
• the terms “compact Cas9 protein”, “compact napDNAbp” and “compact variant [of a Cas protein]” refers to a Cas9 protein or variant that has an amino acid length of less than about 1250 amino acids.
• a compact Cas9 protein or compact napDNAbp contains less than 1250 amino acids, less than 1240 amino acids, less than 1230 amino acids, less than 1220 amino acids, less than 1210 amino acids, less than 1200 amino acids, less than 1190 amino acids, less than 1180 amino acids, less than 1170 amino acids, less than 1160 amino acids, less than 1150 amino acids, less than 1140 amino acids, less than 1130 amino acids, less than 1120 amino acids, less than 1110 amino acids, less than 1100 amino acids, less than 1050 amino acids, less than 1000 amino acids, less than 950 amino acids, less than 900 amino acids, less than 850 amino acids, less than 800 amino acids, less than 750 amino acids, less than 700 amino acids, less than 650 amino acids, less than 600 amino acids, less than 550 amino acids, or less than 500 amino acids in length.
• the base editors of the disclosure may comprise compact napDNAbps and/or compact Cas9 proteins.
• the compact Cas9 protein is about 350 amino acids shorter than a SpCas9.
• the compact Cas9 protein is about 1000 amino acids in length.
• the compact protein is a compact variant of S.
• a “compact variant” may refer to a Cas9 protein hat has one or more truncations, or one or more deletions, relative to a wild-type Cas9 protein, such as a wild-type SpCas9 or Cpf1.
• the base editors of the present disclosure may use any suitable napDNAbp, including any suitable Cas9 or Cas9 equivalent.
• napDNAbp nickases [00158]
• the disclosed base editors may comprise a napDNAbp domain that comprises a nickase.
• the base editors described herein comprise a Cas9 nickase.
• Cas9 nickase refers to a variant of Cas9 which is capable of introducing a single-strand break in a double strand DNA molecule target.
• the Cas9 nickase comprises only a single functioning nuclease domain.
• the wild type Cas9 e.g., the canonical SpCas9
• the wild type Cas9 comprises two separate nuclease domains, namely, the RuvC domain (which cleaves the non-protospacer DNA strand) and HNH domain (which cleaves the protospacer DNA strand).
• the Cas9 nickase comprises a mutation in the RuvC domain which inactivates the RuvC nuclease activity.
• nickase mutations in the RuvC domain could include D10X, H983X, D986X, or E762X, wherein X is any amino acid other than the wild type amino acid.
• the nickase could be D10A, of H983A, or D986A, or E762A or a combination thereof.
• the napDNAbp domain of any of the disclosed base editors comprises an S. pyogenes Cas9 nickase (SpCas9n).
• the napDNAbp domain of any of the disclosed based editors is comprises at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity to SEQ ID NO: 365 or 370.
• the napDNAbp domain of any of the disclosed base editors comprises the amino acid sequence of SEQ ID NO: 365.
• the napDNAbp domain of any of the disclosed base editors comprises the amino acid sequence of SEQ ID NO: 370.
• the napDNAbp domain of any of the disclosed base editors comprises an S. aureus Cas9 nickase (SaCas9n).
• the napDNAbp domain of any of the disclosed based editors is comprises at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity to SEQ ID NO: 438.
• the napDNAbp domain of any of the disclosed base editors comprises the amino acid sequence of SEQ ID NO: 438.
• the Cas9 nickase can having a mutation in the RuvC nuclease domain and have one of the following amino acid sequences, or a variant thereof having an amino acid sequence that has at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity thereto.
• Compact Cas9 variants with modified PAM specificities [00162]
• the napDNAbp comprises a compact Cas protein, such as a Cas9 derived from C. jejuni, S. auricularis, N. meningitidis, or S. aureus.
• the napDNAbp comprises a CjCas9 nickase, a SauriCas9 nickase, an Nme2Cas9 nickase, an SaCas9 nickase, or an SaKKH-Cas9 nickase.
• the napDNAbp is not an Nme2Cas9 protein or nickase.
• the napDNAbp is not a SaCas9 protein or nickase.
• the base editors of the present disclosure may also comprise Cas9 variants with modified PAM specificities.
• Cas9 proteins that exhibit activity on a target sequence that does not comprise the canonical PAM (5′-NGG-3′, where N is A, C, G, or T) at its 3′-end.
• the Cas9 protein exhibits activity on a target sequence comprising a 5′-NGG-3′ PAM sequence at its 3′-end.
• the Cas9 protein exhibits activity on a target sequence comprising a 5 ⁇ -NNG- 3 ⁇ PAM sequence at its 3′-end.
• the Cas9 protein exhibits activity on a target sequence comprising a 5′-NNA-3′ PAM sequence at its 3 ⁇ -end.
• the Cas9 protein exhibits activity on a target sequence comprising a 5′-NNC-3′ PAM sequence at its 3 ⁇ -end. In some embodiments, the Cas9 protein exhibits activity on a target sequence comprising a 5 ⁇ -NNT-3 ⁇ PAM sequence at its 3 ⁇ -end. In some embodiments, the Cas9 protein exhibits activity on a target sequence comprising a 5 ⁇ -NGT-3 ⁇ PAM sequence at its 3 ⁇ -end. In some embodiments, the Cas9 protein exhibits activity on a target sequence comprising a 5 ⁇ -NGA-3 ⁇ PAM sequence at its 3 ⁇ -end.
• the Cas9 protein exhibits activity on a target sequence comprising a 5 ⁇ -NGC-3 ⁇ PAM sequence at its 3 ⁇ -end. In some embodiments, the Cas9 protein exhibits activity on a target sequence comprising a 5 ⁇ - NAA-3 ⁇ PAM sequence at its 3 ⁇ -end. In some embodiments, the Cas9 protein exhibits activity on a target sequence comprising a 5 ⁇ -NAC-3 ⁇ PAM sequence at its 3′-end. In some embodiments, the Cas9 protein exhibits activity on a target sequence comprising a 5 ⁇ -NAT-3 ⁇ PAM sequence at its 3 ⁇ -end.
• the Cas9 protein exhibits activity on a target sequence comprising a 5 ⁇ -NAG-3 ⁇ PAM sequence at its 3 ⁇ -end.
• the disclosed base editors comprise a napDNAbp domain comprising a SpCas9-NG, which has a PAM that corresponds to NGN.
• the disclosed base editors comprise a napDNAbp domain that has a sequence that is at least 90%, at least 95%, at least 98%, or at least 99% identical to SpCas9-NG.
• the disclosed base editors comprise a napDNAbp domain that has a sequence that is at least 90%, at least 95%, at least 98%, or at least 99% identical to SaCas9-KKH.
• the length of SaCas9 (and SaKKH-Cas9) is 1053 amino acids.
• SaCas9-KKH The sequence of SaCas9-KKH (nickase) is illustrated below: [00166] S aureus Cas9 nickase KKH (SaCas9-KKH) MGKRNYILGLAIGITSVGYGIIDYETRDVIDAGVRLFKEANVENNEGRRSKRGARRL KRRRRHRIQRVKKLLFDYNLLTDHSELSGINPYEARVKGLSQKLSEEEFSAALLHLAK RRGVHNVNEVEEDTGNELSTKEQISRNSKALEEKYVAELQLERLKKDGEVRGSINRF KTSDYVKEAKQLLKVQKAYHQLDQSFIDTYIDLLETRRTYYEGPGEGSPFGWKDIKE WYEMLMGHCTYFPEELRSVKYAYNADLYNALNDLNNLVITRDENEKLEYYEKFQII ENVFKQKKKPTLKQIAKEILVNEEDIKGYRVTSTGKPEFTNLKV
• the disclosed base editors comprise a SauriCas9 nickase.
• SauriCas9 recognizes NNGG and NNNGG PAMs.
• the sequence of SauriCas9 (nickase) is set forth as SEQ ID NO: 479.
• the disclosed base editors comprise a napDNAbp domain that has a sequence that is at least 90%, at least 95%, at least 98%, or at least 99% identical to SEQ ID NO: 479.
• the disclosed base editors comprise a napDNAbp comprising SEQ ID NO: 479. The length of this protein is 1061 amino acids.
• the disclosed base editors comprise a napDNAbp domain comprising an S. pyogenes Cas9 nickase KKH, or SpCas9-KKH, which has a PAM that corresponds to NNNRRT.
• the disclosed base editors comprise a napDNAbp comprising a compact Cas9 ortholog from derived from Neisseria meningitidis (Nme, or Nme2).
• the napDNAbp comprises Nme2Cas9.
• the disclosed base editors comprise an Nme2Cas9 nickase. Nme2Cas9 recognizes recognizes a simple dinucleotide PAM, NNNNCC, or N 4 CC (where N is any nucleotide), as described in Edraki et al., Molecular Cell 73, 714-726, incorporated herein by reference. The sequence of Nme2Cas9 is set forth as SEQ ID NO: 5.
• the disclosed base editors comprise a napDNAbp domain that has a sequence that is at least 90%, at least 95%, at least 98%, or at least 99% identical to SEQ ID NO: 5.
• the disclosed base editors comprise a napDNAbp comprising SEQ ID NO: 5.
• the length of this protein is 1082 amino acids.
• the disclosed base editors comprise a napDNAbp domain that has a sequence that is at least 90%, at least 95%, at least 98%, or at least 99% identical to SEQ ID NO: 6.
• the disclosed base editors comprise a napDNAbp comprising SEQ ID NO: 6. The length of this protein is 1083 amino acids.
• the napDNAbp comprises CjCas9.
• the disclosed base editors comprise a CjCas9 nickase.
• CjCas9 recognizes recognizes NNNNACA and NNNNACAC PAMs. See Kim et al., Nature Communications 8(14500):1-12 (2017), which is incorporated herein by reference.
• the sequence of CjCas9 (nickase) is set forth as SEQ ID NO: 379.
• the disclosed base editors comprise a napDNAbp domain that has a sequence that is at least 90%, at least 95%, at least 98%, or at least 99% identical to SEQ ID NO: 379.
• the disclosed base editors comprise a napDNAbp comprising SEQ ID NO: 379.
• the length of this protein is 984 amino acids.
• the napDNAbp may comprise a compact Cas9 ortholog from Staphylococcus lugdunensis Cas9 (SlugCas9), Staphylococcus lutrae Cas9 (SlutrCas9), or Staphylococcus haemolyticus Cas9 (ShaCas9).
• SlugCas9 Staphylococcus lugdunensis Cas9
• SlutrCas9 Staphylococcus lutrae Cas9
• Shaphylococcus haemolyticus Cas9 ShaCas9
• the Cas protein may include any CRISPR associated protein, including but not limited to, Cas12a, Cas12b, Cas1, Cas1B, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9 (also known as Csn1 and Csx12), Cas10, Csy1, Csy2, Csy3, Cse1, Cse2, Csc1, Csc2, Csa5, Csn2.
• a nickase mutation e.g., a mutation corresponding to the D10A mutation of the wild type SpCas9 polypeptide of SEQ ID NO: 326.
• the base editors contemplated herein can include a Cas9 protein that is of smaller molecular weight than the canonical SpCas9 sequence.
• the smaller-sized Cas9 variants may facilitate delivery to cells, e.g., by an AAV vector, expression vector, or other means of delivery.
• the canonical SpCas9 protein is 1368 amino acids in length and has a predicted molecular weight of 158 kilodaltons.
• small-sized Cas9 variant refers to any Cas9 variant—naturally occurring, engineered, or otherwise—that is less than about 1300 amino acids, or at least less than 1290 amino acids, or than less than 1280 amino acids, or less than 1270 amino acid, or less than 1260 amino acid, or less than 1250 amino acids, or less than 1240 amino acids, or less than 1230 amino acids, or less than 1220 amino acids, or less than 1210 amino acids, or less than 1200 amino acids, or less than 1190 amino acids, or less than 1180 amino acids, or less than 1170 amino acids, or less than 1160 amino acids, or less than 1150 amino acids, or less than 1140 amino acids, or less than 1130 amino acids, or less than 1120 amino acids, or less than 1110 amino acids, or less than 1100 amino acids, or less than 1050 amino acids, or less than 1000 amino acids, or less than 950 amino acids, or less than 900 amino acids, or less than 850 amino acids, or less than 800 amino acids, or
• the base editors disclosed herein may comprise one of the small-sized Cas9 variants described as follows, or a Cas9 variant thereof having at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to any reference small-sized Cas9 protein.
• Exemplary small-sized Cas9 variants include, but are not limited to, SauriCas9, SaCas9, CjCas9, Nme2Cas9, AsCas12a, and LbCas12a.
• the napDNAbp domain of any of the disclosed base editors comprises an LbCas12a, such as a wild-type LbCas12a.
• the napDNAbp domain of any of the disclosed based editors is comprises at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity to SEQ ID NO: 381
• the napDNAbp domain of any of the disclosed base editors comprises the amino acid sequence of SEQ ID NO: 381.
• the napDNAbp domain of any of the disclosed base editors comprises an AsCas12a, such as a wild-type AsCas12a.
• the napDNAbp domain of any of the disclosed base editors comprises a mutant AsCas12a, such as an engineered AsCas12a, or enAsCas12a.
• the napDNAbp domain of any of the disclosed based editors is comprises at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity to SEQ ID NO: 383.
• the napDNAbp domain of any of the disclosed base editors comprises the amino acid sequence of SEQ ID NO: 383.
• the base editors described herein may also comprise Cas12a/Cpf1 (dCpf1) variants that may be used as a guide nucleotide sequence-programmable DNA-binding protein domain.
• the Cas12a/Cpf1 protein has a RuvC-like endonuclease domain that is similar to the RuvC domain of Cas9 but does not have a HNH endonuclease domain, and the N- terminal of Cpf1 does not have the alfa-helical recognition lobe of Cas9. It was shown in Zetsche et al., Cell, 163, 759–771, 2015 (which is incorporated herein by reference) that, the RuvC-like domain of Cpf1 is responsible for cleaving both DNA strands and inactivation of the RuvC-like domain inactivates Cpf1 nuclease activity.
• the base editor comprises a deaminase that is a cytosine deaminase.
• the cytosine deaminase domain is fused to the N-terminus of the napDNAbp domain.
• the deaminase is an apolipoprotein B mRNA-editing complex (APOBEC) family deaminase.
• APOBEC apolipoprotein B mRNA-editing complex
• the deaminase is an APOBEC1 deaminase, an APOBEC2 deaminase, an APOBEC3A deaminase, an APOBEC3B deaminase, an APOBEC3C deaminase, an APOBEC3D deaminase, an APOBEC3F deaminase, an APOBEC3G deaminase, an APOBEC3H deaminase, or an APOBEC4 deaminase.
• the deaminase is an activation-induced deaminase (AID).
• the deaminase is a Lamprey CDA1 (pmCDA1) deaminase.
• the deaminase is from a human, chimpanzee, gorilla, monkey, cow, dog, rat, or mouse.
• the deaminase is from a human.
• the deaminase is from a rat.
• the deaminase is a human APOBEC1 deaminase.
• the deaminase is pmCDA1.
• the deaminase is human APOBEC3G .
• the deaminase is a human APOBEC3G variant . In some embodiments, the deaminase is rat APOBEC1.
• the cytidine deaminase domain is a “FERNY” polypeptide having an amino acid sequence according to SEQ ID NO: 393 or an amino acid sequence that is at least 80%, 85%, 90%, 95, 98%, 99%, or 99.5% identical to SEQ ID NO: 393, as follows: MFERNYDPRELRKETYLLYEIKWGKSGKLWRHWCQNNRTQHAEVYFLENIFNARRF NPSTHCSITWYLSWSPCAECSQKIVDFLKEHPNVNLEIYVARLYYHEDERNRQGLRD LVNSGVTIRIMDLPDYNYCWKTFVSDQGGDEDYWPGHFAPWIKQYSLKL (SEQ ID NO: 393) [00185] In certain other embodiment, the cytidine dea
• the cytidine deaminase domain is an “evoFERNY” polypeptide having an amino acid sequence according to SEQ ID NO: 394 or an amino acid sequence that is at least 85%, 90%, 95, 98%, 99%, or 99.5% identical to SEQ ID NO: 394, which contains H102P and D104N substitutions relative to SEQ ID NO: 393, as follows: MFERNYDPRELRKETYLLYEIKWGKSGKLWRHWCQNNRTQHAEVYFLENIFNARRF NPSTHCSITWYLSWSPCAECSQKIVDFLKEHPNVNLEIYVARLYYPENERNRQGLRD LVNSGVTIRIMDLPDYNYCWKTFVSDQGGDEDYWPGHFAPWIKQYSLKL (SEQ ID NO: 394).
• the FERNY and evoFERNY deaminase domains are 162 amino acids in length. These domains are thus shorter than those of any one of SEQ ID NOs: 276-277, 281, 133- 134, 292-295, and 487.
• the disclosed CBEs comprise a FERNY or evoFERNY deaminase domain.
• the disclosed CBEs comprise a deaminase domain that comprises the amino acid sequence of SEQ ID NO: 393 or 394.
• the state-of-the-art cytosine base editor BE3.9 contains a rat APOBEC1 (rAPOBEC1) cytidine deaminase domain.
• FERNY is an N- and C-terminally truncated ancestral sequence reconstruction based on an APOBEC family phylogenetic tree.
• rAPOBEC1 229 aa; FERNY: 161 aa.
• the sequence similarity to rAPOBEC1 is 55%.
• the evolved FERNY genotype also has high GC activity and is comparably active to APOBEC despite being a shorter protein. Evolved FERNY is described in greater detail in PCT Publication No.
• WO 2019/023680 published January 31, 2019, which is incorporated herein by reference. Additional exemplary cytidine deaminases are disclosed in PCT Publication No. WO 2021/108717, published June 3, 2021.
• suitable cytosine deaminase domains are provided below, as SEQ ID NOs: 276-277, 281, 133-134, 292-295, and 487.
• the deaminase is at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to any one of the amino acid sequences set forth below.
• the variants provided herein are deoxyadenosine deaminases.
• the disclosed adenosine deaminases are variants of known adenosine deaminase TadA7.10, which comprises the following mutations as compared to wild-type ecTadA (SEQ ID NO: 325): W23R, H36L, P48A, R51L, L84F, A106V, D108N, H123Y, S146C, D147Y, R152P, E155V, I156F, and K157N.
• the disclosed adenosine deaminases are variants of a TadA derived from a species other than E.
• the disclosed adenosine deaminase domain comprises TadA-8e, a variant of E. coli TadA 7.10.
• TadA-8e (set forth as SEQ ID NO: 433) contains the following substitutions: T111, D119, F149, R26, V88, A109, H122, T166, and D167, relative to TadA7.10 (SEQ ID NO: 315).
• TadA-8e is disclosed in PCT Publication No.
• the adenosine deaminase domain comprises TadA-8e(V106W), which contains a V106W substitution relative to TadA-8e.
• the disclosed adenosine deaminases hydrolytically deaminate a targeted adenosine in a nucleic acid of interest to an inosine, which is read as a guanosine (G) by DNA polymerase enzymes.
• G guanosine
• These variants may comprise a domain of any of the disclosed base editors (i.e., an adenosine deaminase domain of an adenine base editor).
• any of the disclosed adenine base editors are capable of deaminating adenosine in a nucleic acid sequence (e.g., DNA or RNA).
• the disclosed adenine base editors are further capable of deaminating adenine in DNA.
• Exemplary, non-limiting, embodiments of adenosine deaminases are provided herein.
• the adenosine deaminase domain of any of the disclosed base editors comprises a single adenosine deaminase, or a monomer.
• the adenosine deaminase domain comprises 2 3 4 or 5 adenosine deaminases In some embodiments, the adenosine deaminase domain comprises two adenosine deaminases, or a dimer. In some embodiments, the deaminase domain comprises a dimer of an engineered (or evolved) deaminase and a wild-type deaminase, such as a wild-type E. coli-derived deaminase.
• mutations provided herein may be applied to adenosine deaminases in other adenine base editors, for example, those provided in PCT Publication No. WO 2018/027078, published August 2, 2018; PCT Publication No. WO 2019/079347 on April 25, 2019; International Application No PCT/US2019/033848, filed May 23, 2019, which published as PCT Publication No. WO 2019/226593 on November 28, 2019; U.S. Patent Publication No.2018/0073012, published March 15, 2018, which issued as U.S. Patent No.10,113,163, on October 30, 2018; U.S.
• Patent Publication No.2017/0121693 published May 4, 2017, which issued as U.S. Patent No.10,167,457 on January 1, 2019; PCT Publication No. WO 2017/070633, published April 27, 2017; U.S. Patent Publication No.2015/0166980, published June 18, 2015; U.S. Patent No.9,840,699, issued December 12, 2017; and U.S. Patent No.10,077,453, issued September 18, 2018; PCT Application No. PCT/US2020/28568, filed April 16, 2020, and PCT Publication No. WO 2021/158921, published August 12, 2021; all of which are incorporated herein by reference in their entireties.
• any of the adenosine deaminases provided herein are capable of deaminating adenine, e.g., deaminating adenine in a deoxyadenosine nucleoside of DNA.
• the adenosine deaminase may be derived from any suitable organism (e.g., E. coli).
• the adenosine deaminase is a naturally-occurring adenosine deaminase that includes one or more mutations corresponding to any of the mutations provided herein (e.g., mutations in ecTadA).
• TadA deaminases derived from Bacillus subtilis (set forth in full as SEQ ID NO: 318), S. aureus (SEQ ID NO: 317), and S. pyogenes (SEQ ID NO: 448) are provided.
• SEQ ID NO: 318 S. aureus
• S. pyogenes SEQ ID NO: 448 are provided.
• the amino acid substitutions in E. coli TadA-8e, and the homologous mutations in the B. subtilis, S. aureus, and S. pyogenes TadA deaminases, are shown.
• adenosine deaminase e.g., having homology to ecTadA
• the adenosine deaminase is derived from a prokaryote .
• the adenosine deaminase is from a bacterium.
• the adenosine deaminase is from Escherichia coli, Staphylococcus aureus, Salmonella typhi, Shewanella putrefaciens, Haemophilus influenzae, Caulobacter crescentus, or Bacillus subtilis. In some embodiments, the adenosine deaminase is from E. coli. [00205] In some embodiments, the adenosine deaminase comprises TadA9, or a variant thereof. TadA9 contains V82S and Q154R substitutions relative to TadA-8e.
• the adenosine deaminase comprises an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to the amino acid sequence of TadA9 (SEQ ID NO: 33).
• TadA9 may be referred to in the art as TadA*8.9.
• An ABE containing the TadA9 deaminase is referred to herein as ABE9.
• TadA9 is is described in additional detail in Gaudelli et al., Nat Biotechnol.2020 Jul;38(7):892-900 and PCT Publication No. WO 2021/050571, published March 18, 2021, each of which are incorporated herein by reference.
• the adenosine deaminase comprises TadA20, or a variant thereof.
• TadA20 contains I76Y, V82S, Y123H, Y147R and Q154R substitutions relative to TadA7.10.
• TadA20 is described in additional detail in Gaudelli et al., Nat Biotechnol.2020 Jul;38(7):892-900 and WO 2021/050571, published March 18, 2021.
• TadA20 may be referred to in the art as TadA*8.20.
• the adenosine deaminase comprises an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to the amino acid sequence of TadA20 (SEQ ID NO: 326).
• An ABE containing the TadA20 deaminase is referred to herein as ABE20. It may be referred to in the art as ABE8.20, ABE8.20-d, or ABE8.20-m.
• the adenosine deaminase comprises an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to any of the amino acid sequences of SEQ ID NOs: 33, 315, 317-326, 433 or 448-449.
• adenosine deaminases provided herein may include one or more mutations (e.g., any of the mutations provided herein). The disclosure provides adenosine deaminases with a certain percent identity plus any of the mutations or combinations thereof described herein.
• any of the adenosine deaminases described herein may be a truncated variant of any of the other adenosine deaminases described herein, e.g., any of the adenosine deaminases of SEQ ID NOs: 33, 315, 317-326, 433 or 448-449.
• Exemplary truncated adenosine deaminases may comprise truncations of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or more than 15 amino acids from the N-terminus.
• exemplary truncated adenosine deaminases may comprise truncations of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or more than 15 amino acids from the C-terminus.
• the adenosine deaminase domain comprises a trunacted version of the wild- type ecTadA, as set forth in SEQ ID NO: 324. Any of the adenosine deaminases described herein may include an N-terminal methionine (M) amino acid residue.
• any of the mutations provided herein may be introduced into other adenosine deaminases, such as S. aureus TadA (saTadA), A. aeolicus TadA (AaTadA), or another adenosine deaminase (e.g., another bacterial adenosine deaminase), such as those sequences provided below.
• adenosine deaminases such as S. aureus TadA (saTadA), A. aeolicus TadA (AaTadA), or another adenosine deaminase (e.g., another bacterial adenosine deaminase), such as those sequences provided below.
• any of the mutations identified in ecTadA may be made in other adenosine deaminases that have homologous amino acid residues.
• Any of the mutations provided herein may be made individually or in any combination in ecTadA or another adenosine deaminase.
• Any of the mutated deaminases provided herein may be used in the context of adenine base editor.
• the deaminases provided herein may have a sequence that begins with a methionine (“M”) before the first amino acid shown in the sequences below.
• M methionine
• Exemplary adenosine deaminase variants of the disclosure are described below.
• the adenosine deaminase domain comprises an adenosine deaminase that has a sequence with at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or at least 99.5% sequence identity to one of the following: [00212] TadA 7.10 (E.
• TadA MPPAFITGVTSLSDVELDHEYWMRHALTLAKRAWDEREVPVGAVLVHNHRVIGEG WNRPIGRHDPTAHAEIMALRQGGLVLQNYRLLDTTLYVTLEPCVMCAGAMVHSRIG RVVFGARDAKTGAAGSLIDVLHHPGMNHRVEIIEGVLRDECATLLSDFFRMRRQEIK ALKKADRAEGAGPAV (SEQ ID NO: 319) [00219] Shewanella putrefaciens (S.
• TadA MDEYWMQVAMQMAEKAEAAGEVPVGAVLVKDGQQIATGYNLSISQHDPTAHAEI LCLRSAGKKLENYRLLDATLYITLEPCAMCAGAMVHSRIARVVYGARDEKTGAAGT VVNLLQHPAFNHQVEVTSGVLAEACSAQLSRFFKRRRDEKKALKLAQRAQQGIE (SEQ ID NO: 320) [00220] Haemophilus influenzae F3031 (H influenzae) TadA: MDAAKVRSEFDEKMMRYALELADKAEALGEIPVGAVLVDDARNIIGEGWNLSIVQS DPTAHAEIIALRNGAKNIQNYRLLNSTLYVTLEPCTMCAGAILHSRIKRLVFGASDYK TGAIGSRFHFFDDYKMNHTLEITSGVLAEECSQKLSTFFQKRREEKKIEKALLKSLSD K (SEQ ID NO: 321) [00221] Ca
• TadA MRTDESEDQDHRMMRLALDAARAAAEAGETPVGAVILDPSTGEVIATAGNGPIAAH DPTAHAEIAAMRAAAAKLGNYRLTDLTLVVTLEPCAMCAGAISHARIGRVVFGADD PKGGAVVHGPKFFAQPTCHWRPEVTGGVLADESADLLRGFFRARRKAKI (SEQ ID NO: 322) [00222] Geobacter sulfurreducens (G.
• TadA MSSLKKTPIRDDAYWMGKAIREAAKAAARDEVPIGAVIVRDGAVIGRGHNLREGSN DPSAHAEMIAIRQAARRSANWRLTGATLYVTLEPCLMCMGAIILARLERVVFGCYDP KGAAGSLYDLSADPRLNHQVRLSPGVCQEECGTMLSDFFRDLRRRKKAKATPALFI DERKVPPEP (SEQ ID NO: 323) [00223] Streptococcus pyogenes (S.
• the adenosine deaminase domain comprises an N-terminal truncated E. coli TadA.
• the adenosine deaminase comprises the amino acid sequence: MSEVEFSHEYWMRHALTLAKRAWDEREVPVGAVLVHNNRVIGEGWNRPIGRHDPT AHAEIMALRQGGLVMQNYRLIDATLYVTLEPCVMCAGAMIHSRIGRVVFGARDAKT GAAGSLMDVLHHPGMNHRVEITEGILADECAALLSDFFRMRRQEIKAQKKAQSSTD (SEQ ID NO: 324).
• the TadA deaminase is a full-length E. coli TadA deaminase (ecTadA).
• the adenosine deaminase domain comprises a deaminase that comprises the amino acid sequence: MRRAFITGVFFLSEVEFSHEYWMRHALTLAKRAWDEREVPVGAVLVHNNRVIGEG WNRPIGRHDPTAHAEIMALRQGGLVMQNYRLIDATLYVTLEPCVMCAGAMIHSRIG RVVFGARDAKTGAAGSLMDVLHHPGMNHRVEITEGILADECAALLSDFFRMRRQEI KAQKKAQSSTD (SEQ ID NO: 325) [00227]
• the base editor comprises an adenosine deaminase monomer.
• the base editor comprises an adenosine deaminase dimer.
• the base editor may comprise a heterodimer of a first adenosine deaminase and a second adenosine deaminase.
• the first adenosine deaminase is N-terminal to the second adenosine deaminase in the base editor.
• the first adenosine deaminase is C-terminal to the second adenosine deaminase in the base editor.
• the first adenosine deaminase and the second deaminase are fused directly to each other or via a linker.
• the first adenosine deaminase is fused N- terminal to the napDNAbp via a linker
• the second deaminase is fused C-terminal to the napDNAbp domain via a linker.
• the second adenosine deaminase is fused N-terminal to the napDNAbp domain via a linker
• the first deaminase is fused C- terminal to the napDNAbp via a linker.
• the base editing methods of the disclosure comprise the use of an adenine base editor.
• Exemplary adenine base editors of this disclosure comprise the monomer and dimer versions of the following editors: Sauri-ABE8e, SaKKH-ABE8e, SaABE8e, CjCas9-ABE8e and Nme2Cas9-ABE8e; SaKKH-ABE8e(V106W), SauriCas9- ABE8e(V106W), CjCas9-ABE8e(V106W), Nme2Cas9-ABE8e(V106W), and SaCas9- ABE8e(V106W); SaKKH-ABE9, SauriCas9-ABE9, CjCas9-ABE9, Nme2Cas9-ABE9, and SaCas9-ABE9; SaKKH-ABE20, SauriCas
• the ABE is Sauri- ABE8e, SaKKH-ABE8e, or SaABE8e. These base editors are 1298, 1291, and 1291 amino acids in length, respectively. Additional base editors are 1221 amino acids (CjABE8e) and 1319 amino acids (Nme2ABE8e) in length.
• the ABE is SaKKH- ABE8e.
• Exemplary ABEs contain an adenosine deaminase domain that comprises a TadA8e and does not comprise a second adenosine deaminase (i.e., the adenosine deaminase domain consists of a deaminase monomer).
• ABE8e may be referred to in the art as “ABE8” or “ABE8.0”.
• the ABE8e base editor and variants thereof may comprise an adenosine deaminase domain containing a TadA- 8e adenosine deaminase monomer (monomer form) or a TadA-8e adenosine deaminase homodimer or heterodimer (dimer form).
• the architecture of base editors comprising an adenosine deaminase domain and a napDNAbp is as follows: NH2- [adenosine deaminase]-[napDNAbp domain]-COOH; or NH 2 -[napDNAbp domain]- [adenosine deaminase]-COOH.
• the base editors comprise an ABE8e monomer architecture, which comprises NH2-[NLS]-[adenosine deaminase]-[napDNAbp domain]-[NLS]-COOH, wherein “NLS” is a nuclear localization sequence.
• the disclosure provides complexes of adenine base editors and guide RNAs.
• Exemplary disclosed complexes comprise any of the following ABEs in conjunction with a guide RNA (such as a single-guide RNA): Sauri-ABE8e, SaKKH-ABE8e, SaABE8e, CjCas9-ABE8e and Nme2Cas9-ABE8e; SaKKH-ABE8e(V106W), SauriCas9- ABE8e(V106W), CjCas9-ABE8e(V106W), Nme2Cas9-ABE8e(V106W), and SaCas9- ABE8e(V106W); SaKKH-ABE9, SauriCas9-ABE9, CjCas9-ABE9, Nme2Cas9-ABE9, and SaCas9-ABE9; SaKKH-ABE20, SauriCas9-ABE20, CjCas9-ABE20, Nme2Cas9-ABE20
• ABEs may be used to deaminate a A nucleobase in accordance with the disclosed complexes.
• the ABE is CjCas9-ABE8e.
• this editor exhibited higher context preference for pyrimidines in the nucleotide position 5 ⁇ of the target adenine base (YA >> RA).
• “preference” and “context preference” refer to a product purity of above 40% with respect to the target adenosine.
• the disclosure provides ABEs having pyrimidine (“Y”) context preference, where “context” refers to the presence of a pyrimidine or a purine (“R”) immediately 5′ of the adenine base to be edited (or the target adenine base), such as CjABE8e editors and variants thereof.
• Y pyrimidine
• R purine
• These ABEs may have a preference for editing an adenosine in a target nucleic acid sequence of 5′-YAN-3′, wherein Y is C or T; N is A, T, C, G, or U; and A is the target adenosine.
• an ABE having context preference for deaminating an adenosine in a target nucleic acid sequence of 5′-YAN-3′, wherein Y is C or T, and N is A, T, C, G, or U; and A is the target adenosine.
• FIG.2A An exemplary AAV-encoded adenine base editor construct is shown in FIG.2A. This construct contains an SaABE8e base editor operably controlled by an EFS promoter and a bGH polyA sequence. It also contains a guide RNA encoded in the reverse orientation, as indicated by the arrow pointing away from the 3 ⁇ terminus.
• the disclosed complexes of ABEs may possess an on-target editing efficiency of more than 50% after being contacted with a nucleic acid molecule comprising a target sequence. Further exemplary ABE complexes possess an on-target editing efficiency of more than 60% after being contacted with a nucleic acid molecule comprising a target sequence. Further exemplary ABEs possess an on-target editing efficiency of more than 65%, more than 70%, more than 75%, more than 80%, more than 82.5%, or more than 85% after being contacted with a nucleic acid molecule comprising a target sequence.
• the disclosed ABE complexes may exhibit indel frequencies of less than 2.5%, less than 2.4%, less than 2.2%, less than 2.0%, less than 1.75%, less than 1.5%, less than 1.3%, less than 1.1%, or less than 1.0% after being contacted with a nucleic acid molecule containing a target sequence.
• the disclosure provide base editors comprising a napDNAbp domain and an adenosine deaminase domain as described herein.
• the Cas9 domain may be any of the Cas9 domains or Cas9 proteins (e.g., a Cas9 nickase, or nCas9) provided herein.
• any of the Cas9 domains or Cas9 proteins may be fused with any of the adenosine deaminase domains provided herein.
• the base editors comprising adenosine deaminases and a napDNAbp do not include a linker sequence.
• a linker is present between the adenosine deaminase domain and/or between an adenosine deaminase and the napDNAbp.
• the “]-[” used in the general architecture above indicates the presence of an optional linker.
• an adenosine deaminase domain and the napDNAbp domain are fused via any of the linkers provided herein.
• the adenosine deaminase domain (which may include one or more adenosine deaminases) and the napDNAbp are fused via any of the linkers provided below in the section entitled “Linkers” [00237]
• the adenine base editors comprise adenosine deaminases comprising comprises a sequence with at least 80%, 85%, 90%, 95%, 98%, 99%, or 99.5% sequence identity to SEQ ID NO: 433 (TadA-8e).
• the adenine base editors comprise the sequence of SEQ ID NO: 433. [00238] In some embodiments, the adenine base editor of the disclosure comprises the sequence of SEQ ID NO: 181. In some embodiments, the adenine base editor of the disclosure comprises the sequence of SEQ ID NO: 182. In other embodiments, the adenine base editor of the disclosure comprises the sequence of SEQ ID NO: 183. In other embodiments, the adenine base editors of the disclosure comprises the sequence of SEQ ID NOs: 171 or 172.
• any of the adenine base editors described herein may comprise an amino acid sequence having 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, or more than 30 amino acids that differ relative to the amino acid sequence of any of SEQ ID NOs: 171-172 and 181-183. These differences may comprise amino acids that have been inserted, deleted, or substituted relative to the reference sequence.
• the disclosed adenosine deaminase domains contain stretches of about 50, about 75, about 100, about 125, about 150, about 175, about 200, about 300, about 400, about 500, or more than 500 consecutive amino acids in common with either of SEQ ID NOs: 171- 172 and 181-183.
• Exemplary base editors comprise sequences that are at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or at least 99.5% identical to any of the following amino acid sequences (SEQ ID NOs: 171-172 and 181-183).
• the disclosed base editors have a sequence comprising any of the following amino acid sequences: [00241] SaABE8e: NLS, linker, TadA-8e, SaCas9 MKRTADGSEFESPKKKRKVSEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVI GEGWNRAIGLHDPTAHAEIMALRQGGLVMQNYRLIDATLYVTFEPCVMCAGAMIHSRIGR VVFGVRNSKRGAAGSLMNVLNYPGMNHRVEITEGILADECAALLCDFYRMPRQVFNAQK KAQSSINSGGSSGGSSGSETPGTSESATPESSGGSSGGSGKRNYILGLAIGITSVGYGIIDYET RDVIDAGVRLFKEANVENNEGRRSKRGARRLKRRRRHRIQRVKKLLFDYNLLTDHSELSGI NPYEARVKGLSQKLSEEEFSAALLHLAKRRGVHNVNEVEEDTGNELSTKEQISRNSKALEE KYVAELQ
• CBEs examples include CjCas9-BE3.9, CjCas9-FERNY-BE3.9, and CjCas9-evoFERNY- BE3.9
• the CBEs of the disclosure may be a variant of any of CjCas9-BE3.9, CjCas9- FERNY-BE3.9, and CjCas9-evoFERNY-BE3.9.
• the disclosed cytosine base editors may comprise a fusion protein comprising: (i) a nucleic acid programmable DNA binding protein (napDNAbp) domain; (ii) a cytidine deaminase domain; and (iii) a uracil glycosylase inhibitor domain (UGI).
• the disclosed CBEs contain a single UGI domain.
• the disclosed CBEs can be arranged structurally in a variety of configurations, which include but are not limited to: NH2-[cytidine deaminase domain]-[napDNAbp domain]-[UGI]-COOH; NH 2 -[cytidine deaminase domain]-[UGI]-[napDNAbp domain]-COOH; NH 2 -[napDNAbp domain]-[UGI]-[cytidine deaminase domain]-COOH; NH2-[napDNAbp domain]-[cytidine deaminase domain]-[UGI]-COOH; NH 2 -[UGI]-[cytidine deaminase domain]-[napDNAbp domain]-COOH; or NH 2 -[UGI]-[napDNAbp domain]-[cytidine deaminase domain]-COOH, wherein each instance of “]-
• FIG.14 An exemplary construct encoding a single AAV-CBE is shown in FIG.14.
• This CBE contains a BE3.9 architecture, with the deaminase FERNY (or evoFERNY) as the cytidine deaminase domain positioned 5 ⁇ of the napDNAbp domain.
• the cytosine base editor contains a CjCas9 napDNAbp domain.
• a human U6-controlled (“hU6”) sgRNA is positioned at the 3 ⁇ end, in the reverse orientation to the base editor.
• This construct contains an EFS promoter driving the base editor, and an SV40 late polyA sequence.
• the construct has a length of 5.012 kb.
• BE3.9 refers to the BE3.9 CBE architecture, i.e., NH 2 -[first nuclear localization sequence]-[cytosine deaminase domain]- [32aa linker]-[napDNAbp domain]-[9aa linker]-[first UGI domain]-[second nuclear localization sequence]-COOH.
• the disclosed CBEs may further comprise one or more nuclear localization signals (NLSs).
• NLSs nuclear localization signals
• the disclosed CBEs may comprise modified (or evolved) cytosine deaminase domains, such as deaminase domains that recognize an expanded PAM sequence, have improved efficiency of deaminating 5′-GC targets, and/or make edits in a narrower target window,
• the disclosed cytidine nucleobase editors comprise evolved nucleic acid programmable DNA binding proteins (napDNAbp), such as an evolved Cas9.
• the disclosure provides complexes of cytosine base editors and guide RNAs, e.g., complexes of any of CjCas9-BE3.9, CjCas9-FERNY-BE3.9, and CjCas9- evoFERNY-BE39 and a sgRNA [00252]
• CBEs are provided below, as SEQ ID NOs: 19 and 20, which are FERNY-BE3.9 editors. These editors contain SpCas9 as a napDNAbp domain.
• Exemplary AAV-encoded CBEs of the disclosure contain a CjCas9 domain (SEQ ID NO: 379) in place of the SpCas9 domain of the below-described FERNY-BE3.9 editors.
• the following base editor (SEQ ID NO: 19) contains wild-type FERNY, which may be used as a reference base editor. This base editor was evolved to generate the evoFERNY base editor shown as SEQ ID NO: 20.
• These base editors contain a bpNLS and a single UGI domain.
• the disclosed base editors comprise CjCas9-evoFERNY-BE3.9, which is provided below as SEQ ID NO: 22.
• Any of the disclosed base editors may comprise a sequence having at least 80%, 85%, 90%, 92.5%, 95%, 97%, 98% or 99% identity to any of SEQ ID NOs: 21 and 22.
• the base editors may comprise the sequence of SEQ ID NO: 21 or 22. These base editors contain a bpNLS and a single UGI domain. The FERNY deaminase is italicized.
• the rAAV particles of the present disclosure comprise a rAAV vector (i.e., a recombinant genome of the rAAV) encapsidated in the viral capsid proteins.
• a rAAV vector i.e., a recombinant genome of the rAAV
• the AAV nucleic acid vector is single-stranded.
• the AAV nucleic acid vector is self-complementary.
• the rAAV vectors of the disclosure do not contain any inteins.
• viral sequences that facilitate integration comprise Inverted Terminal Repeat (ITR) sequences.
• ITR Inverted Terminal Repeat
• nucleic acid molecule is flanked on each side by an ITR sequence.
• the nucleic acid vector further comprises a region encoding an AAV Rep protein as described herein, either contained within the region flanked by ITRs or outside the region.
• the ITR sequences can be derived from any AAV serotype (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10) or can be derived from more than one serotype.
• the ITR sequences are derived from AAV8 or AAV9.
• a nucleic acid plasmid such as a helper plasmid, that comprises a region encoding a Rep protein and/or a Cap (capsid) protein is provided.
• the rAAV particles disclosed herein comprise an rAAV2 particle, rAAV6 particle, rAAV8 particle, rPHP.B particle, rPHP.eB particle, or rAAV9 particle, or a variant thereof.
• the disclosed rAAV particles are rAAV8 or rAAV9 particles.
• Exemplary rAAV particles provided herein include, but are not limited to, an rAAV8-Sauri-ABE8e, rAAV9-Sauri-ABE8e, rAAV8-SaKKH-ABE8e, rAAV9-SaKKH- ABE8e, rAAV8-CjCas9-ABE8e, rAAV9-CjCas9-ABE8e, rAAV8-Nme2Cas9-ABE8e, or an rAAV9-Nme2Cas9-ABE8e particle.
• the rAAV particle comprises an rAAV8-SaKKH-ABE8e particle. In some embodiments, the rAAV particle comprises a rAAV9-CjBE3.9 particle or an rAAV8-CjBE3.9 particle.
• ITR sequences and plasmids containing ITR sequences are known in the art and commercially available (see, e.g., products and services available from Vector Biolabs, Philadelphia PA; Cellbiolabs San Diego CA; Agilent Technologies Santa Clara Ca; and Addgene, Cambridge, MA; and Gene delivery to skeletal muscle results in sustained expression and systemic delivery of a therapeutic protein.
• Kessler PD Podsakoff GM, Chen X, McQuiston SA, Colosi PC, Matelis LA, Kurtzman GJ, Byrne BJ. Proc Natl Acad Sci USA.1996 Nov 26;93(24):14082-7; and Curtis A. Machida. Methods in Molecular MedicineTM. Viral Vectors for Gene Therapy Methods and Protocols.10.1385/1-59259-304- 6:201 ⁇ Humana Press Inc.2003. Chapter 10. Targeted Integration by Adeno-Associated Virus. Matthew D. Weitzman, Samuel M. Young Jr., Toni Cathomen and Richard Jude Samulski; U.S. Pat.
• the rAAV vector of the present disclosure comprises one or more regulatory elements to control the expression of the heterologous nucleic acid region (e.g., promoters, transcriptional terminators, and/or other regulatory elements).
• the first and/or second nucleotide sequence is operably linked to one or more (e.g., 1, 2, 3, 4, 5, or more) transcriptional terminators.
• transcriptional terminators include transcription terminators (or polyadenylation signals) of the bovine growth hormone gene (bGH), human growth hormone gene (hGH), SV40, CW3, ⁇ , or combinations thereof.
• the transcriptional terminator is an SV40 polyadenylation signal.
• the transcriptional terminator does not contain a posttranscription response element, such as WPRE element.
• Methods of packaging are known in the art and reagents are commercially available (see, e.g., Zolotukhin et al. Production and purification of serotype 1, 2, and 5 recombinant adeno-associated viral vectors. Methods 28 (2002) 158– 167; and U.S. Patent Publication Numbers US 2007-0015238 and US 2012-0322861, which are incorporated herein by reference; and plasmids and kits available from ATCC and Cell Biolabs, Inc.).
• a plasmid comprising a gene of interest may be combined with one or more helper plasmids, e.g., that contain a rep gene (e.g., encoding Rep78, Rep68, Rep52 and Rep40) and a cap gene (encoding VP1, VP2, and VP3, including a modified VP2 region as described herein), and transfected into a recombinant cells such that the rAAV particle can be packaged and subsequently purified.
• Packaging cells or host cells
• Such cells include 293 cells, which package adenovirus, and ⁇ 2 cells or PA317 cells, which package retrovirus.
• Viral vectors used in gene therapy are usually generated by producing a cell line that packages a nucleic acid vector into a viral particle.
• the vectors typically contain the minimal viral sequences required for packaging and subsequent integration into a host, other viral sequences being replaced by an expression cassette for the polynucleotide(s) to be expressed.
• the missing viral functions are typically supplied in trans by the packaging cell line.
• AAV vectors used in gene therapy typically only possess ITR sequences from the AAV genome which are required for packaging and integration into the host genome.
• Viral DNA is packaged in a cell line, which contains a helper plasmid encoding the other AAV genes, namely rep and cap, but lacking ITR sequences.
• the cell line may also be infected with adenovirus as a helper.
• the helper virus promotes replication of the AAV vector and expression of AAV genes from the helper plasmid.
• the helper plasmid is not packaged in significant amounts due to a lack of ITR sequences. Contamination with adenovirus can be reduced by, e.g., heat treatment to which adenovirus is more sensitive than AAV.
• Additional methods for the delivery of nucleic acids to cells are known to those skilled in the art, such as those disclosed in US 2003/0087817, published May 8, 2003, PCT Application No. WO 2016/205764, published December 22, 2016, and PCT Application No. WO 2018/071868, published April 19, 2018.
• the base editor constructs may be engineered for delivery in one or more rAAV vectors.
• An rAAV as related to any of the methods and compositions provided herein may be of any serotype including any derivative or pseudotype (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 2/1, 2/5, 2/8, 2/9, 3/1, 3/5, 3/8, or 3/9).
• An rAAV may comprise a genetic payload (i.e., a recombinant nucleic acid vector that expresses a transgene of interest, such as a whole base editor that is carried by the rAAV into a cell) that is to be delivered to a cell.
• an rAAV may be chimeric.
• the serotype of an rAAV refers to the serotype of the capsid proteins of the recombinant virus.
• Non-limiting examples of derivatives and pseudotypes include rAAV2/1, rAAV2/5, rAAV2/8, rAAV2/9, AAV2-AAV3 hybrid, AAVrh.10, AAVrh.74, AAVhu.14, AAV3a/3b, AAVrh32.33, AAV-HSC15, AAV-HSC17, AAVhu.37, AAVrh.8, CHt-P6, AAV2.5, AAV6.2, AAV2i8, AAV-HSC15/17, AAVM41, AAV9.45, AAV6(Y445F/Y731F), AAV2.5T, AAV-HAE1/2, AAV clone 32/83, AAVShH10, AAV2 (Y->F) AAV8 (Y73
• compositions comprising a plurality of any of the disclosed rAAV particles are provided herein.
• compositions contain a plurality of any of the disclosed rAAV8 particles, rAAV9 particles, rAAV2 particles, rAAV6 particles, rAAVPHP.B particles, and rAAVPHP.eB particles.
• tissues not well-transduced by intravenous AAV9 injections may be transduced by other existing AAV variants, such as AAV4 transduction of the lung, or by different delivery routes, such as AAV9 transduction of kidney cellsby retrograde ureteral infusion.
• AAV derivatives/pseudotypes, and methods of producing such derivatives/pseudotypes are known in the art (see, e.g., Mol. Ther.2012 Apr;20(4):699-708. doi: 10.1038/mt.2011.287. Epub 2012 Jan 24.
• the AAV vector toolkit poised at the clinical crossroads. Asokan A1, Schaffer DV, Samulski RJ.).
• Methods for producing and using pseudotyped rAAV vectors are known in the art (see, e.g., Duan et al., J. Virol., 75:7662- 7671, 2001; Halbert et al., J.
• the disclosure provides compositions containing a plurality of any of the disclosed rAAV particles.
• the disclosure provides host cells containing a plurality of any of the disclosed rAAV particles.
• the host cells are mammalian cells, such as human cells.
• the host cells are yeast cells, plant cells, or bacterial cells.
• any of the disclosed rAAV particles, host cells, or compositions are delivered to a subject, such as a mammalian subject.
• the rAAV particles are delivered to a human subject
• the disclosed rAAV particles and compositions are administered to a subject in a single injection, such as a single systemic injection.
• the disclosed rAAV particles and compositions are administered to a subject in multiple injections.
• any of the disclosed rAAV particles or compositions are known to transduce target tissues within days, but are typically allowed three to four weeks to complete transduction, genome integration, and clearance, from the cell. Accordingly, in some aspects, any of the disclosed rAAV particles or compositions are administered to a subject for a period of three weeks. In some aspects, any of the disclosed rAAV particles or compositions are administered to a subject for a period of between three and four weeks. [00275] In some embodiments, any of the disclosed rAAV particles or compositions is administered to a subject or a target tissue in a therapeutically effective amount of about 10 15 , about 10 14 , about 10 13 , about 10 12 , about 10 11 , or less than about 10 11 vector genomes (vg) per kg weight of the subject.
• vg vector genomes
• the rAAV particles are administered in an amount of between 10 15 and 10 14 , between 10 14 and 10 13 , between 10 13 and 10 12 , between 10 12 and 10 11 , or between 10 12 and 10 11 vgs per kg. In some embodiments, the rAAV particles are administered in an amount of between 10 14 and 10 11 vgs per kg. In some embodiments, any of the disclosed rAAV particles or compositions is administered to a target tissue of a subject in a lower dose than is convention for dual AAV particle delivery, such as that described in PCT Publication No. WO 2020/236982, published November 26, 2020 and Levy, J.M., et al. Nat Biomed Eng 4, 97-110 (2020).
• the present disclosure provides single AAV vector delivery of base editors to target tissues, such as liver, neuronal, heart, muscular, or ocular tissue.
• any of the disclosed rAAV particles or compositions is administered to the liver (hepatic) tissue of a subject.
• any of the disclosed rAAV particles or compositions is administered to the cardiac tissue of a subject.
• any of the disclosed rAAV particles or compositions is administered to the neuronal tissue of a subject.
• any of the disclosed rAAV particles or compositions is administered to the muscular, or neuromuscular, tissue of a subject.
• any of the disclosed rAAV particles or compositions is administered to the ocular tissue of a subject.
• the disclosed rAAV particles provide for transduction of the target tissue to achieve expression and translation of the payload or transgene, e.g., a base editor in accordance with the present disclosure for a sufficient duration to install desired mutations in the genome of a target cell.
• the desired mutatation is an A to G mutation. In some embodiments, the desired mutatation is a C to T mutation.
• the disclosed rAAV particles provide for sufficient expression and translation of the base editor transgene for a sufficient duration to install desired (on-target) mutations in the genome with a tolerable degree of off-target effects, such as bystander edits. In some embodiments, the disclosed rAAV particles provide for sufficient expression and translation of the base editor transgene for a sufficient duration to install desired mutations in the genome without appreciable off-target editing. In some embodiments, the disclosed rAAV particles provide for sufficient expression and translation of the base editor transgene for a sufficient duration to install desired mutations in the genome without appreciable bystander editing.
• Suitable routes of administrating the disclosed compositions of rAAV particles include, without limitation: topical, subcutaneous, transdermal, intradermal, intralesional, intraarticular, intraperitoneal, intravesical, transmucosal, gingival, intradental, intracochlear, transtympanic, intraorgan, epidural, intrathecal, intramuscular, intravenous, systemic, intravascular, intraosseus, periocular, intratumoral, intracerebral, parenteral, and intracerebroventricular administration.
• the route of administration is systemic (intravenous).
• the pharmaceutical composition described herein is administered locally to a diseased site.
• compositions comprising any of the disclosed compositions and a pharmaceutically acceptable carrier are provided herein.
• the pharmaceutical composition is formulated for delivery to a subject, e.g., for base editing in a genome.
• the disclosed compositions are formulated in accordance with routine procedures as a composition adapted for intravenous or subcutaneous administration to a subject, e.g., a human.
• compositions provided herein are formulated for delivery to a subject, for example, to a human subject, in order to effect a targeted genomic modification within the subject.
• cells are obtained from the subject and contacted with a any of the pharmaceutical compositions provided herein.
• cells removed from a subject and contacted ex vivo with a pharmaceutical composition are re-introduced into the subject, optionally after the desired genomic modification has been effected or detected in the cells.
• Subjects to which administration of the pharmaceutical compositions is contemplated include but are not limited to humans and/or other primates; mammals domesticated animals, pets, and commercially relevant mammals such as cattle, pigs, horses, sheep, cats, dogs, mice, and/or rats; and/or birds, including commercially relevant birds such as chickens, ducks, geese, and/or turkeys.
• Formulations of the pharmaceutical compositions described herein may be prepared by any method known or hereafter developed in the art of pharmacology.
• Such preparatory methods include the step of bringing the active ingredient(s) into association with an excipient and/or one or more other accessory ingredients, and then, if necessary and/or desirable, shaping and/or packaging the product into a desired single- or multi-dose unit.
• Pharmaceutical formulations may additionally comprise a pharmaceutically acceptable excipient, which, as used herein, includes any and all solvents, dispersion media, diluents, or other liquid vehicles, dispersion or suspension aids, surface active agents, isotonic agents, thickening or emulsifying agents, preservatives, solid binders, lubricants and the like, as suited to the particular dosage form desired.
• compositions of rAAV particles for administration by injection are solutions in sterile isotonic aqueous buffer.
• the pharmaceutical can also include a solubilizing agent and a local anesthetic such as lignocaine to ease pain at the site of the injection.
• the ingredients are supplied either separately or mixed together in unit dosage form, for example, as a dry lyophilized powder or water free concentrate in a hermetically sealed container such as an ampoule or sachette indicating the quantity of active agent.
• the pharmaceutical is to be administered by infusion, it can be dispensed with an infusion bottle containing sterile pharmaceutical grade water or saline.
• the term “pharmaceutically acceptable carrier” means a pharmaceutically-acceptable material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, manufacturing aid (e.g., lubricant, talc magnesium, calcium or zinc stearate, or steric acid), or solvent encapsulating material, involved in carrying or transporting the compound from one site (e.g., the delivery site) of the body, to another site (e.g., organ, tissue or portion of the body).
• a pharmaceutically-acceptable material, composition or vehicle such as a liquid or solid filler, diluent, excipient, manufacturing aid (e.g., lubricant, talc magnesium, calcium or zinc stearate, or steric acid), or solvent encapsulating material, involved in carrying or transporting the compound from one site (e.g., the delivery site) of the body, to another site (e.g., organ, tissue or portion of the body).
• a pharmaceutically acceptable carrier is “acceptable” in the sense of being compatible with the other ingredients of the formulation and not injurious to the tissue of the subject (e.g., physiologically compatible, sterile, physiologic pH, etc.).
• materials which can serve as pharmaceutically-acceptable carriers include: (1) sugars, such as lactose, glucose and sucrose; (2) starches, such as corn starch and potato starch; (3) cellulose, and its derivatives, such as sodium carboxymethyl cellulose, methylcellulose, ethyl cellulose, microcrystalline cellulose and cellulose acetate; (4) powdered tragacanth; (5) malt; (6) gelatin; (7) lubricating agents, such as magnesium stearate, sodium lauryl sulfate and talc; (8) excipients, such as cocoa butter and suppository waxes; (9) oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; (10) glycols
• the rAAV particle pharmaceutical compositions of this disclosure may be administered or packaged as a unit dose, for example.
• unit dose ⁇ when used in reference to a pharmaceutical composition of the present disclosure refers to physically discrete units suitable as unitary dosage for the subject, each unit containing a predetermined quantity of active material calculated to produce the desired therapeutic effect in association with the required diluent, i.e., a carrier or vehicle.
• the disclosure provides the rAAV vector nucleic acid sequences set forth below.
• the disclosed vectors comprise a nucleic acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or at least 99.5% sequence identity to any of SEQ ID NOs: 100-102.
• the disclosed vectors the nucleic acid sequence of any of SEQ ID NOs: 100- 102. The components of each sequence, along with the ITR-to-ITR length, is indicated.
• any of the vectors described herein may comprise a nucleic acid sequence having 1-5 5-10 10-15 15-20 20-25 25-30 30-35 35-40 40-45 45-50 or more than 50 nucleotides that differ relative to the sequence of any of SEQ ID NOs: 100-102. These differences may comprise nucleotides that have been inserted, deleted, or substituted relative to any of SEQ ID NOs: 100-102.
• the disclosed vectors contain stretches of about 50, about 75, about 100, about 125, about 150, about 175, about 200, about 300, about 400, about 500, or more than 500 consecutive nucleotides in common with any of SEQ ID NOs: 100-102.
• the nucleic acid molecule comprises a DNA, e.g., a single-stranded DNA or a double-stranded DNA.
• the target sequence of the nucleic acid molecule may comprise a target nucleobase pair containing an adenine (A).
• the target sequence of the nucleic acid molecule may comprise a target nucleobase pair containing a cytosine (C).
• the target sequence may be a genomic sequence, e.g., a human genomic sequence.
• the target sequence may comprise a sequence, e.g., a target sequence with point mutation, associated with a disease or disorder.
• the target sequence with a point mutation may be associated with cardiovascular disease.
• the target nucleotide sequence is a DNA sequence in a genome, e.g., a eukaryotic genome.
• the target nucleotide sequence is in a mammalian (e.g., a human) genome.
• the target nucleotide sequence is in a human genome.
• the target nucleotide sequence is in the genome of a rodent, such as a mouse or a rat.
• the target nucleotide sequence is in the genome of a domesticated animal, such as a horse, cat, dog, or rabbit.
• the target nucleotide sequence is in the genome of a research animal.
• the target nucleotide sequence is in the genome of a genetically engineered non-human subject. In some embodiments, the target nucleotide sequence is in the genome of a plant. In some embodiments, the target nucleotide sequence is in the genome of a microorganism, such as a bacteria. [00291] In some embodiments, the disclosed AAV-encoded base editors exhibit low off- target effects, such as low off-target editing frequencies. In some embodiments, the disclosed AAV-encoded base editors exhibit low off-target editing frequencies while exhibiting high on-target editing efficiencies.
• use of the TadA-8e deaminase or TadA-8e(V106W) deaminase in any fo the disclosed AAV-encoded adenine base editors may exhibit off-target editing frequencies of 0.32% or less while maintaining on-target editing efficiencies of about 80% or more. See PCT Publication No. WO 2021/158921, published August 12, 2021. [00292]
• the disclosed base editors may provide (or yield) on-target editing efficiencies of greater than 50% or greater than 60% (such as greater than 70%, greater than 75%, greater than 80%, or greater than 85%) at the target nucleobase pair for one or more base editors under evaluation.
• any of the disclosed methods of editing may yield an on-target editing efficiency of at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, or at least about 85%.
• the disclosed BEs and editing methods comprising the step of contacting a cell comprising a target DNA sequence with any of the disclosed BEs result in an actual or average off-target DNA editing frequency of about 2.0% or less, 1.75% or less, 1.5% or less, 1.2% or less, 1% or less, 0.9% or less, 0.8% or less, 0.75% or less, 0.7% or less, 065% or less or 06% or less
• These off-target editing frequencies may be obtained in sequences having any level of sequence identity to the target sequence.
• the modifier “average” refers to a mean value over all editing events detected at sites other than a given target nucleobase pair (e.g., as detected by high-throughput sequencing).
• the disclosed editing methods result in an on-target DNA base editing efficiency of at least about 35%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 95%, 98%, or 99% at the target nucleobase pair.
• the step of contacting may result in in a DNA base editing efficiency of at least about 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, or 75%.
• the step of contacting results in on- target base editing efficiencies of greater than 75%.
• the step of contacting may result in in a DNA base editing efficiencies of between 60 and 85%.
• base editing efficiencies of greater than 85% may be realized.
• any of the disclosed rAAV vectors or particle Upon administration of any of the disclosed rAAV vectors or particle to cardiac tissue or muscle tissue (e.g., skeletal muscle tissue), editing efficiencies of at least about 20%, at least about 22%, at least about 24%, at least about 27%, at least about 30%, at least about 33%, or at least about 36%, may be realized. These editing efficiencies represent between 2- and 2.5-fold increases relative to the editing efficiencies in cardiac and muscle tissues reported for dual AAV vectors.
• indel rates of 2.5% or less, 2.0% or less, 1.5% or less, 1.2% or less, or 1.0% or less in the cardiac cell or muscle cell may be realized.
• the disclosed editing methods result in a ratio of on- target:off-target editing of about 25:1, 50:1, 65:1, 75:1, 80:1, 85:1, 90:1, 95:1, 100:1, 110:1, 125:1, or more than 125:1.
• the disclosed editing methods result in a ratio of on-target:off-target editing of about 150:1, 200:1, 300:1, 400:1, 500:1, 600:1, 700:1, 800:1, 900:1, 1000:1, 1100:1, 1200:1, 1250:1, 1275:1, 1300:1, 1325:1, 1350:1, 1400:1, 1500:1, or more than 1500:1.
• a ratio of on-target:off-target editing is equivalent to a ratio of sequencing reads reflecting on-target deaminations relative to deaminations of known or predicted off-target sites, or candidate off-target sites.
• Candidate off-target sites may be identified and hence the ratio of on-target:off-target editing may be measured, using an experimental assay or a computation algorithm (e.g., Cas-OFFinder).
• candidate off-target sites may be identified using an experimental assay such as EndoV-Seq, GUIDE-Seq, or CIRCLE-Seq.
• the ratios of on-target editing:off-target editing relies on the use of EndoV-Seq.
• the disclosed editing methods result in, and the disclosed base editors generate, a minimal degree of bystander edits (i.e., synonymous off-target point mutations at nucleobases that are near the target base and do not change the outcome of the intended editing method).
• the disclosed editing methods result in less than 10, less than 9, less than 8, less than 7, less than 6, less than 5, less than 4, less than 3, less than 2, less than 1, or zero non-silent bystander edits.
• editing methods using the disclosed single-AAV encoded SaKKH-ABE8e editor in liver tissue may result in few (i.e., minimal) non-silent bystander edits.
• adenine base editors are capable of modifying a specific DNA base without generating a significant proportion of indels.
• An “indel”, as used herein, refers to the insertion or deletion of a nucleotide base within a DNA substrate. Such insertions or deletions can lead to frame shift mutations within a coding region of a gene.
• it is desirable to generate adenine base editors that efficiently modify e.g.
• the disclosed editing methods that use the disclosed BEs may result in less than 20%, 19%, 18%, 16%, 14%, 12%, 10%, 8%, 6%, 4%, 2%, 1.5%, 1%, 0.5%, 0.2%, or 0.1% indel formation in a a nucleic acid (e.g., a DNA) comprising a target sequence.
• a nucleic acid e.g., a DNA
• the disclosed editing methods result in an indel rate of 2.5% or less, 2.0% or less, 1.5% or less, 1.2% or less, or 1.0% or less. See FIGs.11A, 11B, and 15.
• the disclosed editing methods result in a base edit:indel ratio of at least about 5:1, 7:1, 8:1, 9:1, 10:1, 11:1, 12:1, 13:1 or greater than about 15:1.
• Some aspects of the disclosure are based on the recognition that any of the base editors provided herein are capable of efficiently generating an intended mutation, such as a point mutation, in DNA (e.g.
• an intended mutation is a mutation that is generated by a specific base editor bound to a gRNA, specifically designed to generate the intended mutation (e.g. deamination).
• the intended mutation is a mutation associated with a disease or disorder, such as sickle cell disease.
• the intended mutation is an adenine (A) to guanine (G) point mutation associated with a disease or disorder.
• the intended mutation is a thymine (T) to cytosine (C) point mutation associated with a disease or disorder.
• the intended mutation is an adenine (A) to guanine (G) point mutation within the coding region of a gene. In some embodiments, the intended mutation is a thymine (T) to cytosine (C) point mutation within the coding region of a gene. [00303] In some embodiments, the intended mutation is a deamination that generates a stop codon, for example, a premature stop codon within the coding region of a gene. In some embodiments, the intended mutation is a mutation that eliminates a stop codon. In some embodiments, the intended mutation eliminates a stop codon comprising the nucleic acid sequence 5′-TAG-3′, 5′-TAA-3′, or 5′-TGA-3′.
• the intended mutation is a deamination that alters the regulatory sequence of a gene (e.g., a gene promoter or gene repressor).
• the intended mutation is a deamination introduced into the gene promoter.
• the deamination introduced into the gene promoter leads to a decrease in the transcription of a gene operably linked to the gene promoter.
• the deamination leads to an increase in the transcription of a gene operably linked to the gene promoter.
• the intended mutation is a deamination that alters the splicing of a genetic sequence, or gene.
• the intended deamination results in the introduction of a splice site in a gene. In other embodiments, the intended deamination results in the removal of a splice site. In some embodiments, the intended deamination results in the introduction of a stop codon in a gene. In other embodiments, the intended deamination results in the removal of a stop codon. [00306] In some embodiments, any of the base editors provided herein are capable of generating a ratio of intended mutations to unintended mutations (e.g., intended point mutations:unintended point mutations) that is greater than 1:1.
• any of the base editors provided herein are capable of generating a ratio of intended mutations to unintended mutations (eg intended point mutations:unintended point mutations) that is at least 1.5:1, at least 2:1, at least 2.5:1, at least 3:1, at least 3.5:1, at least 4:1, at least 4.5:1, at least 5:1, at least 5.5:1, at least 6:1, at least 6.5:1, at least 7:1, at least 7.5:1, at least 8:1, at least 10:1, at least 12:1, at least 15:1, at least 20:1, at least 25:1, at least 30:1, at least 40:1, at least 50:1, at least 100:1, at least 150:1, at least 200:1, at least 250:1, at least 500:1, or at least 1000:1, or more.
• intended point mutations:unintended point mutations eg intended point mutations:unintended point mutations
• RNA editing effects refers to the introduction of modifications (e.g. deaminations) of nucleotides within cellular RNA, e.g., messenger RNA (mRNA).
• modifications e.g. deaminations
• mRNA messenger RNA
• RNA editing effects are “low” or “reduced” when a detected mutation is introduced into RNA molecules at a frequency of 0.3% or less.
• the present disclosure further provides methods of administering the disclosed base editors wherein the method yields reduced and/or low RNA editing effects.
• the present disclosure further provides base editors (such as the disclosed ABEs) that induce (or yield, provide or cause) low and/or undetectable RNA editing effects (see FIG.17).
• the base editors provide an average adenosine (A) to inosine (I) (A-to-I) editing frequency in cellular mRNA transcripts of 0.3% or less. In some embodiments, the base editors provide an average adenosine (A) to inosine (I) (A-to-I) actual and/or consistent editing frequencies in RNA of about 0.3% or less. The base editors may provide actual or average A-to-I editing frequencies in RNA of about 0.5% or less, 0.4% or less, 0.35% or less, 0.25% or less, 0.2% or less, 0.15% or less, 0.12% or less, 0.1% or less, 0.08% or less, or 0.075% or less.
• Guide sequences (e.g., guide RNAs) [00309]
• the present disclosure further provides guide RNAs for use in accordance with the disclosed methods of editing.
• the disclosure provides guide RNAs that are designed to recognize target sequences.
• Such gRNAs may be designed to have guide sequences (or “spacers”) having complementarity to a protospacer within the target sequence.
• Guide RNAs are also provided for use with one or more of the disclosed base editors, e.g., in the disclosed methods of editing a nucleic acid molecule.
• Such gRNAs may be designed to have guide sequences having complementarity to a protospacer within a target sequence to be edited, and to have backbone sequences that interact specifically with the napDNAbp domains of any of the disclosed base editors, such as Cas9 nickase domains of the disclosed base editors.
• Guide RNAs in accordance with the disclosed methods of editing may have complementarity to any of the protospacer sequences listed in Table 1 (SEQ ID NOs: 430-565).
• the base editors may be complexed, bound, or otherwise associated with (e.g., via any type of covalent or non-covalent bond) one or more guide sequences.
• the guide sequence becomes associated or bound to the base editor and directs its localization to a specific target sequence having complementarity to the guide sequence or a portion thereof.
• the particular design embodiments of a guide sequence will depend upon the nucleotide sequence of a genomic target sequence (i.e., the desired site to be edited) and the type of napDNAbp (e.g., type of Cas9 protein) present in the base editor, among other factors, such as PAM sequence locations, percent G/C content in the target sequence, the degree of microhomology regions, secondary structures, etc.
• a guide sequence is any polynucleotide sequence having sufficient complementarity with a target polynucleotide sequence to hybridize with the target sequence and direct sequence-specific binding of the napDNAbp (e.g., a Cas9 or Cas9 variant) to the target sequence.
• the degree of complementarity between a guide sequence and its corresponding target sequence when optimally aligned using a suitable alignment algorithm, is about or more than about 50%, 60%, 75%, 80%, 85%, 90%, 95%, 97.5%, 99%, or more.
• Optimal alignment may be determined with the use of any suitable algorithm for aligning sequences, non-limiting example of which include the Smith- Waterman algorithm, the Needleman-Wunsch algorithm, algorithms based on the Burrows- Wheeler Transform (e.g., the Burrows Wheeler Aligner), ClustalW, Clustal X, BLAT, Novoalign (Novocraft Technologies, ELAND (Illumina, San Diego, Calif.), SOAP (available at soap.genomics.org.cn), and Maq (available at maq.sourceforge.net).
• any suitable algorithm for aligning sequences non-limiting example of which include the Smith- Waterman algorithm, the Needleman-Wunsch algorithm, algorithms based on the Burrows- Wheeler Transform (e.g., the Burrows Wheeler Aligner), ClustalW, Clustal X, BLAT, Novoalign (Novocraft Technologies, ELAND (Illumina, San Diego, Calif.), SOAP (available at soap.genomics.org
• a guide sequence is about or more than about 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 75, or more nucleotides in length. In some embodiments, a guide sequence is less than about 75, 50, 45 40 35 30 25 20 15 12 or fewer nucleotides in length. In some embodiments the guide RNA is 15-300, 25-300, 50-300, 25-250, 25-200, 15-200, or 15-100 nucleotides in length. In some embodiments, the guide RNA is between about 25 and 200 nucleotides in length.
• the guide RNA is between about 15 and 200, or between 15 and 100, nucleotides in length.
• the ability of a guide sequence to direct sequence-specific binding of a base editor to a target sequence may be assessed by any suitable assay.
• the components of a base editor, including the guide sequence to be tested may be provided to a host cell having the corresponding target sequence, such as by transfection with vectors encoding the components of a base editor disclosed herein, followed by an assessment of preferential cleavage within the target sequence.
• cleavage of a target polynucleotide sequence may be evaluated in situ by providing the target sequence, components of a base editor, including the guide sequence to be tested and a control guide sequence different from the test guide sequence, and comparing binding or rate of cleavage at the target sequence between the test and control guide sequence reactions.
• Other assays are possible, and will occur to those skilled in the art.
• a guide sequence may be selected to target any target sequence.
• the target sequence is a sequence within a genome of a cell.
• Exemplary target sequences include those that are unique in the target genome.
• a guide sequence is selected to reduce the degree of secondary structure within the guide sequence.
• Secondary structure may be determined by any suitable polynucleotide folding algorithm. Some programs are based on calculating the minimal Gibbs free energy. An example of one such algorithm is mFold, as described by Zuker & Stiegler (Nucleic Acids Res.9 (1981), 133-148). Another example folding algorithm is the online webserver RNAfold, developed at Institute for Theoretical Chemistry at the University of Vienna, using the centroid structure prediction algorithm (see, e.g., A. R. Gruber et al., 2008, Cell 106(1): 23-24; and PA Carr & GM Church, 2009, Nature Biotechnology 27(12): 1151-62). Additional algorithms may be found in Chuai, G.
• the guide sequence of the gRNA is linked to a tracr mate (also known as a “backbone”) sequence which in turn hybridizes to a tracr sequence.
• tracr mate also known as a “backbone”
• a tracr mate sequence includes any sequence that has sufficient complementarity with a tracr sequence to promote one or more of: (1) excision of a guide sequence flanked by tracr mate sequences in a cell containing the corresponding tracr sequence; and (2) formation of a complex at a target sequence, wherein the complex comprises the tracr mate sequence hybridized to the tracr sequence.
• degree of complementarity is with reference to the optimal alignment of the tracr mate sequence and tracr sequence, along the length of the shorter of the two sequences.
• Optimal alignment may be determined by any suitable alignment algorithm, and may further account for secondary structures, such as self-complementarity within either the tracr sequence or tracr mate sequence.
• the degree of complementarity between the tracr sequence and tracr mate sequence along the length of the shorter of the two when optimally aligned is about or more than about 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97.5%, 99%, or higher.
• the tracr sequence is about or more than about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50, or more nucleotides in length.
• the tracr sequence and tracr mate sequence are contained within a single transcript, such that hybridization between the two produces a transcript having a secondary structure, such as a hairpin.
• Preferred loop forming sequences for use in hairpin structures are four nucleotides in length, and most preferably have the sequence GAAA. However, longer or shorter loop sequences may be used, as may alternative sequences.
• the sequences preferably include a nucleotide triplet (for example, AAA), and an additional nucleotide (for example C or G). Examples of loop forming sequences include CAAA and AAAG.
• the transcript or transcribed polynucleotide sequence has at least two or more hairpins. In certain embodiments, the transcript has two, three, four or five hairpins. In a further embodiment of the invention, the transcript has at most five hairpins.
• the single transcript further includes a transcription termination sequence; preferably this is a polyT sequence, for example six T nucleotides.
• the guide RNAs for use in accordance with the disclosed methods of editing comprise synthetic single guide RNAs (sgRNAs) containing modified ribonucleotides.
• the guide RNAs contain modifications such as 2′-O- methylated nucleotides and phosphorothioate linkages.
• the guide RNAs contain 2′-O-methyl modifications in the first three and last three nucleotides, and phosphorothioate bonds between the first three and last three nucleotides.
• the guide RNAs for use in accordance with the disclosed methods of editing comprise a backbone structure that is recognized by an N. meningitis Cas9 protein or domain, such as an Nme2Cas9 domain.
• the backbone structure (or scaffold) recognized by an Nme2Cas9 protein may comprise the sequence provided below: 5′-[guide sequence]- gttgtagctccctttctcatttcggaaacgaaatgagaaccgttgctacaataaggccgtctgaaagatgtgccgcaacgctctgcccc ttaaagcttctgcttttaaggggcatcgtttta-3′ (SEQ ID NO: 719).
• This scaffold sequence is recognized by the NmeCas9, Nme1Cas9, Nme2Cas9, and Nme3Cas9 proteins.
• guide RNAs for editing with base editors containing Nme2Cas9 domains and variants thereof are described in Edraki et al., Molecular Cell 73, 714-726, incorporated herein by reference.
• the guide RNAs for use in accordance with the disclosed methods of editing comprise a backbone structure that is recognized by an S. pyogenes Cas9 protein or domain, such as an SpCas9 domain of the disclosed base editors.
• the backbone structure recognized by an SpCas9 protein may comprise the sequence 5′-[guide sequence]- guuuuagagcuagaaauagcaaguuaaaauaaggcuaguccguuaucaacuugaaaaaguggcaccgagucggugcuuu uu-3′ (SEQ ID NO: 339), wherein the guide sequence comprises a sequence that is complementary to the protospacer of the target sequence. See U.S. Publication No. 2015/0166981, published June 18, 2015, the disclosure of which is incorporated herein by reference.
• the guide sequence is typically 20 nucleotides long.
• the guide RNAs for use in accordance with the disclosed methods of editing comprise a backbone structure that is recognized by an C. jejuni Cas9 protein or domain, such as a CjCas9 domain of the disclosed base editors.
• the backbone structure recognized by a CjCas9 protein may comprise the sequence 5′-[guide sequence]- gttttagtccctgaaaagggactaaaataaagagtttgcgggactctgcggggttacaatcccctaaaccgctttttttt-3′ (SEQ ID NO: 340), wherein the guide sequence comprises a sequence that is complementary to the protospacer of the target sequence.
• the guide RNAs for use in accordance with the disclosed methods of editing comprise a backbone structure that is recognized by an S. aureus Cas9 protein.
• the backbone structure recognized by an SaCas9 protein may comprise the sequence 5′-[guide sequence]- guuuuaguacucuguaaugaaaauuacagaaucuacuaaaacaaggcaaaaugccguguuuaucucgucaacuuguugg cgagauuuuuuuuu-3′ (SEQ ID NO: 78).
• the guide RNAs for use in accordance with the disclosed methods of editing may comprise a backbone structure as listed in Table 2 (SEQ ID NOs: 566-571)..
• the sequences of suitable guide RNAs for targeting the disclosed BEs to specific genomic target sites will be apparent to those of skill in the art based on the present disclosure.
• Such suitable guide RNA sequences typically comprise guide sequences that are complementary to a nucleic sequence within 50 nucleotides upstream or downstream of the target nucleobase pair to be edited.
• Some exemplary guide RNA sequences suitable for targeting any of the provided BEs to specific target sequences are provided herein.
• Additional guide sequences are well known in the art and may be used with the base editors described herein. Additional exemplary guide sequences are disclosed in, for example, Jinek M., et al., Science 337:816-821(2012); Mali P, Esvelt KM & Church GM (2013) Cas9 as a versatile tool for engineering biology, Nature Methods, 10, 957-963; Li JF et al., (2013) Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9, Nature Biotechnology, 31, 688-691; Hwang, W.Y.
• the invention further relates in various aspects to methods of making the disclosed improved base editors by various modes of manipulation that include, but are not limited to, codon optimization to achieve greater expression levels in a cell, and the use of nuclear localization sequences (NLSs), preferably at least two NLSs, e.g., two bipartite NLSs, to increase the localization of the expressed base editors into a cell nucleus.
• NLSs nuclear localization sequences
• the base editors contemplated herein can include modifications that result in increased expression, for example, through codon optimization.
• the base editors (or a component thereof) is codon optimized for expression in particular cells, such as eukaryotic cells.
• the eukaryotic cells may be those of or derived from a particular organism, such as a mammal, including, but not limited to, human, mouse, rat, rabbit, dog, or non-human primate.
• codon optimization refers to a process of modifying a nucleic acid sequence for enhanced expression in the host cells of interest by replacing at least one codon (e.g.
• Codon bias differences in codon usage between organisms
• mRNA messenger RNA
• tRNA transfer RNA
• genes can be tailored for optimal gene expression in a given organism based on codon optimization.
• Codon usage tables are readily available, for example, at the “Codon Usage Database”, and these tables can be adapted in a number of ways. See Nakamura, Y., et al. “Codon usage tabulated from the international DNA sequence databases: status for the year 2000” Nucl. Acids Res.28:292 (2000).
• Computer algorithms for codon optimizing a particular sequence for expression in a particular host cell are also available, such as Gene Forge (Aptagen; Jacobus, Pa.), are also available.
• one or more codons in a sequence encoding a CRISPR enzyme correspond to the most frequently used codon for a particular amino acid.
• the base editors provided herein further comprise one or more nuclear targeting sequences, for example, a nuclear localization sequence (NLS).
• a NLS comprises an amino acid sequence that facilitates the importation of a protein, that comprises an NLS, into the cell nucleus (e.g., by nuclear transport).
• any of the base editors provided herein further comprise one or more nuclear localization sequences (NLSs).
• any of the base editors comprise two NLSs.
• one or more of the NLSs are bipartite NLSs (“bpNLS”).
• the disclosed base editors comprise two bipartite NLSs.
• the disclosed base editors comprise more than two bipartite NLSs.
• the NLS is fused to the N-terminus of the base editor.
• the NLS is fused to the C-terminus of the base editor.
• the NLS is fused to the C-terminus of the napDNAbp.
• the NLS is fused to the N-terminus of the adenosine deaminase.
• the NLS is fused to the C-terminus of the adenosine deaminase. In some embodiments, the NLS is fused to the base editor via one or more linkers. In some embodiments, the NLS is fused to the base editor without a linker. [00330] In some embodiments, the NLS comprises an amino acid sequence of any one of the NLS sequences provided or referenced herein. In some embodiments, the NLS comprises an amino acid sequence as set forth in SEQ ID NO: 408 or SEQ ID NO: 409. Additional nuclear localization sequences are known in the art and would be apparent to the skilled artisan.
• a NLS comprises the amino acid sequence PKKKRKV (SEQ ID NO: 408), MDSLLMNRRKFLYQFKNVRWAKGRRETYLC (SEQ ID NO: 409), KRTADGSEFESPKKKRKV (SEQ ID NO: 410), or KRTADGSEFEPKKKRKV (SEQ ID NO: 411).
• the NLS comprises the amino acid sequence: NLSKRPAAIKKAGQAKKKK (SEQ ID NO: 482), PAAKRVKLD (SEQ ID NO: 483), RQRRNELKRSF (SEQ ID NO: 484), or NQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGY (SEQ ID NO: 485).
• the base editor comprises a bpNLS.
• the bpNLS may comprise an amino acid sequence selected from the group consisting of: KRTADGSEFEPKKKRKV (SEQ ID NO: 398), KRPAATKKAGQAKKKK (SEQ ID NO: 344), KKTELQTTNAENKTKKL (SEQ ID NO: 345), KRGINDRNFWRGENGRKTR (SEQ ID NO: 346), and RKSGKIAAIVVKRPRK (SEQ ID NO: 347).
• the bpNLA comprises the amino acid sequence set forth in SEQ ID NO: 344 or 398.
• the base editors provided herein do not comprise a linker.
• a linker is present between one or more of the domains or proteins (e.g., deaminase, napDNAbp, and/or NLS).
• the “]-[” used in the general architecture above indicates the presence of an optional linker [00333]
• the general architecture of exemplary base editors with a first adenosine deaminase, a second adenosine deaminase, and a napDNAbp domain comprises any one of the following structures, where NLS is a nuclear localization sequence (e.g., any NLS provided herein), NH2 is the N-terminus of the base editor, and COOH is the C-terminus of the base editor.
• Exemplary base editors comprising a deaminase, a napDNAbp domain, and an NLS (e.g., any NLS provided herein) may have the following architecture: NH 2 -[deaminase domain]-[napDNAbp domain]-[NLS]-COOH; NH 2 -[napDNAbp domain]-[deaminase domain]-[NLS]-COOH; NH2-[NLS]-[deaminase domain]-[napDNAbp domain]-COOH; or NH2-[NLS]-[napDNAbp domain]-[deaminase domain]-COOH.
• the disclosed base editors comprise the ABE architecture that follows, where TadA-8e is the adenosine deaminase domain: NH2-[bpNLS]-[TadA-8e]-[napDNAbp domain]-[bpNLS]-COOH; NH 2 -[bpNLS]-[napDNAbp domain]-[TadA-8e]-[bpNLS]-COOH; NH 2 -[bpNLS]-[TadA-8e]-[napDNAbp domain]-[bpNLS]-COOH; or NH2-[bpNLS]-[napDNAbp domain]-[TadA-8e]-[bpNLS]-COOH.
• Exemplary base editors comprising a cytidine deaminase, a napDNAbp domain, a UGI domain, and an NLS (e.g., any NLS provided herein) may have the following architecture: NH2-[napDNAbp domain]-[cytidine deaminase domain]-[UGI domain]- [bpNLS]-COOH; or NH2-[bpNLS]-[napDNAbp domain]-[cytidine deaminase domain]-[UGI domain]-COOH; NH 2 -[cytidine deaminase domain]-[napDNAbp domain]-[UGI domain]- [bpNLS]-COOH; or NH2-[bpNLS]-[cytidine deaminase domain]-[napDNAbp domain]-[UGI domain]-COOH.
• a representative nuclear localization signal is a peptide sequence that directs the protein to the nucleus of the cell in which the sequence is expressed.
• a nuclear localization signal is predominantly basic, can be positioned almost anywhere in a protein's amino acid sequence, generally comprises a short sequence of four amino acids (Autieri & Agrawal, (1998) J. Biol. Chem.273: 14731-37, incorporated herein by reference) to eight amino acids, and is typically rich in lysine and arginine residues (Magin et al., (2000) Virology 274: 11-16, incorporated herein by reference). Nuclear localization signals often comprise proline residues.
• NLSs can be classified in three general groups: (i) a monopartite NLS exemplified by the SV40 large T antigen NLS (PKKKRKV (SEQ ID NO: 408)); (ii) a bipartite motif consisting of two basic domains separated by a variable number of spacer amino acids and exemplified by the Xenopus nucleoplasmin NLS (KRXXXXXXXXXKKKL (SEQ ID NO: 486)); and (iii) noncanonical sequences such as M9 of the hnRNP Al protein, the influenza virus nucleoprotein NLS, and the yeast Gal4 protein NLS (Dingwall and Laskey, Trends Biochem Sci.1991 Dec;16(12):478-81).
• Nuclear localization signals appear at various points in the amino acid sequences of proteins. NLSs have been identified at the N-terminus, the C-terminus, and in the central region of proteins. Thus, the specification provides base editors that may be modified with one or more NLSs at the C-terminus, the N-terminus, as well as at in internal region of the base editor. The residues of a longer sequence that do not function as component NLS residues should be selected so as not to interfere, for example tonically or sterically, with the nuclear localization signal itself. Therefore, although there are no strict limits on the composition of an NLS-comprising sequence, in practice, such a sequence can be functionally limited in length and composition.
• the present disclosure contemplates any suitable means by which to modify a fusion protein (or base editor) to include one or more NLSs.
• the base editors can be engineered to express a fusion protein that is translationally fused at its N-terminus or its C-terminus (or both) to one or more NLSs, i.e., to form a fusion protein-NLS fusion construct.
• the fusion protein-encoding nucleotide sequence can be genetically modified to incorporate a reading frame that encodes one or more NLSs in an internal region of the encoded fusion protein.
• the NLSs may include various amino acid linkers or spacer regions encoded between the fusion protein and the N- terminally, C-terminally, or internally-attached NLS amino acid sequence.
• the present disclosure also provides for nucleotide constructs, vectors, and host cells for expressing base editors that comprise a fusion protein and one or more NLSs.
• the base editors described herein may also comprise nuclear localization signals which are linked to a fusion protein through one or more linkers, e.g., polymeric, amino acid, polysaccharide chemical or nucleic acid linker element
• the NLS is linked to a fusion protein using an XTEN linker, as set forth in SEQ ID NO: 412.
• linkers within the contemplated scope of the disclosure are not intented to have any limitations and can be any suitable type of molecule (e.g., polymer, amino acid, polysaccharide, nucleic acid, lipid, or any synthetic chemical linker domain) and be joined to the fusion protein by any suitable strategy that effectuates forming a bond (e.g., covalent linkage, hydrogen bonding) between the fusion protein and the one or more NLSs.
• the base editors described herein also may include one or more additional elements.
• an additional element may comprise an effector of base repair, such as an inhibitor of base repair.
• the base editors described herein may comprise one or more heterologous protein domains (e.g., about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more domains in addition to the base editors components).
• a base editor may comprise any additional protein sequence, and optionally a linker sequence between any two domains.
• Other exemplary features that may be present are localization sequences, such as cytoplasmic localization sequences, export sequences, such as nuclear export sequences, or other localization sequences, as well as sequence tags.
• heterologous protein domains that may be fused to a base editor or component thereof (e.g., the napDNAbp domain, the nucleotide modification domain, or the NLS domain) include, without limitation, epitope tags and reporter gene sequences.
• epitope tags include histidine (His) tags, V5 tags, FLAG tags, influenza hemagglutinin (HA) tags, Myc tags, VSV-G tags, and thioredoxin (Trx) tags.
• reporter genes include, but are not limited to, glutathione-5-transferase (GST), horseradish peroxidase (HRP), chloramphenicol acetyltransferase (CAT), beta-galactosidase, beta- glucuronidase, luciferase, green fluorescent protein (GFP), HcRed, DsRed, cyan fluorescent protein (CFP), yellow fluorescent protein (YFP), and autofluorescent proteins including blue fluorescent protein (BFP).
• GST glutathione-5-transferase
• HRP horseradish peroxidase
• CAT chloramphenicol acetyltransferase
• beta-galactosidase beta-galactosidase
• beta-glucuronidase beta-galactosidase
• luciferase green fluorescent protein
• GFP green fluorescent protein
• HcRed HcRed
• DsRed cyan fluorescent protein
• YFP
• a base editor may be fused to a gene sequence encoding a protein or a fragment of a protein that binds DNA molecules or binds other cellular molecules, including, but not limited to, maltose binding protein (MBP), S-tag, Lex A DNA binding domain (DBD) fusions, GAL4 DNA binding domain fusions, and herpes simplex virus (HSV) BP16 protein fusions. Additional domains that may form part of a base editor are described in US Patent Publication No.2011/0059502, published March 10, 2011, and incorporated herein by reference in its entirety.
• a reporter gene which includes, but is not limited to, glutathione-5-transferase (GST), horseradish peroxidase (HRP), chloramphenicol acetyltransferase (CAT) beta-galactosidase, beta-glucuronidase, luciferase, green fluorescent protein (GFP), HcRed, DsRed, cyan fluorescent protein (CFP), yellow fluorescent protein (YFP), and autofluorescent proteins including blue fluorescent protein (BFP), may be introduced into a cell to encode a gene product which serves as a marker by which to measure the alteration or modification of expression of the gene product.
• GST glutathione-5-transferase
• HRP horseradish peroxidase
• CAT chloramphenicol acetyltransferase
• beta-galactosidase beta-galactosidase
• beta-glucuronidase beta-galactosidase
• the gene product is luciferase. In a further embodiment of the disclosure the expression of the gene product is decreased.
• Other exemplary features that may be present are tags that are useful for solubilization, purification, or detection of the base editor.
• Suitable protein tags include, but are not limited to, biotin carboxylase carrier protein (BCCP) tags, myc- tags, calmodulin-tags, FLAG-tags, hemagglutinin (HA)-tags, bgh-PolyA tags, polyhistidine tags, and also referred to as histidine tags or His-tags, maltose binding protein (MBP)-tags, nus-tags, glutathione-S-transferase (GST)-tags, green fluorescent protein (GFP)-tags, thioredoxin-tags, S-tags, Softags (e.g., Softag 1, Softag 3), strep-tags , biotin ligase tags, FlAsH tags, V5 tags, and SBP-tags.
• BCCP biotin carboxylase carrier protein
• MBP maltose binding protein
• GST glutathione-S-transferase
• GFP green fluorescent protein
• Softags e.g.,
• the base editor comprises one or more His tags.
• Linkers may be used to link any of the peptides or peptide domains or domains of the base editor (e.g., a napDNAbp domain covalently linked to an adenosine deaminase domain which is covalently linked to an NLS domain).
• the base editors described herein may comprise linkers of 32 amino acids in length.
• the linker may be as simple as a covalent bond, or it may be a polymeric linker many atoms in length. In certain embodiments, the linker is a polypeptide or based on amino acids.
• the linker is not peptide-like.
• the linker is a covalent bond (e.g., a carbon-carbon bond, disulfide bond, carbon-heteroatom bond, etc.).
• the linker is a carbon-nitrogen bond of an amide linkage.
• the linker is a cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic or heteroaliphatic linker.
• the linker is polymeric (e.g., polyethylene, polyethylene glycol, polyamide, polyester, etc.).
• the linker comprises a monomer, dimer, or polymer of aminoalkanoic acid.
• the linker comprises an aminoalkanoic acid (e.g., glycine, ethanoic acid, alanine, beta-alanine, 3-aminopropanoic acid, 4-aminobutanoic acid, 5- pentanoic acid, etc.).
• the linker comprises a monomer, dimer, or polymer of aminohexanoic acid (Ahx).
• the linker is based on a carbocyclic moiety (e.g., cyclopentane, cyclohexane).
• the linker comprises a polyethylene glycol moiety (PEG). In other embodiments, the linker comprises amino acids. In certain embodiments, the linker comprises a peptide. In certain embodiments, the linker comprises an aryl or heteroaryl moiety. In certain embodiments, the linker is based on a phenyl ring.
• the linker may include functionalized moieties to facilitate attachment of a nucleophile (e.g., thiol, amino) from the peptide to the linker. Any electrophile may be used as part of the linker.
• Exemplary electrophiles include, but are not limited to, activated esters, activated amides, Michael acceptors, alkyl halides, aryl halides, acyl halides, and isothiocyanates.
• the linker is 5-100 amino acids in length, for example, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35-40, 40-45, 45-50, 50-60, 60-70, 70-80, 80-90, 90-100, 100-110, 110-120, 120-130, 130-140, 140-150, or 150-200 amino acids in length. Longer or shorter linkers are also contemplated.
• the linker is 32 amino acids in length.
• the linker comprises the 32-amino acid sequence SGGSSGGSSGSETPGTSESATPESSGGSSGGS (SEQ ID NO: 412), also known as an XTEN linker.
• the linker comprises the 9-amino acid sequence SGGSGGSGGS (SEQ ID NO: 413).
• the linker comprises the 4- amino acid sequence SGGS (SEQ ID NO: 414).
• the linker comprises the amino acid sequence (GGGGS)n (SEQ ID NO: 415), (G) n (SEQ ID NO: 416), (EAAAK) n (SEQ ID NO: 417), (GGS) n (SEQ ID NO: 418), (SGGS) n (SEQ ID NO: 419), (XP) n (SEQ ID NO: 420), or any combination thereof, wherein n is independently an integer between 1 and 30, and wherein X is any amino acid.
• the linker comprises the amino acid sequence (GGS) n (SEQ ID NO: 421), wherein n is 1, 3, or 7.
• the linker comprises the amino acid sequence SGSETPGTSESATPES (SEQ ID NO: 422). [00351] In some embodiments, a linker comprises SGSETPGTSESATPES (SEQ ID NO: 422), and SGGS (SEQ ID NO: 414). In some embodiments, a linker comprises SGGSSGSETPGTSESATPESSGGS (SEQ ID NO: 423) In some embodiments a linker comprises SGGSSGGSSGSETPGTSESATPESSGGSSGGS (SEQ ID NO: 412).
• a linker comprises GGSGGSPGSPAGSPTSTEEGTSESATPESGPGTSTEPSEGSAPGSPAGSPTSTEEGTSTE PSEGSAPGTSTEPSEGSAPGTSESATPESGPGSEPATSGGSGGS (SEQ ID NO: 424). In some embodiments, the linker is 24 amino acids in length. In some embodiments, the linker comprises the amino acid sequence SGGSSGGSSGSETPGTSESATPES (SEQ ID NO: 425). In some embodiments, the linker is 40 amino acids in length. In some embodiments, the linker comprises the amino acid sequence SGGSSGGSSGSETPGTSESATPESSGGSSGGSSGGSSGGS (SEQ ID NO: 426). In some embodiments, the linker is 64 amino acids in length.
• the linker comprises the amino acid sequence SGGSSGGSSGSETPGTSESATPESSGGSSGGSSGGSSGGSSGSETPGTSESATPESSGGS SGGS (SEQ ID NO: 427). In some embodiments, the linker is 92 amino acids in length. In some embodiments, the linker comprises the amino acid sequence PGSPAGSPTSTEEGTSESATPESGPGTSTEPSEGSAPGSPAGSPTSTEEGTSTEPSEGSAP GTSTEPSEGSAPGTSESATPESGPGSEPATS (SEQ ID NO: 428).
• any of the linkers provided herein may be used to link a first adenosine deaminase and a second adenosine deaminase; an adenosine deaminase domain (comprising, e.g., a first and/or a second adenosine deaminase) and a napDNAbp; a napDNAbp and an NLS; or an adenosine deaminase domain and an NLS.
• any of the base editors provided herein comprise an adenosine deaminase and a napDNAbp that are fused to each other via a linker.
• any of the base editors provided herein comprise a first adenosine deaminase and a second adenosine deaminase that are fused to each other via a linker.
• any of the base editors provided herein comprise an NLS, which may be fused to an adenosine deaminase (e.g., a first and/or a second adenosine deaminase) and a nucleic acid programmable DNA binding protein (napDNAbp).
• adenosine deaminase e.g., a first and/or a second adenosine deaminase
• napDNAbp nucleic acid programmable DNA binding protein
• adenosine deaminase e.g., an engineered ecTadA
• a napDNAbp e.g., a Cas9 domain
• first adenosine deaminase and a second adenosine deaminase may be employed (e.g., ranging from very flexible linkers of the form of SEQ ID NOs: 119, 121-124 (see, e.g., Guilinger JP, Thompson DB, Liu DR. Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nat.
• n is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15.
• the linker comprises a (GGS) n (SEQ ID NO: 421) motif, wherein n is 1, 3, or 7.
• the adenosine deaminase and the napDNAbp, and/or the first adenosine deaminase and the second adenosine deaminase of any of the base editors provided herein are fused via a linker comprising an amino acid sequence selected from SEQ ID NOs: 119-132.
• the linker is 24 amino acids in length.
• the linker comprises the amino acid sequence (SGGS) 2 - SGSETPGTSESATPES-(SGGS) 2 (SEQ ID NO: 412), which may also be referred to as (SGGS)2-XTEN-(SGGS)2 (SEQ ID NO: 429).
• the linker comprises the amino acid sequence, wherein n is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments, the linker is 40 amino acids in length. In some embodiments, the linker is 64 amino acids in length. In some embodiments, the linker is 92 amino acids in length. [00353] The above description is meant to be non-limiting with regard to making base editors having increased expression, and thereby increase editing efficiencies. Methods of Treatment and Uses [00354] Other aspects of the present disclosure provide methods of delivering the base editor into a cell to form a complete and functional Cas9 protein or nucleobase editor.
• a cell is contacted with a composition described herein (e.g., compositions comprising nucleotide sequences encoding the base editor or AAV particles containing nucleic acid vectors comprising such nucleotide sequences).
• the contacting results in the delivery of such nucleotide sequences into a cell, wherein the N-terminal portion of the Cas9 protein or the nucleobase editor and the C- terminal portion of the Cas9 protein or the nucleobase editor are expressed in the cell and are joined to form a complete Cas9 protein or a complete nucleobase editor.
• any rAAV particle, nucleic acid molecule or composition provided herein may be introduced into the cell in any suitable way, either stably or transiently.
• the disclosed proteins may be transfected into the cell.
• the cell may be transduced or transfected with a nucleic acid molecule.
• a cell may be transduced (e.g., with a virus encoding a protein), or transfected (e.g., with a plasmid encoding a protein) with a nucleic acid molecule that encodes a protein, or an rAAV particle containing a viral genome encoding one or more nucleic acid molecules.
• transduction may be a stable or transient transduction.
• cells expressing a protein or containing a protein may be transduced or transfected with one or more guide RNA sequences, for example in delivery of a base editor.
• a plasmid expressing a protein may be introduced into cells through electroporation, transient (e.g., lipofection) and stable genome integration (e.g., nucleofection or piggybac) and viral transduction or other methods known to those of skill in the art.
• the invention provides methods comprising delivering one or more base editor-encoding polynucleotides, one or more transcripts thereof, and/or one or proteins transcribed therefrom, to a cell using a non-viral delivery method.
• Methods of non- viral delivery of nucleic acids include lipofection, nucleofection, microinjection, biolistics, virosomes, liposomes, immunoliposomes, polycation or lipid:nucleic acid conjugates, naked DNA, artificial virions, and agent-enhanced uptake of DNA. Lipofection is described in e.g., U.S. Pat.
• compositions provided herein comprise a lipid and/or polymer.
• the lipid and/or polymer is cationic. The preparation of such lipid particles is well known.
• the target nucleotide sequence is a DNA sequence in a genome, e.g. a eukaryotic genome. In certain embodiments, the target nucleotide sequence is in a mammalian (e.g. a human) genome.
• the target nucleotide sequence may comprise a target sequence (e.g., a point mutation) associated with a disease, disorder, or condition.
• the target sequence may comprise a T to C (or A to G) point mutation associated with a disease, disorder, or condition, and wherein the deamination of the mutant C base results in mismatch repair-mediated correction to a sequence that is not associated with a disease, disorder, or condition.
• the target sequence may otherwise comprise a G to A (or C to T) point mutation associated with a disease, disorder, or condition, and wherein the deamination of the mutant A base results in mismatch repair-mediated correction to a sequence that is not associated with a disease disorder, or condition.
• the target sequence may encode a protein, and where the point mutation is in a codon and results in a change in the amino acid encoded by the mutant codon as compared to a wild-type codon.
• the target sequence may also be at a splice site, and the point mutation results in a change in the splicing of an mRNA transcript as compared to a wild-type transcript.
• the target may be at a non-coding sequence of a gene, such as a promoter, and the point mutation results in increased or decreased expression of the gene.
• the deamination of a mutant C results in a change of the amino acid encoded by the mutant codon, which in some cases can result in the expression of a wild-type amino acid.
• the deamination of a mutant A results in a change of the amino acid encoded by the mutant codon, which in some cases can result in the expression of a wild-type amino acid.
• the methods described herein involving contacting a cell with a composition or rAAV particle can occur in vitro, ex vivo, or in vivo.
• the step of contacting a cell occurs in a subject.
• the subject has been diagnosed with a disease, disorder, or condition.
• the step of contacting a cell occurs ex vivo, or outside of a subject.
• the methods disclosed herein involve contacting a mammalian cell with a composition or rAAV particle.
• the methods involve contacting a retinal cell, cortical cell or cerebellar cell.
• compositions described herein may be administered to a subject in need thereof in a therapeutically effective amount to treat and/or prevent a disease or disorder the subject is suffering from. Any disease or disorder that maybe treated and/or prevented using CRISPR/Cas9-based genome-editing technology may be treated by the base editor described herein. It is to be understood that, if the nucleotide sequences encoding the base editor does not further encode a gRNA, a separate nucleic acid vector encoding the gRNA may be administered together with the compositions described herein.
• Exemplary suitable diseases, disorders or conditions include, without limitation, cardiovascular disease, cystic fibrosis, phenylketonuria, epidermolytic hyperkeratosis (EHK), chronic obstructive pulmonary disease (COPD), Charcot-Marie-Toot disease type 4J, neuroblastoma (NB), von Willebrand disease (vWD), myotonia congenital, hereditary renal amyloidosis, dilated cardiomyopathy, hereditary lymphedema, familial Alzheimer’s disease, prion disease chronic infantile neurologic cutaneous articular syndrome (CINCA) congenital deafness, Niemann-Pick disease type C (NPC) disease, and desmin-related myopathy (DRM).
• cardiovascular disease cystic fibrosis
• phenylketonuria epidermolytic hyperkeratosis (EHK), chronic obstructive pulmonary disease (COPD), Charcot-Marie-Toot disease type 4J, neuroblastoma (NB),
• the disease or condition is cardiovascular disease. In some embodiments, the disease or condition is Niemann-Pick disease type C (NPC) disease.
• NPC Niemann-Pick disease type C
• the disease, disorder or condition is associated with a point mutation that introduces a stop codon, for example, a premature stop codon within the coding region of a gene.
• the desired base edit removes a stop codon within the coding region of a gene. In some embodiments, the desired base edit disrupts a splice acceptor site or a splice donor site.
• the desired base edit is associated with disruption of a splice acceptor site or a splice donor site in a PCSK9 gene, or an Angptl3 gene. In certain embodiments, the desired base edit is associated with the disruption of a splice acceptor site at W8 in a PCKS9 gene. In some embodiments, the desired base edit is an A to G edit that disrupts the splice acceptor site at residue 8, generating a W8R substitution.
• cystic fibrosis See, e.g., Schwank et al., Functional repair of CFTR by CRISPR/Cas9 in intestinal stem cell organoids of cystic fibrosis patients. Cell stem cell.2013; 13: 653-658; and Wu et. al., Correction of a genetic disease in mouse via use of CRISPR-Cas9.
• phenylketonuria e.g., phenylalanine to serine mutation at position 835 (mouse) or 240 (human) or a homologous residue in phenylalanine hydroxylase gene (T>C mutation) – see, e.g., McDonald et al., Genomics.1997; 39:402-405; Bernard-Soulier syndrome (BSS) – e.g., phenylalanine to serine mutation at position 55 or a homologous residue, or cysteine to arginine at residue 24 or a homologous residue in the platelet membrane glycoprotein IX (T>C mutation) – see, e.g., Noris et al., British Journal of Haematology.1997; 97: 312-320, and Ali et al., Hematol.2014; 93:
• J. Haematol.1992 see also accession number P04275 in the UNIPROT database; 82: 66-72; myotonia congenital – e.g., cysteine to arginine mutation at position 277 or a homologous residue in the muscle chloride channel gene CLCN1 (T>C mutation) – see, e.g., Weinberger et al., The J.
• hereditary renal amyloidosis e.g., stop codon to arginine mutation at position 78 or a homologous residue in the processed form of apolipoprotein AII or at position 101 or a homologous residue in the unprocessed form (T>C mutation) – see, e.g., Yazaki et al., Kidney Int.2003; 64: 11-16; dilated cardiomyopathy (DCM) – e.g., tryptophan to Arginine mutation at position 148 or a homologous residue in the FOXD4 gene (T>C mutation), see, e.g., Minoretti et.
• DCM dilated cardiomyopathy
• CINCA chronic infantile neurologic cutaneous articular syndrome
• DRM desmin-related myopathy
• the entire contents of all references and database entries is incorporated herein by reference.
• Treatment of a disease or disorder includes delaying the development or progression of the disease, or reducing disease severity.
• Treating the disease does not necessarily require curative results [00369]
• “delaying” the development of a disease means to defer, hinder, slow, retard, stabilize, and/or postpone progression of the disease. This delay can be of varying lengths of time, depending on the history of the disease and/or individuals being treated.
• a method that “delays” or alleviates the development of a disease, or delays the onset of the disease is a method that reduces probability of developing one or more symptoms of the disease in a given time frame and/or reduces extent of the symptoms in a given time frame, when compared to not using the method. Such comparisons are typically based on clinical studies, using a number of subjects sufficient to give a statistically significant result.
• “Development” or “progression” of a disease means initial manifestations and/or ensuing progression of the disease. Development of the disease can be detectable and assessed using standard clinical techniques as well known in the art. However, development also refers to progression that may be undetectable. For purpose of this disclosure, development or progression refers to the biological course of the symptoms. “Development” includes occurrence, recurrence, and onset. [00371] As used herein “onset” or “occurrence” of a disease includes initial onset and/or recurrence. Conventional methods, known to those of ordinary skill in the art of medicine, can be used to administer the isolated polypeptide or pharmaceutical composition to the subject, depending upon the type of disease to be treated or the site of the disease.
• the present disclosure provides uses of any one of the disclosed base editors described herein and a guide RNA targeting this nucleobase editor to a target in the manufacture of a medicament.
• uses of any one of the nucleobase editors and guide RNAs described herein are provided in the manufacture of a kit for base editing, wherein the base editing comprises contacting the nucleic acid molecule with the base editor and guide RNA under conditions suitable for the substitution of the adenine (A) of a A:T nucleobase pair in the target with a guanine (G), or for the substitution of the cytosine (C) of a C:T nucleobase pair in the target with a thymine (T).
• A adenine
• G guanine
• C cytosine
• the step of contacting of induces separation of the double-stranded DNA at a target region. In some embodiments, the step of contacting further comprises nicking one strand of the double- stranded DNA, wherein the one strand comprises an unmutated strand.
• the step of contacting is performed in vitro. In other embodiments, the step of contacting is performed in vivo. In some embodiments, the step of contacting is performed in a subject (e.g., a human subject or a non- human animal subject) In some embodiments the step of contacting is performed in a human or non-human animal cell. In some embodiments, the step of contacting is performed in a plant cell.
• the present disclosure also provides uses of any one of the nucleobase editors or any one of the complexes of nucleobase editors and guide RNAs described herein as a medicament.
• the present disclosure also provides uses of the described pharmaceutical compositions or cells comprising, and vectors or rAAV particles encoding, any of the disclosed nucleobase editors or complexes herein as a medicament.
• the medicament is for treatment of cardiovascular disease.
• the present disclosure provides uses of any one of the base editors described herein and a guide RNA targeting this base editor to a target base pair in a nucleic acid molecule in the manufacture of a kit for nucleic acid editing, wherein the nucleic acid editing comprises contacting the nucleic acid molecule with the base editor and guide RNA under conditions suitable for the desired base edit.
• the desired base edit is the substitution of the adenine (A) of a target A:T base pair with a guanine (G).
• the nucleic acid molecule is a double-stranded DNA molecule.
• the step of contacting induces separation of the double- stranded DNA at a target region.
• the step of contacting thereby comprises nicking one strand of the double-stranded DNA, wherein the one strand comprises an unmutated strand that comprises the T of the target A:T nucleobase pair.
• the step of contacting is performed in vitro. In other embodiments, the step of contacting is performed in vivo. In some embodiments, the step of contacting is performed in a subject (e.g., a human subject or a non- human animal subject). In some embodiments, the step of contacting is performed in a human or non-human animal cell. In some embodiments, the step of contacting is performed in a plant cell.
• kits [00377] The present disclosure also provides uses of any one of the adenine base editors described herein as a medicament. The present disclosure also provides uses of any one of the complexes of adenine base editors and guide RNAs described herein as a medicament.
• Kits [00378] The compositions of the present disclosure may be assembled into kits.
• the kit comprises nucleic acid vectors for the expression of the nucleobase editors described herein.
• the kit further comprises appropriate guide nucleotide sequences (e.g., gRNAs) or nucleic acid vectors for the expression of such guide nucleotide sequences, to target the Cas9 protein or nucleobase editor to the desired target sequence.
• gRNAs guide nucleotide sequences
• the kit described herein may include one or more containers housing components for performing the methods described herein and optionally instructions for use. Any of the kit described herein may further comprise components needed for performing the assay methods.
• Each component of the kits where applicable, may be provided in liquid form (e.g., in solution) or in solid form, (e.g., a dry powder). In certain cases, some of the components may be reconstitutable or otherwise processible (e.g., to an active form), for example, by the addition of a suitable solvent or other species (for example, water), which may or may not be provided with the kit.
• the kits may optionally include instructions and/or promotion for use of the components provided.
• instructions can define a component of instruction and/or promotion, and typically involve written instructions on or associated with packaging of the disclosure. Instructions also can include any oral or electronic instructions provided in any manner such that a user will clearly recognize that the instructions are to be associated with the kit, for example, audiovisual (e.g., videotape, DVD, etc.), Internet, and/or web-based communications, etc.
• the written instructions may be in a form prescribed by a governmental agency regulating the manufacture, use, or sale of pharmaceuticals or biological products, which can also reflect approval by the agency of manufacture, use or sale for animal administration.
• kits includes all methods of doing business including methods of education, hospital and other clinical instruction, scientific inquiry, drug discovery or development, academic research, pharmaceutical industry activity including pharmaceutical sales, and any advertising or other promotional activity including written, oral and electronic communication of any form, associated with the disclosure. Additionally, the kits may include other components depending on the specific application, as described herein. [00381] The kits may contain any one or more of the components described herein in one or more containers. The components may be prepared sterilely, packaged in a syringe and shipped refrigerated. Alternatively it may be housed in a vial or other container for storage. A second container may have other components prepared sterilely.
• kits may include the active agents premixed and shipped in a vial tube or other container
• the kits may have a variety of forms, such as a blister pouch, a shrink wrapped pouch, a vacuum sealable pouch, a sealable thermoformed tray, or a similar pouch or tray form, with the accessories loosely packed within the pouch, one or more tubes, containers, a box or a bag.
• the kits may be sterilized after the accessories are added, thereby allowing the individual accessories in the container to be otherwise unwrapped.
• the kits can be sterilized using any appropriate sterilization techniques, such as radiation sterilization, heat sterilization, or other sterilization methods known in the art.
• kits may also include other components, depending on the specific application, for example, containers, cell media, salts, buffers, reagents, syringes, needles, a fabric, such as gauze, for applying or removing a disinfecting agent, disposable gloves, a support for the agents prior to administration, etc.
• Host Cells [00383] Cells that may contain any of the compositions described herein include prokaryotic cells and eukaryotic cells. The methods described herein are used to deliver a Cas9 protein or a nucleobase editor into a eukaryotic cell (e.g., a mammalian cell, such as a human cell). In some embodiments, the cell is in vitro (e.g., cultured cell.
• the cell is in vivo (e.g., in a subject such as a human subject). In some embodiments, the cell is ex vivo (e.g., isolated from a subject and may be administered back to the same or a different subject).
• Mammalian cells of the present disclosure include human cells, primate cells (e.g., vero cells), rat cells (e.g., GH3 cells, OC23 cells) or mouse cells (e.g., MC3T3 (“3T3”) cells or mouse neuroblastoma neuro-2A (“N2A”) cells).
• human cell lines including, without limitation, human embryonic kidney (HEK, or HEK293T) cells, HeLa cells, cancer cells from the National Cancer Institute’s 60 cancer cell lines (NCI60), DU145 (prostate cancer) cells, Lncap (prostate cancer) cells, MCF-7 (breast cancer) cells, MDA-MB- 438 (breast cancer) cells, PC3 (prostate cancer) cells, T47D (breast cancer) cells, THP-1 (acute myeloid leukemia) cells, U87 (glioblastoma) cells, SHSY5Y human neuroblastoma cells (cloned from a myeloma) and Saos-2 (bone cancer) cells.
• HEK human embryonic kidney
• HEK293T human embryonic kidney
• HeLa cells cancer cells from the National Cancer Institute’s 60 cancer cell lines (NCI60)
• DU145 (prostate cancer) cells Lncap (prostate cancer) cells
• MCF-7 breast cancer
• rAAV vectors are delivered into human embryonic kidney (HEK) cells (e.g., HEK 293 or HEK 293T cells).
• HEK human embryonic kidney
• rAAV vectors are delivered into stem cells (e.g., human stem cells) such as, for example, pluripotent stem cells (e.g., human pluripotent stem cells including human induced pluripotent stem cells (hiPSCs)).
• stem cell refers to a cell with the ability to divide for indefinite periods in culture and to give rise to specialized cells.
• a pluripotent stem cell refers to a type of stem cell that is capable of differentiating into all tissues of an organism, but not alone capable of sustaining full organismal development.
• a human induced pluripotent stem cell refers to a somatic (e.g., mature or adult) cell that has been reprogrammed to an embryonic stem cell-like state by being forced to express genes and factors important for maintaining the defining properties of embryonic stem cells (see, e.g., Takahashi and Yamanaka, Cell 126 (4): 663–76, 2006, incorporated herein by reference).
• Human induced pluripotent stem cell cells express stem cell markers and are capable of generating cells characteristic of all three germ layers (ectoderm, endoderm, mesoderm).
• Examples of cell lines that may be used in accordance with the present disclosure include 293-T, 293-T, 3T3, N2A, 4T1, 721, 9L, A-549, A172, A20, A253, A2780, A2780ADR, A2780cis, A431, ALC, B16, B35, BCP-1, BEAS-2B, bEnd.3, BHK-21, BR 293, BxPC3, C2C12, C3H-10T1/2, C6, C6/36, Cal-27, CGR8, CHO, CML T1, CMT, COR- L23, COR-L23/5010, COR-L23/CPR, COR-L23/R23, COS-7, COV-434, CT26, D17, DH82, DU145, DuCaP, E14Tg2a, EL4, EM2, EM3, EMT6/AR1, EMT6/AR10.0, FM3, H1299, H69, HB54,
• ABE8e variants that use compact CjCas9, Nme2Cas9 and SauriCas9 domains were characterized to develop a suite of single-AAV, high-activity adenine base editors that collectively offered compatibility with a broad range of PAM sequences, including commonly occurring N4CC and N2GG PAMs, enabling base editing of approximately 82% of adenines in the human genome in principle (see FIG.4D).
• high-efficiency guide RNAs targeting Pcsk9 to allow evaluation of in vivo genome editing (irrespective of protein knockdown) in N2A and 3T3 cells were identified by transfecting plasmids encoding SaABE8e or SaKKH-ABE8e and corresponding sgRNAs with spacers that targeted the endogenous Pcsk9 gene.
• the editing efficiency of each sgRNA was analyzed by targeted high-throughput DNA sequencing (HTS) (FIG.6).
• the most efficient guide RNA installed a W8R coding mutation in Pcsk9 using SaABE8e (FIG.6).
• AAV genome architectures were designed and compared for delivery of SaABE8e to assess the impact of modifying the EFS promoter by adding a minimal minute virus of mice (MVM) intron 37 , modifying the terminator by removing the truncated WPRE gamma subunit W3, or replacing the bGH polyadenylation signal with an SV40 late polyadenylation signal.
• VMM minimal minute virus of mice
• AAV expression cassettes were designed and produced: (1) EFS-SaABE8e-W3bGH, (2) EFS-MVM-SaABE8e-W3bGH, (3) EFS-MVM-SaABE8e-bGH, (4) EFS-SaABE8e-bGH, and (5) EFS-SaABE8e-W3-SV40.
• Each of the five AAV candidates were administered to 6- to 7-week-old wild-type C57BL/6J mice by retro-orbital injection at a high dose (4x10 11 vg editor AAV plus 4x10 11 vg sgRNA AAV) or low dose (4x10 10 vg editor AAV plus 4x10 10 vg sgRNA AAV) (FIG 2C) [00393]
• a high dose (4x10 11 vg editor AAV plus 4x10 11 vg sgRNA AAV
• low dose 4x10 10 vg editor AAV plus 4x10 10 vg sgRNA AAV
• This single-AAV9 SaABE8e was injected retro-orbitally into 6-8-week-old C57BL/6J mice at a dose of 4x10 11 vg or 4x10 10 vg, matching the dose of base editor AAV used in previous experiments, and corresponding to half the previously used total AAV dose since the sgRNA was now expressed from the same AAV as the base editor.
• Single-AAV SaABE8e performed similarly at half the total AAV dose to intact SaABE8e and sgRNA expressed from two different AAVs in the liver at both the high and low doses.
• Single-AAV SaABE8e yielded 64% and 55% editing of bulk liver at high and low dose, respectively (FIG.
• the single-AAV ABE construct was assessed at a dose of 8x10 11 vg per mouse, equal in total AAV dose per mouse to that of the high-dose experiments described above requiring two AAVs. Further improvements in editing were observed compared to the lower doses, especially in heart and muscle, which were edited with 33% and 22% average efficiency, respectively (FIG.2C, FIGs.8A and 8B).
• the relatively wide editing window of SaABE8e is maintained in vivo, and indels remain low in each tissue (FIGs.8A and 8B).
• plasmids encoding each editor and a corresponding sgRNA targeting a PAM-matched site were transfected into HEK293T cells. Three days later, the cells were analyzed by targeted high-throughput DNA sequencing (FIGs.3A-3C). [00399] All three of the tested small ABEs supported efficient base editing in HEK293T cells, with peak efficiencies at each target site generally ranging from 40-70%.
• CjABE8 the smallest of the three small-Cas variants tested, the window was even larger, spanning positions 2 to 18, counting the PAM as positions 24-31, with optimal editing occurring between positions 3 and 15 (FIGs.3B and 4B).
• CjABE8e also appeared to be more sensitive to the context preferences of the fused deaminase than the other tested ABEs.
• the editing efficiency varied substantially depending on the nucleobase 5 ⁇ of the target adenine (YA >> RA).
• SauriCas9-ABE8e typically ranged from protospacer positions 3-16 (counting the PAM as positions 22-25) with improved editing occurring between positions 5-15 (FIGs.3C and 4C), which resembled the wide editing window enabled by the related SaCas9.
• the collective targeting scope of four small ABE8e variants (SaKKHABE8e, Nme2ABE8e, CjABE8e, and SauriABE8e) were assessed by determining the number of adenines in the entire hg38 human reference genome that were targetable by at least one of these variants.
• the sequence context surrounding each adenine was analyzed for the presence of a small ABE8e-targetable PAM that would place each adenine within an appropriate base editing window. This analysis revealed that 82% of all adenines in the human genome were targetable in principle by at least one of these four small ABE8e variants.
• SaABE8e, SaKKH-ABE8e, and newly designed SauriABE8e were used to disrupt start codons, splice donors, and splice acceptors 53 to block production of the targeted protein without relying on double-strand breaks or indel formation.
• Single-AAV Adenine base editing of Pcsk9 and Angptl3 in mice [00403] To assess in vivo editing activity with sgRNAs targeting PCSK9, Pcsk9, and Angptl3 together with the corresponding size-minimized ABE8e variant, single-AAV ABEs were prepared in AAV8, a serotype that efficiently transduced murine hepatocytes 54 , and administered to 6- to 8-week old mice systemically via retroorbital injection at a dose of 1x10 11 vg per mouse (5x10 12 vg/kg).
• AAV8 encoding SaKKH-ABE8e and sgRNA targeting the exon 1 splice donor of human PCSK9 were injected into humanized mice containing the human PCSK9 sequence 55 .
• AAV8 encoding SaKKH-ABE8e, SaKKH- ABE8e(V106W), or SauriABE8e and editor-matched sgRNA targeting exon 1 splice donor of mouse Pcsk9 or SaKKH-ABE8e and sgRNA targeting the exon 6 splice donor of mouse Angptl3 were injected to wild-type C57BL/6J mice. After four weeks bulk liver tissue was analyzed by HTS.
• SaKKH- ABE8e(V106W) which uses a mutant of evolved TadA-8e deaminase that reduces guide- independent DNA and mRNA off-target editing 76 , maintained high editing efficiency in vivo.
• These single-AAV in vivo base editing efficiencies approached those of reported LNP- mediated ABE mRNA liver delivery methods targeting Pcsk9 and Angptl3 reported in pre- clinical studies in mice 41,58 .
• the disruption of Pcsk9 exon 1 spice donor was measured in liver four weeks after administration by HTS.
• the maximum vg/kg dose used (5x10 12 vg/kg for a 20-g mouse) was comparable to or lower than those used in gene therapy non-human primate studies and human clinical trials 6,60 . It was observed that the single- and dual-AAV ABE systems performed similarly at each dose, with the single-AAV yielding 54%, 38%, and 3.7% average editing in liver at a dose of 1x10 11 vg, 1x10 10 vg, and 1x10 9 vg, respectively (FIG.4C), and editing via dual-AAV SpABE8e in liver at the same dose of AAV averaging 57%, 35%, and 1.0%, respectively.
• Example 3 Reduction in circulating protein and lipids upon editing of Pcsk9 and Angptl3 [00406] To assess whether the efficient editing observed in the liver translated into efficient target gene knockdown and concomitant reduction in circulating lipid levels, editor treated mice were serially bled and plasma levels of the targeted protein and total cholesterol were measured. A non-targeting control of dual AAV ABE7.10 targeting Dnmt1, an edit not expected to affect cholesterol or lipid metabolism, was included for comparison (FIGs.11A and 11B).
• Dnmt1 encodes DNA methyltransferase 1.
• single-AAV ABE treatment at this dose resulted in 99%, 91%, and 94% knockdown of human PCSK9, mouse Pcsk9, and mouse Angptl3 protein levels, respectively, compared to control animals treated with AAV encoding the Dnmt1- targeting guide RNA.
• Plasma triglycerides were measured in Angptl3-targeted mice, as loss-of-function alleles of Angptl3 are known to reduce levels of both cholesterol and triglycerides 62 .
• Angptl3-targeted mice a 45% decrease in circulating triglycerides was observed compared to nontargeting control to 25 mg/dL after four weeks (FIG.5K).
• the editing and reduction of circulating Angptl3, cholesterol, and triglycerides achieved here with single AAV ABE is likely the highest reported upon targeted genome editing to knockdown Angptl3 58,63 .
• mice treated with single-AAV ABEs were assessed. Histology performed on livers from mice treated with single-AAV8 SaKKH-ABE8e and guide targeting PCSK9 exon 1 donor at 1x10 11 vg four weeks after administration did not indicate morphological changes relative to untreated mice (FIGs.19A and 19B).
• liver tissue of 6- to 8-week-old C57BL/6J mice treated with 1x10 11 vg single-AAV8 SaKKH-ABE8e, 1x10 11 vg single-AAV8 SaKKH-ABE8e(V106W), or 5x10 10 vg of each half of dual-AAV8 intein-split SaKKH-ABE8e targeting mouse Pcsk9 exon 1 four weeks after administration of these three editors.
• the top three computationally predicted sites 77,78 from these livers were sequenced.
• FIG.16B HEK293T cells were transfected with plasmids encoding full-length SpABE8e or intein-split SpABE8e and sgRNA targeting the human PCSK9 exon 1 splice donor site.
• AAV platform may be especially preferable when targeting non-liver tissues such as heart and skeletal muscle, or when toxicity limits AAV dosage (FIG. 2C).
• Single-AAV ABEs having serotypes AAV8 and AAV9 were packaged in multiple serotypes which facilitated editing in a variety of tissues and cell types outside the liver or with alternate administration routes. Even for base editing in the liver, the organ for which LNP-mediated mRNA delivery is the most potent, single-AAV ABEs resulted in editing efficiencies, target protein knockdown, and desired phenotypic changes comparable to reported preclinical LNP-mediated mRNA delivery efforts 41,59 .
• Single-AAV base editor delivery is currently limited to ABEs that use small Cas enzymes ⁇ 32 kb in gene size
• the activity of a variety of size-reduced ABEs that together cover a targetable genome similar to that targetable by SpCas9-ABE has been demonstrated. It is estimated that roughly 82% of genomic adenines can be edited using the suite of size- minimized ABEs described in this disclosure.
• Plasmid Plus Maxiprep or Midiprep kits Qiagen
• ZymoPURE II Midiprep kit Zymo Research
• PureYield plasmid miniprep kits Promega
• HEK293T cells ATCC CRL-3216
• Neuro-2A cells ATCC CCL-131
• Dulbecco’s Modified Eagle’s Medium plus GlutaMax Thermo Fisher Scientific
• 10% (v/v) FBS at 37 °C with 5% CO 2 .16–24 hours before transfection
• HEK293T cells or N2A cells were seeded on 96-well plates (Corning) at 1.4 ⁇ 10 4 –2.0 ⁇ 10 4 cells/well at >90% viability, or for SauriABE transfections
• HEK293T cells were seeded in 48-well plates (Corning) at 4.0 ⁇ 10 4 cells/well, >90% viability.
• Cells in 96- well plates were transfected at approximately 70–85% confluency with 0.5 ⁇ L of Lipofectamine 2000 (Thermo Fisher Scientific) and 187.5 ng of base editor plasmid, 37.5 ng of sgRNA plasmid per well (180 ng editor and 60 ng sgRNA for SauriABE8e).
• Cells in 48- well plates were transfected with 1.5 ⁇ L Lipofectamine 2000 with 750 ng editor and 250 ⁇ L sgRNA. Cells were cultured for 72 hours after transfection.
• Barcodes for Illumina sequencing were added via a second PCR step, using 1 ⁇ L of the first PCR as a template. Total PCR cycles were kept to a minimum to avoid PCR bias. Barcoded PCR products were pooled according to amplicon. The gel was extracted (MinElute; Qiagen) and quantified by qPCR (KAPA; KK4824) or Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific). Sequencing of pooled libraries was performed using Illumina MiSeq according to the manufacturer’s instructions. Primers for amplification of each locus from genomic DNA are compiled in Table 3. [00424] Sequencing reads were demultiplexed using MiSeq Reporter (Illumina).
• Alignment of amplicon sequences to reference sequence was performed using CRISPResso2 78 with “discard_indel_reads” on.
• efficiency was calculated as percentage of (reads containing an A to G edit at given position without indels)/(number of total reads).
• Indels were calculated explicitly as (discarded reads)/(total aligned reads) ⁇ 100.
• Base editing at a given position was calculated explicitly as: (frequency of specified point mutation in non-discarded reads) ⁇ 100 ⁇ (100 – (indel reads))/100).
• AAV production [00425] AAV was produced as previously described 35 .
• HEK293T clone 17 cells (ATCC CRL-11268) were maintained in Dulbecco’s Modified Eagle’s Medium plus GlutaMax (Thermo Fisher Scientific) supplemented with 10% (v/v) FBS without antibiotic in 150-mm dishes (Thermo Fisher Scientific; 157150) at 37 °C with 5% CO 2 and passaged every 2– 3 days. Cells were split 1:3 the day before polyethyleneimine transfection with 5.7 ⁇ g AAV genome plasmid, 11.4 ⁇ g pHelper (Chlontech) and 22.8 ⁇ g rep-cap plasmid per plate. Media was exchanged for DMEM 5% FBS the day after transfection.
• the media was decanted and combined with a 5 ⁇ solution of 40% poly(ethylene glycol) 8,000 (PEG 8k, Sigma-Aldrich 89510) in 2.5 M NaCl for a final concentration of 8% PEG/500 mM NaCl, incubated on ice for 2 hours, and then centrifuged at 3200 g for 30 minutes. The pellet was resuspended in 500 ⁇ L of hypertonic lysis buffer per plate and added to the cell lysate. Crude lysates were either incubated at 4 °C overnight or taken immediately to ultracentrifugation.
• PEG 8k poly(ethylene glycol) 8,000
• Phenol red at a final concentration of 1 ⁇ g/mL was added to the 15, 25 and 60% layers to facilitate identification.
• Ultracentrifugation was performed using a Ti 70 rotor in a Sorvall wX+ Ultracentrifuge (Thermo Scientific) at 58,000 rpm for 2 hours 15 minutes at 18 °C. Immediately following centrifugation, 3 mL of solution was withdrawn from the 40–60% iodixanol interface via an 18-gauge needle. The solution was exchanged into cold PBS containing 0.001% F-68 using PES 100 kD MWCO columns (Thermo Scientific, Pierce 88533) and concentrated.
• the concentrated AAV solution was sterile filtered using a 0.22 ⁇ m filter, quantified by qPCR (AAVpro Titration Kit version 2; Clontech), and stored at 4 °C until use.
• Animals [00427] All experiments in live animals were approved by the Broad Institute and University of Pennsylvania Institutional Animal Care and Use Committees and were consistent with local, state, and federal regulations as applicable, including the National Institutes of Health Guide for the Care and Use of Laboratory Animals. C57BL/6J mice (stock no.000664) for use in experiments were purchased from The Jackson Laboratory. Humanized PCSK9 mice were reported previously 57 .
• mice were housed in a room maintained on a 12-hour light and dark cycle with ad libitum access to standard rodent diet and water except for 4-hour fasts just prior to bleeds for plasma analysis.
• Retro-orbital injections [00428] AAV was diluted into 100 ⁇ L of sterile 0.9% NaCl USP (Fresenius Kabi; 918610) before injection. Anesthesia was induced with 2-4% isoflurane. Following induction, as measured by unresponsiveness to bilateral toe pinch, the right eye was protruded by gentle pressure on the skin, and an insulin syringe was advanced, with the bevel facing away from the eye, into the retrobulbar sinus where AAV solution was slowly injected.
• mice were euthanized by carbon dioxide asphyxiation. Genomic DNA was purified from minced tissue using gDNAdvance kit (Beckman Coulter A48705) according to the manufacturer’s instructions and used as template for high throughput sequencing.
• RNA was purified from 30 mg of snap frozen liver tissue with RNeasy Plus Mini kit (Qiagen 74134) according to the manufacturer’s instructions, then reverse transcribed to cDNA using SuperScript III first-strand synthesis supermix (Invitrogen 18080-450) with an oligo dT primer, which was used as template for high-throughput sequencing.
• Digital droplet PCR [00429] Genomic DNA was purifyied from tissue using Beckman gDNAdvance kit (Beckman Coulter A48705) according to the manufacturer’s instructions and used as template for digital droplet PCR.
• ddPCR was carried out using ddPCR Supermix for Probes (BioRad 1863026) with 10 ng of genomic DNA as template and 3 units NEB EcoRI-HF (R3101S) per reaction. Droplets were autogenerated and PCR was performed at an annealing and extension temperature of 61 °C for 2 minutes for a total of 60 cycles Droplets were analyzed on a QX200 droplet analyzer and droplet fluorescence was quantified using QuantaSoft (BioRad). Calculation of targetable genomic adenosines [00430] A custom Python script, shown in Example 5, was used to analyze the targetability of all adenosines in the hg38 human reference genome.
• adenosine was counted as targetable if the surrounding genomic sequence context contained a small ABE8e-targetable PAM that would place that adenosine within an appropriate base editing window.
• the PAM sequences, protospacer lengths, and base editing windows associated with each small ABE8e variant are provided in in Table 4A (Example 4).
• the percentage of calculated genomic adenines on each chromosome is shown in Table 4B.
• mice were euthanized by carbon dioxide asphyxiation after a 4-hour fast.
• Whole livers were harvested for genomic DNA isolation and analysis and for hematoxylin/eosin staining, and terminal blood samples were collected.
• Pre-treatment and post-treatment plasma human PCSK9, mouse Pcsk9, or mouse ANGPTL3 was measured using the Human Proprotein Convertase 9/PCSK9 Quantikine ELISA Kit, Mouse Proprotein Convertase 9/PCSK9 Quantikine ELISA Kit, or Human Angiopoietin-like 3 Quantikine ELISA Kit, respectively, according to the manufacturer’s instructions (R&D Systems).
• Total cholesterol or triglyceride levels were measured using the Infinity Cholesterol Reagent or Infinity Triglycerides Reagent, respectively, according to the manufacturer’s instructions (Thermo Fisher Scientific).
• Liver tissue fixation & histology [00433] A portion of the left medial lobe was fixed in 4% paraformaldehyde at 4 °C overnight, washed with PBS, then dehydrated gradually by serial substitution of PBS for 30%, 50%, 70%, then 100% ethanol. Samples were kept at -20 °C until analysis, when they were paraffinized by the Rodent Histopathology Core of Harvard Medical School.
• 1% alkaline agarose gel (1% agarose in water with 50 mM NaOH and 1mM EDTA) was prepared by dissolving agarose in water, allowing to cool but not solidify, then adding a 50 ⁇ solution of NaOH and EDTA.
• the formed gel was submerged in 1 ⁇ alkaline running buffer (50 mM NaOH, 1 mM EDTA) in a submarine style gel electrophoresis setup at 4 °C.5x10 10 vg of AAV was treated with DNAse I (NEB M0303S) then lysed in 1 ⁇ alkaline lysis buffer (50 mM NaOH, 1 mM EDTA, 0.3% SDS, 5% glycerol, 0.0025% xylene cyanol) for 3 minutes at 95 °C, then cooled on ice. Samples were loaded into the gel then electrophoresed at 20 V for 15 hours. The gel was neutralized in 0.1 M Tris pH 8 for 1 hour at 4 °C with rocking.
• Table 2 sgRNA scaffolds
• Table 3 Primer sequences used to amplify genomic DNA and cDNA for high throughput sequencing
• Table 4A Summary of the base editing activity windows of size-minimized ABEs developed in this manuscript and the percentages of targetable genomic adenines.
• Table 4B Window widths used for the calculation of targetable genomic adenines. Window widths are shown with respect to the standard protospacer lengths of each editor, with position 1 being defined as the 5 ⁇ end of the protospacer.
• the invention includes embodiments in which exactly one member of the group is present in, employed in, or otherwise relevant to a given product or process.
• the invention also includes embodiments in which more than one, or all of the group members are present in, employed in, or otherwise relevant to a given product or process.
• the invention encompasses all variations, combinations, and permutations in which one or more limitations, elements, clauses, descriptive terms, etc., from one or more of the claims or from relevant portions of the description is introduced into another claim. For example, any claim that is dependent on another claim can be modified to include one or more limitations found in any other claim that is dependent on the same base claim.
• values that are expressed as ranges can assume any specific value within the stated ranges in different embodiments of the invention, to the tenth of the unit of the lower limit of the range, unless the context clearly dictates otherwise. It is also to be understood that unless otherwise indicated or otherwise evident from the context and/or the understanding of one of ordinary skill in the art, values expressed as ranges can assume any subrange within the given range, wherein the endpoints of the subrange are expressed to the same degree of accuracy as the tenth of the unit of the lower limit of the range.

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