Non-viral DNA vectors and uses thereof for expressing Factor IX therapeutics

Abstract

The application describes ceDNA vectors having linear and continuous structure for delivery and expression of a transgene. ceDNA vectors comprise an expression cassette flanked by two ITR sequences, where the expression cassette encodes a transgene encoding FIX protein. Some ceDNA vectors further comprise cis-regulatory elements, including regulatory switches. Further provided herein are methods and cell lines for reliable gene expression of FIX protein in vitro, ex vivo and in vivo using the ceDNA vectors. Provided herein are method and compositions comprising ceDNA vectors useful for the expression of FIX protein in a cell, tissue or subject, and methods of treatment of diseases with said ceDNA vectors expressing FIX protein. Such FIX protein can be expressed for treating disease, e.g., hemophilia B.

Description

NON-VIRAL DNA VECTORS AND USES THEREOF FOR EXPRESSING FACTOR IXTHERAPEUTICSRELATED APPLICATIONS

[0001] The present application claims the benefit of priority to U.S. Provisional Application No. 62 / 993,857, filed on March 24, 2020, the entire contents of which is incorporated by reference in its entirety herein.SEQUENCE LISTING

[0002] The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on March 22, 2021, is named 131698-06520_SL.txt and is 394,694 bytes in size.TECHNICAL FIELD

[0003] The present disclosure relates to the field of gene therapy, including non-viral vectors for expressing a transgene or isolated polynucleotides in a subject or cell. The disclosure also relates to nucleic acid constructs, promoters, vectors, and host cells including the polynucleotides as well as methods of delivering exogenous DNA sequences to a target cell, tissue, organ or organism. For example, the present disclosure provides methods for using non-viral ceDNA vectors to express FIX, from a cell, e.g., expressing the FIX therapeutic protein for the treatment of a subject with a hemophilia B. The methods and compositions can be applied e.g., for the purpose of treating disease by expressing the FIX protein in a cell or tissue of a subject in need thereof.BACKGROUND

[0004] Gene therapy aims to improve clinical outcomes for patients suffering from either genetic mutations or acquired diseases caused by an aberration in the gene expression profile. Gene therapy includes the treatment or prevention of medical conditions resulting from defective genes or abnormal gene regulation or expression, e.g. underexpression or overexpression, that can result in a disorder, disease, malignancy, etc. For example, a disease or disorder caused by a defective gene might be treated, prevented or ameliorated by delivery of a corrective genetic material to a patient, or might be treated, prevented or ameliorated by altering or silencing a defective gene, e.g., with a corrective genetic material to a patient resulting in the therapeutic expression of the genetic material within the patient.

[0005] The basis of gene therapy is to supply a transcription cassette with an active gene product (sometimes referred to as a transgene), e.g., that can result in a positive gain-of-function effect, a negative loss-of-function effect, or another outcome. Such outcomes can be attributed to expression of an activating antibody or fusion protein or an inhibitory (neutralizing) antibody or fusion protein. Genetherapy can also be used to treat a disease or malignancy caused by other factors. Human monogenic disorders, disorders caused by variations in a single gene, can be treated by the delivery and expression of a normal gene to the target cells. Delivery and expression of a corrective gene in the patient's target cells can be carried out via numerous methods, including the use of engineered viruses and viral gene delivery vectors. Among the many virus-derived vectors available (e.g., recombinant retrovirus, recombinant lentivirus, recombinant adenovirus, and the like), recombinant adeno-associated virus (rAAV) is gaining popularity as a versatile vector in gene therapy.

[0006] Adeno-associated viruses (AAVs) belong to the Parvoviridae family and more specifically constitute the Dependoparvovirus genus. Vectors derived from AAV (i.e., rAVV or AAV vectors) are attractive for delivering genetic material because (i) they are able to infect (transduce) a wide variety of non-dividing and dividing cell types including myocytes and neurons; (ii) they are devoid of the virus structural genes, thereby diminishing the host cell responses to virus infection, e.g., interferon- mediated responses; (iii) wild-type viruses are considered non-pathologic in humans; (iv) in contrast to wild type AAV, which are capable of integrating into the host cell genome, replication-deficient AAV vectors lack the replication (rep) gene and generally persist as episomes, thus limiting the risk of insertional mutagenesis or genotoxicity; and (v) in comparison to other vector systems, AAV vectors are generally considered to be relatively poor immunogens and therefore do not trigger a significant immune response (see ii), thus gaining persistence of the vector DNA and potentially, long-term expression of the therapeutic transgenes.

[0007] However, there are several major deficiencies in using AAV particles as a gene delivery vector. One major drawback associated with rAAV is its limited viral packaging capacity of about 4.5 kb of heterologous DNA (Dong et al., 1996; Athanasopoulos et al., 2004; Lai et al., 2010), and as a result, use of AAV vectors has been limited to less than 150,000 Da protein coding capacity. The second drawback is that as a result of the prevalence of wild-type AAV infection in the population, candidates for rAAV gene therapy have to be screened for the presence of neutralizing antibodies that eliminate the vector from the patient. A third drawback is related to the capsid immunogenicity that prevents re-administration to patients that were not excluded from an initial treatment. The immune system in the patient can respond to the vector which effectively acts as a “booster” shot to stimulate the immune system generating high titer anti- AAV antibodies that preclude future treatments. Some recent reports indicate concerns with immunogenicity in high dose situations. Another notable drawback is that the onset of AAV-mediated gene expression is relatively slow, given that single- stranded AAV DNA must be converted to double-stranded DNA prior to heterologous gene expression.

[0008] Additionally, conventional AAV virions with capsids are produced by introducing a plasmid or plasmids containing the AAV genome, rep genes, and cap genes (Grimm et al., 1998). However, such encapsidated AAV virus vectors were found to inefficiently transduce certain cell and tissue types and the capsids also induce an immune response.

[0009] Accordingly, use of adeno-associated virus (AAV) vectors for gene therapy is limited due to the single administration to patients (owing to the patient immune response), the limited range of transgene genetic material suitable for delivery in AAV vectors due to minimal viral packaging capacity (about 4.5kb), and slow AAV-mediated gene expression.

[0010] There is large unmet need for disease-modifying therapies in hemophilia B. Current therapies are burdensome and require frequent intravenous (IV) administrations. First, these Factor IX injectables do not provide continuous delivery of factors, with trough levels allowing bleeding episodes. Second, there are no approved gene therapies for hemophilia B, and AAV based therapies cannot be used by 25% to 40% of patients due to pre-existing antibodies. AAV can only be administered once, and the resulting Factor IX levels might not be high enough to be efficacious, or may be supranormal, dose levels cannot be titrated. Third, some hemophilia B patients cannot utilize these therapies because of the development of neutralizing antibodies to these exogenous, artificial clotting factors.

[0011] Accordingly, there is need in the field for a technology that permits expression of a therapeutic FIX protein in a cell, tissue or subject for the treatment of hemophilia B.BRIEF DESCRIPTION

[0012] The technology described herein relates to methods and compositions for treatment of Hemophilia B by expression of Factor IX (FIX) protein from a capsid-free (e.g., non-viral) DNA vector with covalently-closed ends (referred to herein as a “closed-ended DNA vector” or a “ceDNA vector”), where the ceDNA vector comprises a FIX nucleic acid sequence or codon optimized versions thereof. These ceDNA vectors can be used to produce FIX proteins for treatment, monitoring, and diagnosis. The application of ceDNA vectors expressing FIX to the subject for the treatment of hemophilia B is useful to: (i) provide disease modifying levels of FIX enzyme, be minimally invasive in delivery, be repeatable and dosed-to-effect, have rapid onset of therapeutic effect, result in sustained expression of corrective FIX enzyme in the liver, restoring the coagulation cascade, and / or be titratable to achieve the appropriate pharmacologic levels of the defective enzyme.

[0013] In some embodiments, a ceDNA-vector expressing FIX is optionally present in a liposome nanoparticle formulation (LNP) for the treatment of hemophilia B. A ceDNA LNP formulation described herein can provide one or more benefits, including,: providing disease modifying levels of FIX protein, being minimally invasive in delivery, being repeatable and dosed-to-effect, having a rapid onset of therapeutic effect that is typically within days of therapeutic intervention, having sustained expression of corrective FIX levels in the circulation, be titratable to achieve the appropriate pharmacologic levels of the defective coagulation factor, and / or provide treatments for other types of hemophilia, including but not limited to Factor VII deficiency.

[0014] Accordingly, the present disclosure relates to a capsid-free (e.g., non-viral) DNA vector with covalently-closed ends (referred to herein as a “closed-ended DNA vector” or a “ceDNA vector”)comprising a gene encoding FIX, to permit expression of the FIX therapeutic protein in a cell. In one embodiment, the gene encoding FIX is a heterologous gene.

[0015] The ceDNA vectors for expression of FIX protein production as described herein are capsid- free, linear duplex DNA molecules formed from a continuous strand of complementary DNA with covalently-closed ends (linear, continuous and non-encapsidated structure), which comprise a 5’ inverted terminal repeat (ITR) sequence and a 3’ ITR sequence, where the 5’ ITR and the 3’ ITR can have the same symmetrical three-dimensional organization with respect to each other, (i.e., symmetrical or substantially symmetrical), or alternatively, the 5’ ITR and the 3’ ITR can have different three-dimensional organization with respect to each other (i.e., asymmetrical ITRs). In addition, the ITRs can be from the same or different serotypes. In some embodiments, a ceDNA vector can comprise ITR sequences that have a symmetrical three-dimensional spatial organization such that their structure is the same shape in geometrical space, or have the same A, C-C’ and B-B’ loops in 3D space (i.e., they are the same or are mirror images with respect to each other). In some embodiments, one ITR can be from one AAV serotype, and the other ITR can be from a different AAV serotype.

[0016] Accordingly, some aspects of the technology described herein relate to a ceDNA vector for improved protein expression and / or production of the above described FIX protein that comprise ITR sequences that flank a nucleic acid sequence comprising any FIX nucleic acid sequence disclosed in Table 1 or any open reading frame sequence included in any ceDNA sequence disclosed in Table 12, the ITR sequences being selected from any of: (i) at least one WT ITR and at least one modified AAV inverted terminal repeat (ITR) (e.g., asymmetric modified ITRs); (ii) two modified ITRs where the mod-ITR pair have a different three-dimensional spatial organization with respect to each other (e.g., asymmetric modified ITRs), or (iii) symmetrical or substantially symmetrical WT-WT ITR pair, where each WT-ITR has the same three-dimensional spatial organization, or (iv) symmetrical or substantially symmetrical modified ITR pair, where each mod-ITR has the same three-dimensional spatial organization. The ceDNA vectors disclosed herein can be produced in eukaryotic cells, thus devoid of prokaryotic DNA modifications and bacterial endotoxin contamination in insect cells.

[0017] The methods and compositions described herein relate, in part, to the discovery of a non- viral capsid-free DNA vector with covalently-closed ends (ceDNA vectors) that can be used to express at least one FIX protein, or more than one FIX protein, from a cell, including but not limited to cells of the liver.

[0018] Provided herein in one aspect are DNA vectors (e.g., ceDNA vectors) comprising at least one nucleic acid sequence, wherein the nucleic acid sequence encodes a transgene, operably linked to a promoter positioned between two different AAV inverted terminal repeat sequences (ITRs), one of the ITRs comprising a functional AAV terminal resolution site and a Rep binding site, and one of the ITRs comprising a deletion, insertion, or substitution relative to the other ITR; wherein the transgene encodes an FIX protein; and wherein the DNA when digested with a restriction enzyme having a single recognition site on the DNA vector has the presence of characteristic bands of linear andcontinuous DNA as compared to linear and non-continuous DNA controls when analyzed on a non denaturing gel. Other aspects include delivery of the FIX protein by expressing it in vivo from a ceDNA vector as described herein and further, the treatment of hemophilia B using ceDNA vectors encoding the FIX protein. Also contemplated herein are cells comprising a ceDNA vector encoding an FIX protein as described herein.

[0019] Aspects of the disclosure relate to methods to produce the ceDNA vectors useful for FIX protein expression in a cell as described herein. Other embodiments relate to a ceDNA vector produced by the methods provided herein. In one embodiment, the capsid free (e.g., non-viral) DNA vector (ceDNA vector) for FIX protein production is obtained from a plasmid (referred to herein as a “ceDNA-plasmid”) comprising a polynucleotide expression construct template comprising in this order: a first 5’ inverted terminal repeat (e.g. AAV ITR); a nucleic acid sequence; and a 3’ ITR (e.g. AAV ITR), where the 5’ ITR and 3’ITR can be asymmetric relative to each other, or symmetric (e.g., WT-ITRs or modified symmetric ITRs) as defined herein.

[0020] The ceDNA vector for expression of the FIX protein as disclosed herein is obtainable by a number of means that would be known to the ordinarily skilled artisan after reading this disclosure.For example, a polynucleotide expression construct template used for generating the ceDNA vectors of the present disclosure can be a ceDNA-plasmid, a ceDNA-bacmid, and / or a ceDNA-baculovirus. In one embodiment, the ceDNA-plasmid comprises a restriction cloning site (e.g. SEQ ID NO: 123 and / or 124) operably positioned between the ITRs where an expression cassette comprising e.g., a promoter operatively linked to a transgene, e.g., a nucleic acid encoding FIX can be inserted. In some embodiments, ceDNA vectors for expression of FIX protein are produced from a polynucleotide template (e.g., ceDNA-plasmid, ceDNA-bacmid, ceDNA-baculovirus) containing symmetric or asymmetric ITRs (modified or WT ITRs).

[0021] In a permissive host cell, in the presence of e.g., Rep, the polynucleotide template having at least two ITRs replicates to produce ceDNA vectors expressing the FIX protein. ceDNA vector production undergoes two steps: first, excision (“rescue”) of template from the template backbone (e.g. ceDNA-plasmid, ceDNA-bacmid, ceDNA-baculovirus genome etc.) via Rep proteins, and second, Rep mediated replication of the excised ceDNA vector. Rep proteins and Rep binding sites of the various AAV serotypes are well known to those of ordinary skill in the art. One of ordinary skill understands to choose a Rep protein from a serotype that binds to and replicates the nucleic acid sequence based upon at least one functional ITR. For example, if the replication competent ITR is from AAV serotype 2, the corresponding Rep would be from an AAV serotype that works with that serotype such as AAV2 ITR with AAV2 or AAV4 Rep but not AAV5 Rep, which does not. Upon replication, the covalently-closed ended ceDNA vector continues to accumulate in permissive cells and ceDNA vector is preferably sufficiently stable over time in the presence of Rep protein under standard replication conditions, e.g. to accumulate in an amount that is at least 1 pg / cell, preferably at least 2 pg / cell, preferably at least 3 pg / cell, more preferably at least 4 pg / cell, even more preferably at least 5 pg / cell.

[0022] Accordingly, one aspect of the disclosure relates to a process of producing a ceDNA vector for expression of such FIX proteins comprising the steps of: a) incubating a population of host cells (e.g. insect cells) harboring the polynucleotide expression construct template (e.g., a ceDNA-plasmid, a ceDNA-bacmid, and / or a ceDNA-baculovirus), which is devoid of viral capsid coding sequences, in the presence of a Rep protein under conditions effective and for a time sufficient to induce production of the ceDNA vector within the host cells, and wherein the host cells do not comprise viral capsid coding sequences; and b) harvesting and isolating the ceDNA vector from the host cells. The presence of Rep protein induces replication of the vector polynucleotide with a modified ITR to produce the ceDNA vector for expression of FIX protein in a host cell. Flowever, no viral particles (e.g. AAV virions) are expressed. Thus, there is no virion-enforced size limitation.

[0023] The presence of the ceDNA vector useful for expression of FIX protein is isolated from the host cells can be confirmed by digesting DNA isolated from the host cell with a restriction enzyme having a single recognition site on the ceDNA vector and analyzing the digested DNA material on denaturing and non-denaturing gels to confirm the presence of characteristic bands of linear and continuous DNA as compared to linear and non-continuous DNA.

[0024] Also provided herein are methods of expressing an FIX protein that has therapeutic uses, in a cell or in a subject, using a ceDNA vector. Such FIX proteins can be used for the treatment of hemophilia B. Accordingly, provided herein are methods for the treatment of hemophilia B comprising administering a ceDNA vector encoding a therapeutic FIX protein to a subject in need thereof.

[0025] In some embodiments, one aspect of the technology described herein relates to a non- viral capsid-free DNA vector with covalently-closed ends (ceDNA vector), wherein the ceDNA vector comprises at least one nucleic acid sequence, operably positioned between two ITR sequences where the ITR sequences can be asymmetric, or symmetric, or substantially symmetrical as these terms are defined herein, wherein at least one of the ITRs comprises a functional terminal resolution site (trs) and a Rep binding site, and optionally the nucleic acid sequence encodes a transgene (e.g., FIX protein) and wherein the vector is not in a viral capsid.

[0026] These and other aspects of the disclosure are described in further detail below.DESCRIPTION OF DRAWINGS

[0027] Embodiments of the present disclosure, briefly summarized above and discussed in greater detail below, can be understood by reference to the illustrative embodiments of the disclosure depicted in the appended drawings. Flowever, the appended drawings illustrate only typical embodiments of the disclosure and are therefore not to be considered limiting of scope, for the disclosure may admit to other equally effective embodiments.

[0028] FIG. 1A illustrates an exemplary structure of a ceDNA vector for expression of an FIX protein as disclosed herein, comprising asymmetric ITRs. In this embodiment, the exemplary ceDNA vector comprises an expression cassette containing CAG promoter, WPRE, and BGFlpA. An openreading frame (ORF) encoding the FIX transgene can be inserted into the cloning site (R3 / R4) between the CAG promoter and WPRE. The expression cassette is flanked by two inverted terminal repeats (ITRs) - the wild-type AAV2 ITR on the upstream (5 ’-end) and the modified ITR on the downstream (3’ -end) of the expression cassette, therefore the two ITRs flanking the expression cassette are asymmetric with respect to each other.

[0029] FIG. IB illustrates an exemplary structure of a ceDNA vector for expression of an FIX protein as disclosed herein comprising asymmetric ITRs with an expression cassette containing CAG promoter, WPRE, and BGHpA. An open reading frame (ORF) encoding the FIX transgene can be inserted into the cloning site between CAG promoter and WPRE. The expression cassette is flanked by two inverted terminal repeats (ITRs) - a modified ITR on the upstream (5 ’-end) and a wild-type ITR on the downstream (3 ’-end) of the expression cassette.

[0030] FIG. 1C illustrates an exemplary structure of a ceDNA vector for expression of an FIX protein as disclosed herein comprising asymmetric ITRs, with an expression cassette containing an enhancer / promoter, the FIX transgene, a post transcriptional element (WPRE), and a polyA signal. An open reading frame (ORF) allows insertion of the FIX transgene into the cloning site between CAG promoter and WPRE. The expression cassette is flanked by two inverted terminal repeats (ITRs) that are asymmetrical with respect to each other; a modified ITR on the upstream (5 ’-end) and a modified ITR on the downstream (3 ’-end) of the expression cassette, where the 5’ ITR and the 3 ’ITR are both modified ITRs but have different modifications (i.e., they do not have the same modifications).

[0031] FIG. ID illustrates an exemplary structure of a ceDNA vector for expression of an FIX protein as disclosed herein, comprising symmetric modified ITRs, or substantially symmetrical modified ITRs as defined herein, with an expression cassette containing CAG promoter, WPRE, and BGHpA. An open reading frame (ORF) encoding the FIX transgene is inserted into the cloning site between CAG promoter and WPRE. The expression cassette is flanked by two modified inverted terminal repeats (ITRs), where the 5’ modified ITR and the 3’ modified ITR are symmetrical or substantially symmetrical.

[0032] FIG. IE illustrates an exemplary structure of a ceDNA vector for expression of an FIX protein as disclosed herein comprising symmetric modified ITRs, or substantially symmetrical modified ITRs as defined herein, with an expression cassette containing an enhancer / promoter, a transgene, a post transcriptional element (WPRE), and a polyA signal. An open reading frame (ORF) allows insertion of a transgene (e.g., the FIX) into the cloning site between CAG promoter and WPRE. The expression cassette is flanked by two modified inverted terminal repeats (ITRs), where the 5’ modified ITR and the 3’ modified ITR are symmetrical or substantially symmetrical.

[0033] FIG. IF illustrates an exemplary structure of a ceDNA vector for expression of an FIX protein as disclosed herein, comprising symmetric WT-ITRs, or substantially symmetrical WT-ITRs as defined herein, with an expression cassette containing CAG promoter, WPRE, and BGHpA. An open reading frame (ORF) encoding a transgene (e.g., the FIX) is inserted into the cloning site betweenCAG promoter and WPRE. The expression cassette is flanked by two wild type inverted terminal repeats (WT-ITRs), where the 5’ WT-ITR and the 3’ WT ITR are symmetrical or substantially symmetrical.

[0034] FIG. 1G illustrates an exemplary structure of a ceDNA vector for expression of an FIX protein as disclosed herein, comprising symmetric modified ITRs, or substantially symmetrical modified ITRs as defined herein, with an expression cassette containing an enhancer / promoter, a transgene (e.g., the FIX), a post transcriptional element (WPRE), and a polyA signal. An open reading frame (ORF) allows insertion of a transgene (e.g., the FIX) into the cloning site between CAG promoter and WPRE. The expression cassette is flanked by two wild type inverted terminal repeats (WT-ITRs), where the 5’ WT-ITR and the 3’ WT ITR are symmetrical or substantially symmetrical.

[0035] FIG. 2A provides the T-shaped stem-loop structure of a wild-type left ITR of AAV2 (SEQ ID NO: 52) with identification of A-A’ arm, B-B’ arm, C-C’ arm, two Rep binding sites (RBE and RBE’) and also shows the terminal resolution site (trs). The RBE contains a series of 4 duplex tetramers that are believed to interact with either Rep 78 or Rep 68. In addition, the RBE’ is also believed to interact with Rep complex assembled on the wild-type ITR or mutated ITR in the construct. The D and D’ regions contain transcription factor binding sites and other conserved structure. FIG. 2B shows proposed Rep-catalyzed nicking and ligating activities in a wild-type left ITR (SEQ ID NO: 53), including the T-shaped stem-loop structure of the wild-type left ITR of AAV2 with identification of A-A’ arm, B-B’ arm, C-C’ arm, two Rep Binding sites (RBE and RBE’) and also shows the terminal resolution site (trs), and the D and D’ region comprising several transcription factor binding sites and other conserved structure.

[0036] FIG. 3A provides the primary structure (polynucleotide sequence) (left) and the secondary structure (right) of the RBE-containing portions of the A-A’ arm, and the C-C’ and B-B’ arm of the wild type left AAV2 ITR (SEQ ID NO: 54). FIG. 3B shows an exemplary mutated ITR (also referred to as a modified ITR) sequence for the left ITR. Shown is the primary structure (left) and the predicted secondary structure (right) of the RBE portion of the A-A’ arm, the C arm and B-B’ arm of an exemplary mutated left ITR (ITR-1, left) (SEQ ID NO: 113). FIG. 3C shows the primary structure (left) and the secondary structure (right) of the RBE-containing portion of the A-A’ loop, and the B-B’ and C-C’ arms of wild type right AAV2 ITR (SEQ ID NO: 55). FIG. 3D shows an exemplary right modified ITR. Shown is the primary structure (left) and the predicted secondary structure (right) of the RBE containing portion of the A-A’ arm, the B-B’ and the C arm of an exemplary mutant right ITR (ITR-1, right) (SEQ ID NO: 114). Any combination of left and right ITR (e.g., AAV2 ITRs or other viral serotype or synthetic ITRs) can be used as taught herein. Each of FIGS. 3A-3D polynucleotide sequences refer to the sequence used in the plasmid or bacmid / baculovirus genome used to produce the ceDNA as described herein. Also included in each of FIGS. 3A-3D are corresponding ceDNA secondary structures inferred from the ceDNA vector configurations in the plasmid or bacmid / baculovirus genome and the predicted Gibbs free energy values.

[0037] FIG. 4A is a schematic illustrating an upstream process for making baculovirus infected insect cells (BIICs) that are useful in the production of a ceDNA vector for expression of the FIX as disclosed herein in the process described in the schematic in FIG. 4B. FIG. 4B is a schematic of an exemplary method of ceDNA production and FIG. 4C illustrates a biochemical method and process to confirm ceDNA vector production. FIG. 4D and FIG. 4E are schematic illustrations describing a process for identifying the presence of ceDNA in DNA harvested from cell pellets obtained during the ceDNA production processes in FIG. 4B. FIG. 4D shows schematic expected bands for an exemplary ceDNA either left uncut or digested with a restriction endonuclease and then subjected to electrophoresis on either a native gel or a denaturing gel. The leftmost schematic is a native gel, and shows multiple bands suggesting that in its duplex and uncut form ceDNA exists in at least monomeric and dimeric states, visible as a faster-migrating smaller monomer and a slower-migrating dimer that is twice the size of the monomer. The schematic second from the left shows that when ceDNA is cut with a restriction endonuclease, the original bands are gone and faster-migrating (e.g., smaller) bands appear, corresponding to the expected fragment sizes remaining after the cleavage. Under denaturing conditions, the original duplex DNA is single-stranded and migrates as a species twice as large as observed on native gel because the complementary strands are covalently linked. Thus in the second schematic from the right, the digested ceDNA shows a similar banding distribution to that observed on native gel, but the bands migrate as fragments twice the size of their native gel counterparts. The rightmost schematic shows that uncut ceDNA under denaturing conditions migrates as a single- stranded open circle, and thus the observed bands are twice the size of those observed under native conditions where the circle is not open. In this figure “kb” is used to indicate relative size of nucleotide molecules based, depending on context, on either nucleotide chain length (e.g., for the single stranded molecules observed in denaturing conditions) or number of basepairs (e.g., for the double-stranded molecules observed in native conditions). FIG. 4E shows DNA having a non- continuous structure. The ceDNA can be cut by a restriction endonuclease, having a single recognition site on the ceDNA vector, and generate two DNA fragments with different sizes (lkb and 2kb) in both neutral and denaturing conditions. FIG. 4E also shows a ceDNA having a linear and continuous structure. The ceDNA vector can be cut by the restriction endonuclease, and generate two DNA fragments that migrate as lkb and 2kb in neutral conditions, but in denaturing conditions, the stands remain connected and produce single strands that migrate as 2kb and 4kb.

[0038] FIG. 5 is an exemplary picture of a denaturing gel running examples of ceDNA vectors with (+) or without (-) digestion with endonucleases (EcoRI for ceDNA construct 1 and 2; BamHl for ceDNA construct 3 and 4; Spel for ceDNA construct 5 and 6; and Xhol for ceDNA construct 7 and 8) Constructs 1-8 are described in Example 1 of International Application PCT PCT / US 18 / 49996, which is incorporated herein in its entirety by reference. Sizes of bands highlighted with an asterisk were determined and provided on the bottom of the picture.

[0039] FIG. 6 depicts the results of the experiments described in Example 7 and specifically shows the IVIS images obtained from mice treated with LNP-polyC control (mouse furthest to the left) and four mice treated with LNP-ceDNA-Luciferase (all but the mouse furthest to the left). The four ceDNA-treated mice show significant fluorescence in the liver-containing region of the mouse.

[0040] FIG. 7 depicts the results of the experiment described in Example 8. The dark specks indicate the presence of the protein resulting from the expressed ceDNA transgene and demonstrate association of the administered LNP-ceDNA with hepatocytes.

[0041] FIGS. 8A-8B depict the results of the ocular studies set forth in Example 9. FIG. 8A shows representative IVIS images from let PEI® -ceDNA-Luciferase- injected rat eyes (upper left) versus uninjected eye in the same rat (upper right) or plasmid-Luciferase DNA-injected rat eye (lower left) and the uninjected eye in that same rat (lower right). FIG. 8B shows a graph of the average radiance observed in treated eyes or the corresponding untreated eyes in each of the treatment groups. The ceDNA-treated rats demonstrated prolonged significant fluorescence (and hence luciferase transgene expression) over 99 days, in sharp contrast to rats treated with plasmid-luciferase where minimal relative fluorescence (and hence luciferase transgene expression) was observed.

[0042] FIGS. 9A and 9B depict the results of the ceDNA persistence and redosing study in Rag2 mice described in Example 10. FIG. 9A shows a graph of total flux over time observed in LNP- ceDNA-Luc-treated wild-type c57bl / 6 mice or Rag2 mice. FIG. 9B provides a graph showing the impact of redose on expression levels of the luciferase transgene in Rag2 mice, with resulting increased stable expression observed after redose (arrow indicates time of redose administration).

[0043] FIG. 10 provides data from the ceDNA luciferase expression study in treated mice described in Example 11 , showing total flux in each group of mice over the duration of the study.High levels of unmethylated CpG correlated with lower total flux observed in the mice over time, while use of a liver-specific promoter correlated with durable, stable expression of the transgene from the ceDNA vector over at least 77 days.

[0044] FIGS. 11A and 11B show hydrodynamic delivery of ceDNA vector expressing FIX. FIG 11A shows FIX expression levels in serum samples at day 3 and 7 from mice after hydrodynamic injection of two different ceDNA vectors expressing FIX (LPSl-FIX-vl; LPSl-FIX-v2), or a control ceDNA vector (a ceDNA expressing luciferase only) (shown as Vehicle). Both these FIX ceDNA vectors showed FIX expression. FIG. 11B shows FIX expression levels over a 28 day period in serum samples from mice after hydrodynamic injection of the two different ceDNA vectors expressing FIX (FPSl-FIX-vl; FPSl-FIX-v2), or the vehicle control ceDNA vector (expressing luciferase only).

[0045] FIG. 12 depicts plasma levels of factor IX in mice injected with an FNP formulated FIX ceDNA construct (2.0 mg / kg) at days 0 and 36 and orally dosed with 300 mg / kg of ruxolitinib at day - 2, day -1, day 0, day 1 and day 36.

[0046] FIG. 13A and 13B show FIX expression in male CD-I mice treated with a ceDNA-FIX construct (ceDNA-FIX vl; ceDNA-FIX 2109; or ceDNA-FIX 2112), each of which contains a codon optimized human FIX sequence. FIG. 13A shows human FIX expression levels in CD-I mice treated with 1 pg of ceDNA-FIX vl; ceDNA-FIX 2109; or ceDNA-FIX 2112 via hydrodynamic delivery, measured at Day 3 and Day 7. FIG. 13B shows human FIX expression levels in CD-I mice treated with 10 pg of ceDNA-FIX vl; ceDNA-FIX 2109; or ceDNA-FIX 2112 via hydrodynamic delivery, measured at Day 3 and Day 7.DETAILED DESCRIPTION

[0047] Provided herein is a method for treating hemophilia B using a ceDNA vector comprising one or more nucleic acids that encode an FIX therapeutic protein or fragment thereof. Also provided herein are ceDNA vectors for expression of FIX protein as described herein comprising one or more nucleic acids that encode for the FIX protein. In some embodiments, the expression of FIX protein can comprise secretion of the therapeutic protein out of the cell in which it is expressed. Alternatively, in some embodiments the expressed FIX protein can act or function (e.g., exert its effect) within the cell in which it is expressed. In some embodiments, the ceDNA vector expresses FIX protein in the liver, a muscle (e.g., skeletal muscle) of a subject, or other body part, which can act as a depot for FIX therapeutic protein production and secretion to many systemic compartments.I. Definitions

[0048] Unless otherwise defined herein, scientific and technical terms used in connection with the present application shall have the meanings that are commonly understood by those of ordinary skill in the art to which this disclosure belongs. It should be understood that this disclosure is not limited to the particular methodology, protocols, and reagents, etc., described herein and as such can vary. The terminology used herein is for the purpose of describing particular embodiments only and is not intended to limit the scope of the present disclosure, which is defined solely by the claims. Definitions of common terms in immunology and molecular biology can be found in The Merck Manual of Diagnosis and Therapy, 19th Edition, published by Merck Sharp & Dohme Corp., 2011 (ISBN 978-0- 911910-19-3); Robert S. Porter et al. (eds.), Fields Virology, 6thEdition, published by Lippincott Williams & Wilkins, Philadelphia, PA, USA (2013), Knipe, D.M. and Flowley, P.M. (ed.), The Encyclopedia of Molecular Cell Biology and Molecular Medicine, published by Blackwell Science Ltd., 1999-2012 (ISBN 9783527600908); and Robert A. Meyers (ed.), Molecular Biology and Biotechnology: a Comprehensive Desk Reference, published by VCF1 Publishers, Inc., 1995 (ISBN 1- 56081-569-8); Immunology by Werner Luttmann, published by Elsevier, 2006; Janeway's Immunobiology, Kenneth Murphy, Allan Mowat, Casey Weaver (eds.), Taylor & Francis Limited, 2014 (ISBN 0815345305, 9780815345305); Lewin's Genes XI, published by Jones & Bartlett Publishers, 2014 (ISBN-1449659055); Michael Richard Green and Joseph Sambrook, MolecularCloning: A Laboratory Manual, 4thed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., USA (2012) (ISBN 1936113414); Davis et ai, Basic Methods in Molecular Biology, Elsevier Science Publishing, Inc., New York, USA (2012) (ISBN 044460149X); Laboratory Methods in Enzymology: DNA, Jon Lorsch (ed.) Elsevier, 2013 (ISBN 0124199542); Current Protocols in Molecular Biology (CPMB), Frederick M. Ausubel (ed.), John Wiley and Sons, 2014 (ISBN047150338X, 9780471503385), Current Protocols in Protein Science (CPPS), John E. Coligan (ed.), John Wiley and Sons, Inc., 2005; and Current Protocols in Immunology (CPI) (John E. Coligan, ADA M Kruisbeek, David H Margulies, Ethan M Shevach, Warren Strobe, (eds.) John Wiley and Sons, Inc., 2003 (ISBN 0471142735, 9780471142737), the contents of which are ah incorporated by reference herein in their entireties.

[0049] As used herein, the terms “heterologous nucleic acid sequence” and “transgene” are used interchangeably and refer to a nucleic acid of interest (other than a nucleic acid encoding a capsid polypeptide) that is incorporated into and may be delivered and expressed by a ceDNA vector as disclosed herein. According to some embodiments, the term “heterologous nucleic acid” is meant to refer to a nucleic acid (or transgene) that is not present in, expressed by, or derived from the cell or subject to which it is contacted.

[0050] As used herein, the terms “expression cassette” and “transcription cassette” are used interchangeably and refer to a linear stretch of nucleic acids that includes a transgene that is operably linked to one or more promoters or other regulatory sequences sufficient to direct transcription of the transgene, but which does not comprise capsid-encoding sequences, other vector sequences or inverted terminal repeat regions. An expression cassette may additionally comprise one or more r / 's-acting sequences (e.g., promoters, enhancers, or repressors), one or more introns, and one or more post- transcriptional regulatory elements.

[0051] The terms “polynucleotide” and “nucleic acid,” used interchangeably herein, refer to a polymeric form of nucleotides of any length, either ribonucleotides or deoxyribonucleotides. Thus, this term includes single, double, or multi-stranded DNA or RNA, genomic DNA, cDNA, DNA-RNA hybrids, or a polymer including purine and pyrimidine bases or other natural, chemically or biochemically modified, non-natural, or derivatized nucleotide bases. “Oligonucleotide” generally refers to polynucleotides of between about 5 and about 100 nucleotides of single- or double-stranded DNA. However, for the purposes of this disclosure, there is no upper limit to the length of an oligonucleotide. Oligonucleotides are also known as “oligomers” or “oligos” and may be isolated from genes, or chemically synthesized by methods known in the art. The terms "polynucleotide" and “nucleic acid” should be understood to include, as applicable to the embodiments being described, single-stranded (such as sense or antisense) and double-stranded polynucleotides.

[0052] DNA may be in the form of, e.g., antisense molecules, plasmid DNA, DNA-DNA duplexes, pre -condensed DNA, PCR products, vectors (PI, PAC, BAC, YAC, artificial chromosomes), expression cassettes, chimeric sequences, chromosomal DNA, or derivatives and combinations ofthese groups. DNA may be in the form of minicircle, plasmid, bacmid, minigene, ministring DNA (linear covalently closed DNA vector), closed-ended linear duplex DNA (CELiD or ceDNA), doggybone (dbDNA™) DNA, dumbbell shaped DNA, minimalistic immunological-defined gene expression (MIDGE) -vector, viral vector or nonviral vectors. RNA may be in the form of small interfering RNA (siRNA), Dicer-substrate dsRNA, small hairpin RNA (shRNA), asymmetrical interfering RNA (aiRNA), microRNA (miRNA), mRNA, rRNA, tRNA, viral RNA (vRNA), and combinations thereof. Nucleic acids include nucleic acids containing known nucleotide analogs or modified backbone residues or linkages, which are synthetic, naturally occurring, and non-naturally occurring, and which have similar binding properties as the reference nucleic acid. Examples of such analogs and / or modified residues include, without limitation, phosphorothioates, phosphorodiamidate morpholino oligomer (morpholino), phosphoramidates, methyl phosphonates, chiral-methyl phosphonates, 2’ -O-methyl ribonucleotides, locked nucleic acid (LNA™), and peptide nucleic acids (PNAs). Unless specifically limited, the term encompasses nucleic acids containing known analogues of natural nucleotides that have similar binding properties as the reference nucleic acid. Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions), alleles, orthologs, SNPs, and complementary sequences as well as the sequence explicitly indicated.

[0053] “Nucleotides” contain a sugar deoxyribose (DNA) or ribose (RNA), a base, and a phosphate group. Nucleotides are linked together through the phosphate groups.

[0054] “Bases” include purines and pyrimidines, which further include natural compounds adenine, thymine, guanine, cytosine, uracil, inosine, and natural analogs, and synthetic derivatives of purines and pyrimidines, which include, but are not limited to, modifications which place new reactive groups such as, but not limited to, amines, alcohols, thiols, carboxylates, and alkylhalides.

[0055] The term “nucleic acid construct” as used herein refers to a nucleic acid molecule, either single- or double-stranded, which is isolated from a naturally occurring gene or which is modified to contain segments of nucleic acids in a manner that would not otherwise exist in nature or which is synthetic. The term nucleic acid construct is synonymous with the term “expression cassette” when the nucleic acid construct contains the control sequences required for expression of a coding sequence of the present disclosure. An “expression cassette” includes a DNA coding sequence operably linked to a promoter.

[0056] By “hybridizable” or “complementary” or “substantially complementary” it is meant that a nucleic acid (e.g., RNA) includes a sequence of nucleotides that enables it to non-covalently bind, i.e. form Watson-Crick base pairs and / or G / U base pairs, “anneal”, or “hybridize,” to another nucleic acid in a sequence-specific, antiparallel, manner (i.e., a nucleic acid specifically binds to a complementary nucleic acid) under the appropriate in vitro and / or in vivo conditions of temperature and solution ionic strength. As is known in the art, standard Watson-Crick base-pairing includes: adenine (A) pairingwith thymidine (T), adenine (A) pairing with uracil (U), and guanine (G) pairing with cytosine (C). In addition, it is also known in the art that for hybridization between two RNA molecules (e.g., dsRNA), guanine (G) base pairs with uracil (U). For example, G / U base-pairing is partially responsible for the degeneracy (i.e., redundancy) of the genetic code in the context of tRNA anti-codon base-pairing with codons in mRNA. In the context of this disclosure, a guanine (G) of a protein-binding segment (dsRNA duplex) of a subject DNA-targeting RNA molecule is considered complementary to a uracil (U), and vice versa. As such, when a G / U base-pair can be made at a given nucleotide position a protein-binding segment (dsRNA duplex) of a subject DNA-targeting RNA molecule, the position is not considered to be non-complementary, but is instead considered to be complementary.

[0057] The terms “peptide,” “polypeptide,” and “protein” are used interchangeably herein, and refer to a polymeric form of amino acids of any length, which can include coded and non-coded amino acids, chemically or biochemically modified or derivatized amino acids, and polypeptides having modified peptide backbones.

[0058] A DNA sequence that “encodes” a particular FIX protein is a DNA nucleic acid sequence that is transcribed into the particular RNA and / or protein. A DNA polynucleotide may encode an RNA (mRNA) that is translated into protein, or a DNA polynucleotide may encode an RNA that is not translated into protein (e.g., tRNA, rRNA, or a DNA-targeting RNA; also called “non-coding” RNA or “ncRNA”).

[0001] As used herein, the term “fusion protein” refers to a polypeptide which comprises protein domains from at least two different proteins. For example, a fusion protein may comprise (i) FIX or fragment thereof and (ii) at least one non-gene of interest (GOI) protein. Fusion proteins encompassed herein include, but are not limited to, an antibody, or Fc or antigen-binding fragment of an antibody fused to a FIX protein, e.g., an extracellular domain of a receptor, ligand, enzyme or peptide. The FIX protein or fragment thereof that is part of a fusion protein can be a monospecific antibody or a bispecific or multispecific antibody.

[0059] As used herein, the term “genomic safe harbor gene” or “safe harbor gene” refers to a gene or loci that a nucleic acid sequence can be inserted such that the sequence can integrate and function in a predictable manner (e.g., express a protein of interest) without significant negative consequences to endogenous gene activity, or the promotion of cancer. In some embodiments, a safe harbor gene is also a loci or gene where an inserted nucleic acid sequence can be expressed efficiently and at higher levels than a non-safe harbor site.

[0060] As used herein, the term “gene delivery” means a process by which foreign DNA is transferred to host cells for applications of gene therapy.

[0061] As used herein, the term “terminal repeat” or “TR” includes any viral terminal repeat or synthetic sequence that comprises at least one minimal required origin of replication and a region comprising a palindrome hairpin structure. A Rep-binding sequence (“RBS”) (also referred to as RBE (Rep-binding element)) and a terminal resolution site (“TRS”) together constitute a “minimal requiredorigin of replication” and thus the TR comprises at least one RBS and at least one TRS. TRs that are the inverse complement of one another within a given stretch of polynucleotide sequence are typically each referred to as an “inverted terminal repeat” or “ITR”. In the context of a virus, ITRs mediate replication, virus packaging, integration and provirus rescue. As was unexpectedly found, TRs that are not inverse complements across their full length can still perform the traditional functions of ITRs, and thus the term ITR is used herein to refer to a TR in a ceDNA genome or ceDNA vector that is capable of mediating replication of ceDNA vector. It will be understood by one of ordinary skill in the art that in complex ceDNA vector configurations more than two ITRs or asymmetric ITR pairs may be present. The ITR can be an AAV ITR or a non-AAV ITR, or can be derived from an AAV ITR or a non-AAV ITR. For example, the ITR can be derived from the family Parvoviridae, which encompasses Parvoviruses and Dependoviruses (e.g., canine parvovirus, bovine parvovirus, mouse parvovirus, porcine parvovirus, human parvovirus B-19), or the SV40 hairpin that serves as the origin of SV40 replication can be used as an ITR, which can further be modified by truncation, substitution, deletion, insertion and / or addition. Parvoviridae family viruses consist of two subfamilies: Parvovirinae, which infect vertebrates, and Densovirinae, which infect invertebrates. Dependoparvoviruses include the viral family of the adeno-associated viruses (AAV) which are capable of replication in vertebrate hosts including, but not limited to, human, primate, bovine, canine, equine and ovine species. For convenience herein, an ITR located 5’ to (upstream of) an expression cassette in a ceDNA vector is referred to as a “5’ ITR” or a “left ITR”, and an ITR located 3’ to (downstream of) an expression cassette in a ceDNA vector is referred to as a “3’ ITR” or a “right ITR”.

[0062] A “wild-type ITR” or “WT-ITR” refers to the sequence of a naturally occurring ITR sequence in an AAV or other dependovirus that retains, e.g., Rep binding activity and Rep nicking ability. The nucleic acid sequence of a WT-ITR from any AAV serotype may slightly vary from the canonical naturally occurring sequence due to degeneracy of the genetic code or drift, and therefore WT-ITR sequences encompassed for use herein include WT-ITR sequences as result of naturally occurring changes taking place during the production process (e.g., a replication error).

[0063] As used herein, the term “substantially symmetrical WT-ITRs” or a “substantially symmetrical WT-ITR pair” refers to a pair of WT-ITRs within a single ceDNA genome or ceDNA vector that are both wild type ITRs that have an inverse complement sequence across their entire length. For example, an ITR can be considered to be a wild-type sequence, even if it has one or more nucleotides that deviate from the canonical naturally occurring sequence, so long as the changes do not affect the properties and overall three-dimensional structure of the sequence. In some aspects, the deviating nucleotides represent conservative sequence changes. As one non-limiting example, a sequence that has at least 95%, 96%, 97%, 98%, or 99% sequence identity to the canonical sequence (as measured, e.g., using BLAST at default settings), and also has a symmetrical three-dimensional spatial organization to the other WT-ITR such that their 3D structures are the same shape ingeometrical space. The substantially symmetrical WT-ITR has the same A, C-C’ and B-B’ loops in 3D space. A substantially symmetrical WT-ITR can be functionally confirmed as WT by determining that it has an operable Rep binding site (RBE or RBE’) and terminal resolution site (trs) that pairs with the appropriate Rep protein. One can optionally test other functions, including transgene expression under permissive conditions.

[0064] As used herein, the phrases of “modified ITR” or “mod-ITR” or “mutant ITR” are used interchangeably herein and refer to an ITR that has a mutation in at least one or more nucleotides as compared to the WT-ITR from the same serotype. The mutation can result in a change in one or more of A, C, C’, B, B’ regions in the ITR, and can result in a change in the three-dimensional spatial organization (i.e., its 3D structure in geometric space) as compared to the 3D spatial organization of a WT-ITR of the same serotype.

[0065] As used herein, the term “asymmetric ITRs” also referred to as “asymmetric ITR pairs” refers to a pair of ITRs within a single ceDNA genome or ceDNA vector that are not inverse complements across their full length. As one non-limiting example, an asymmetric ITR pair does not have a symmetrical three-dimensional spatial organization to their cognate ITR such that their 3D structures are different shapes in geometrical space. Stated differently, an asymmetrical ITR pair have the different overall geometric structure, i.e., they have different organization of their A, C-C’ and B- B’ loops in 3D space (e.g., one ITR may have a short C-C’ arm and / or short B-B’ arm as compared to the cognate ITR). The difference in sequence between the two ITRs may be due to one or more nucleotide addition, deletion, truncation, or point mutation. In one embodiment, one ITR of the asymmetric ITR pair may be a wild-type AAV ITR sequence and the other ITR a modified ITR as defined herein (e.g., a non-wild-type or synthetic ITR sequence). In another embodiment, neither ITRs of the asymmetric ITR pair is a wild-type AAV sequence and the two ITRs are modified ITRs that have different shapes in geometrical space (i.e., a different overall geometric structure). In some embodiments, one mod-ITRs of an asymmetric ITR pair can have a short C-C’ arm and the other ITR can have a different modification (e.g., a single arm, or a short B-B’ arm etc.) such that they have different three-dimensional spatial organization as compared to the cognate asymmetric mod-ITR.

[0066] As used herein, the term “symmetric ITRs” refers to a pair of ITRs within a single ceDNA genome or ceDNA vector that are mutated or modified relative to wild-type dependoviral ITR sequences and are inverse complements across their full length. Neither ITRs are wild type ITR AAV2 sequences (i.e., they are a modified ITR, also referred to as a mutant ITR), and can have a difference in sequence from the wild type ITR due to nucleotide addition, deletion, substitution, truncation, or point mutation. For convenience herein, an ITR located 5’ to (upstream of) an expression cassette in a ceDNA vector is referred to as a “5’ ITR” or a “left ITR”, and an ITR located 3’ to (downstream of) an expression cassette in a ceDNA vector is referred to as a “3’ ITR” or a “right ITR”.

[0067] As used herein, the terms “substantially symmetrical modified-ITRs” or a “substantially symmetrical mod-ITR pair” refers to a pair of modified-ITRs within a single ceDNA genome or ceDNA vector that are both that have an inverse complement sequence across their entire length. For example, the modified ITR can be considered substantially symmetrical, even if it has some nucleotide sequences that deviate from the inverse complement sequence so long as the changes do not affect the properties and overall shape. As one non-limiting example, a sequence that has at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to the canonical sequence (as measured using BLAST at default settings), and also has a symmetrical three-dimensional spatial organization to their cognate modified ITR such that their 3D structures are the same shape in geometrical space. Stated differently, a substantially symmetrical modified-ITR pair have the same A, C-C’ and B-B’ loops organized in 3D space. In some embodiments, the ITRs from a mod-ITR pair may have different reverse complement nucleotide sequences but still have the same symmetrical three-dimensional spatial organization - that is both ITRs have mutations that result in the same overall 3D shape. For example, one ITR (e.g., 5’ ITR) in a mod-ITR pair can be from one serotype, and the other ITR (e.g., 3’ ITR) can be from a different serotype, however, both can have the same corresponding mutation (e.g., if the 5 ’ITR has a deletion in the C region, the cognate modified 3 ’ITR from a different serotype has a deletion at the corresponding position in the C’ region), such that the modified ITR pair has the same symmetrical three-dimensional spatial organization. In such embodiments, each ITR in a modified ITR pair can be from different serotypes (e.g., AAV1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, and 12) such as the combination of AAV2 and AAV6, with the modification in one ITR reflected in the corresponding position in the cognate ITR from a different serotype. In one embodiment, a substantially symmetrical modified ITR pair refers to a pair of modified ITRs (mod- ITRs) so long as the difference in nucleotide sequences between the ITRs does not affect the properties or overall shape and they have substantially the same shape in 3D space. As a non-limiting example, a mod-ITR that has at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity to the canonical mod-ITR as determined by standard means well known in the art such as BLAST (Basic Local Alignment Search Tool), or BLASTN at default settings, and also has a symmetrical three-dimensional spatial organization such that their 3D structure is the same shape in geometric space. A substantially symmetrical mod-ITR pair has the same A, C-C’ and B-B’ loops in 3D space, e.g., if a modified ITR in a substantially symmetrical mod-ITR pair has a deletion of a C-C’ arm, then the cognate mod-ITR has the corresponding deletion of the C-C’ loop and also has a similar 3D structure of the remaining A and B-B’ loops in the same shape in geometric space of its cognate mod- ITR.

[0068] The term “flanking” refers to a relative position of one nucleic acid sequence with respect to another nucleic acid sequence. Generally, in the sequence ABC, B is flanked by A and C. The same is true for the arrangement AxBxC. Thus, a flanking sequence precedes or follows a flanked sequencebut need not be contiguous with, or immediately adjacent to the flanked sequence. In one embodiment, the term flanking refers to terminal repeats at each end of the linear duplex ceDNA vector.

[0069] As used herein, the term “ceDNA genome” refers to an expression cassette that further incorporates at least one inverted terminal repeat region. A ceDNA genome may further comprise one or more spacer regions. In some embodiments the ceDNA genome is incorporated as an intermolecular duplex polynucleotide of DNA into a plasmid or viral genome.

[0070] As used herein, the term “ceDNA spacer region” refers to an intervening sequence that separates functional elements in the ceDNA vector or ceDNA genome. In some embodiments, ceDNA spacer regions keep two functional elements at a desired distance for optimal functionality. In some embodiments, ceDNA spacer regions provide or add to the genetic stability of the ceDNA genome within e.g., a plasmid or baculovirus. In some embodiments, ceDNA spacer regions facilitate ready genetic manipulation of the ceDNA genome by providing a convenient location for cloning sites and the like. For example, in certain aspects, an oligonucleotide “polylinker” containing several restriction endonuclease sites, or a non-open reading frame sequence designed to have no known protein (e.g., transcription factor) binding sites can be positioned in the ceDNA genome to separate the cis - acting factors, e.g., inserting a 6mer, 12mer, 18mer, 24mer, 48mer, 86mer, 176mer, etc. between the terminal resolution site and the upstream transcriptional regulatory element. Similarly, the spacer may be incorporated between the polyadenylation signal sequence and the 3 ’-terminal resolution site.

[0071] As used herein, the terms “Rep binding site, “Rep binding element, “RBE” and “RBS” are used interchangeably and refer to a binding site for Rep protein (e.g., AAV Rep 78 or AAV Rep 68) which upon binding by a Rep protein permits the Rep protein to perform its site-specific endonuclease activity on the sequence incorporating the RBS. An RBS sequence and its inverse complement together form a single RBS. RBS sequences are known in the art, and include, for example, 5’- GCGCGCTCGCTCGCTC-3' (SEQ ID NO: 60), an RBS sequence identified in AAV2. Any known RBS sequence may be used in the embodiments of the disclosure, including other known AAV RBS sequences and other naturally known or synthetic RBS sequences. Without being bound by theory it is thought that he nuclease domain of a Rep protein binds to the duplex nucleic acid sequence GCTC, and thus the two known AAV Rep proteins bind directly to and stably assemble on the duplex oligonucleotide, 5’-(GCGC)(GCTC)(GCTC)(GCTC)-3’ (SEQ ID NO: 60). In addition, soluble aggregated conformers (i.e., undefined number of inter-associated Rep proteins) dissociate and bind to oligonucleotides that contain Rep binding sites. Each Rep protein interacts with both the nitrogenous bases and phosphodiester backbone on each strand. The interactions with the nitrogenous bases provide sequence specificity whereas the interactions with the phosphodiester backbone are non- or less- sequence specific and stabilize the protein-DNA complex.

[0072] As used herein, the terms “terminal resolution site” and “TRS” are used interchangeably herein and refer to a region at which Rep forms a tyrosine-phosphodiester bond with the 5’ thymidine generating a 3’ OH that serves as a substrate for DNA extension via a cellular DNA polymerase, e.g.,DNA pol delta or DNA pol epsilon. Alternatively, the Rep-thymidine complex may participate in a coordinated ligation reaction. In some embodiments, a TRS minimally encompasses a non-base-paired thymidine. In some embodiments, the nicking efficiency of the TRS can be controlled at least in part by its distance within the same molecule from the RBS. When the acceptor substrate is the complementary ITR, then the resulting product is an intramolecular duplex. TRS sequences are known in the art, and include, for example, 5’-GGTTGA-3’ (SEQ ID NO: 61), the hexanucleotide sequence identified in AAV2. Any known TRS sequence may be used in the embodiments of the disclosure, including other known AAV TRS sequences and other naturally known or synthetic TRS sequences such as AGTT (SEQ ID NO: 62), GGTTGG (SEQ ID NO: 63), AGTTGG (SEQ ID NO: 64), AGTTGA (SEQ ID NO: 65), and other motifs such as RRTTRR (SEQ ID NO: 66).

[0073] As used herein, the term “ceDNA” refers to capsid-free closed-ended linear double stranded (ds) duplex DNA for non-viral gene transfer, synthetic or otherwise. Detailed description of ceDNA is described in International application of PCT / US2017 / 020828, filed March 3, 2017, the entire contents of which are expressly incorporated herein by reference. Certain methods for the production of ceDNA comprising various inverted terminal repeat (ITR) sequences and configurations using cell-based methods are described in Example 1 of International applications PCT / US 18 / 49996, filed September 7, 2018, and PCT / US2018 / 064242, filed December 6, 2018 each of which is incorporated herein in its entirety by reference. Certain methods for the production of synthetic ceDNA vectors comprising various ITR sequences and configurations are described, e.g., in International application PCT / US2019 / 14122, filed January 18, 2019, the entire content of which is incorporated herein by reference. As used herein, the terms “ceDNA vector” and “ceDNA” are used interchangeably and refer to a closed-ended DNA vector comprising at least one terminal palindrome. In some embodiments, the ceDNA comprises two covalently-closed ends.

[0074] As used herein, the term “ceDNA-plasmid” refers to a plasmid that comprises a ceDNA genome as an intermolecular duplex.

[0075] As used herein, the term “ceDNA-bacmid” refers to an infectious baculovirus genome comprising a ceDNA genome as an intermolecular duplex that is capable of propagating in E. coli as a plasmid, and so can operate as a shuttle vector for baculovirus.

[0076] As used herein, the term “ceDNA-baculovirus” refers to a baculovirus that comprises a ceDNA genome as an intermolecular duplex within the baculovirus genome.

[0077] As used herein, the terms “ceDNA-baculovirus infected insect cell” and “ceDNA-BIIC” are used interchangeably, and refer to an invertebrate host cell (including, but not limited to an insect cell (e.g., an Sf9 cell)) infected with a ceDNA-baculovirus.

[0078] As used herein, the term “closed-ended DNA vector” refers to a capsid-free DNA vector with at least one covalently closed end and where at least part of the vector has an intramolecular duplex structure.

[0079] As defined herein, “reporters” refer to proteins that can be used to provide detectable read outs. Reporters generally produce a measurable signal such as fluorescence, color, or luminescence. Reporter protein coding sequences encode proteins whose presence in the cell or organism is readily observed. For example, fluorescent proteins cause a cell to fluoresce when excited with light of a particular wavelength, luciferases cause a cell to catalyze a reaction that produces light, and enzymes such as b-galactosidase convert a substrate to a colored product. Exemplary reporter polypeptides useful for experimental or diagnostic purposes include, but are not limited to b-lactamase, b - galactosidase (LacZ), alkaline phosphatase (AP), thymidine kinase (TK), green fluorescent protein (GFP) and other fluorescent proteins, chloramphenicol acetyltransferase (CAT), luciferase, and others well known in the art.

[0080] As used herein, the term “effector protein” refers to a polypeptide that provides a detectable read-out, either as, for example, a reporter polypeptide, or more appropriately, as a polypeptide that kills a cell, e.g., a toxin, or an agent that renders a cell susceptible to killing with a chosen agent or lack thereof. Effector proteins include any protein or peptide that directly targets or damages the host cell’s DNA and / or RNA. For example, effector proteins can include, but are not limited to, a restriction endonuclease that targets a host cell DNA sequence (whether genomic or on an extrachromosomal element), a protease that degrades a polypeptide target necessary for cell survival, a DNA gyrase inhibitor, and a ribonuclease-type toxin. In some embodiments, the expression of an effector protein controlled by a synthetic biological circuit as described herein can participate as a factor in another synthetic biological circuit to thereby expand the range and complexity of a biological circuit system’s responsiveness.

[0081] Transcriptional regulators refer to transcriptional activators and repressors that either activate or repress transcription of a gene of interest, such as FIX. Promoters are regions of nucleic acid that initiate transcription of a particular gene Transcriptional activators typically bind nearby to transcriptional promoters and recruit RNA polymerase to directly initiate transcription. Repressors bind to transcriptional promoters and sterically hinder transcriptional initiation by RNA polymerase. Other transcriptional regulators may serve as either an activator or a repressor depending on where they bind and cellular and environmental conditions. Non-limiting examples of transcriptional regulator classes include, but are not limited to homeodomain proteins, zinc -finger proteins, winged- helix (forkhead) proteins, and leucine -zipper proteins.

[0082] As used herein, a “repressor protein” or “inducer protein” is a protein that binds to a regulatory sequence element and represses or activates, respectively, the transcription of sequences operatively linked to the regulatory sequence element. Preferred repressor and inducer proteins as described herein are sensitive to the presence or absence of at least one input agent or environmental input. Preferred proteins as described herein are modular in form, comprising, for example, separable DNA-binding and input agent-binding or responsive elements or domains.

[0083] As used herein, “carrier” includes any and all solvents, dispersion media, vehicles, coatings, diluents, antibacterial and antifungal agents, isotonic and absorption delaying agents, buffers, carrier solutions, suspensions, colloids, and the like. The use of such media and agents for pharmaceutically active substances is well known in the art. Supplementary active ingredients can also be incorporated into the compositions. The phrase “pharmaceutically-acceptable” refers to molecular entities and compositions that do not produce a toxic, an allergic, or similar untoward reaction when administered to a host.

[0084] As used herein, an “input agent responsive domain” is a domain of a transcription factor that binds to or otherwise responds to a condition or input agent in a manner that renders a linked DNA binding fusion domain responsive to the presence of that condition or input. In one embodiment, the presence of the condition or input results in a conformational change in the input agent responsive domain, or in a protein to which it is fused, that modifies the transcription-modulating activity of the transcription factor.

[0085] The term “in vivo ” refers to assays or processes that occur in or within an organism, such as a multicellular animal. In some of the aspects described herein, a method or use can be said to occur “in vivo ” when a unicellular organism, such as a bacterium, is used. The term “ex vivo ” refers to methods and uses that are performed using a living cell with an intact membrane that is outside of the body of a multicellular animal or plant, e.g., explants, cultured cells, including primary cells and cell lines, transformed cell lines, and extracted tissue or cells, including blood cells, among others. The term ” in vitro” refers to assays and methods that do not require the presence of a cell with an intact membrane, such as cellular extracts, and can refer to the introducing of a programmable synthetic biological circuit in a non-cellular system, such as a medium not comprising cells or cellular systems, such as cellular extracts.

[0086] The term “promoter,” as used herein, refers to any nucleic acid sequence that regulates the expression of another nucleic acid sequence by driving transcription of the nucleic acid sequence, which can be a heterologous target gene encoding a protein or an RNA. Promoters can be constitutive, inducible, repressible, tissue-specific, or any combination thereof. A promoter is a control region of a nucleic acid sequence at which initiation and rate of transcription of the remainder of a nucleic acid sequence are controlled. A promoter can also contain genetic elements at which regulatory proteins and molecules can bind, such as RNA polymerase and other transcription factors. In some embodiments of the aspects described herein, a promoter can drive the expression of a transcription factor that regulates the expression of the promoter itself. Within the promoter sequence will be found a transcription initiation site, as well as protein binding domains responsible for the binding of RNA polymerase. Eukaryotic promoters will often, but not always, contain "TATA" boxes and "CAT" boxes. Various promoters, including inducible promoters, may be used to drive the expression of transgenes in the ceDNA vectors disclosed herein. A promoter sequence may be bounded at its 3'terminus by the transcription initiation site and extends upstream (5' direction) to include the minimum number of bases or elements necessary to initiate transcription at levels detectable above background.

[0087] The term “enhancer” as used herein refers to a cis-acting regulatory sequence (e.g., 10-1,500 base pairs) that binds one or more proteins (e.g., activator proteins, or transcription factor) to increase transcriptional activation of a nucleic acid sequence. Enhancers can be positioned up to 1,000,000 base pars upstream of the gene start site or downstream of the gene start site that they regulate. An enhancer can be positioned within an intronic region, or in the exonic region of an unrelated gene.

[0088] A promoter can be said to drive expression or drive transcription of the nucleic acid sequence that it regulates. The phrases “operably linked,” “operatively positioned,” “operatively linked,” “under control,” and “under transcriptional control” indicate that a promoter is in a correct functional location and / or orientation in relation to a nucleic acid sequence it regulates to control transcriptional initiation and / or expression of that sequence. An “inverted promoter,” as used herein, refers to a promoter in which the nucleic acid sequence is in the reverse orientation, such that what was the coding strand is now the non-coding strand, and vice versa. Inverted promoter sequences can be used in various embodiments to regulate the state of a switch. In addition, in various embodiments, a promoter can be used in conjunction with an enhancer.

[0089] A promoter can be one naturally associated with a gene or sequence, as can be obtained by isolating the 5' non-coding sequences located upstream of the coding segment and / or exon of a given gene or sequence. Such a promoter can be referred to as “endogenous.” Similarly, in some embodiments, an enhancer can be one naturally associated with a nucleic acid sequence, located either downstream or upstream of that sequence.

[0090] In some embodiments, a coding nucleic acid segment is positioned under the control of a “recombinant promoter” or “heterologous promoter,” both of which refer to a promoter that is not normally associated with the encoded nucleic acid sequence it is operably linked to in its natural environment. A recombinant or heterologous enhancer refers to an enhancer not normally associated with a given nucleic acid sequence in its natural environment. Such promoters or enhancers can include promoters or enhancers of other genes; promoters or enhancers isolated from any other prokaryotic, viral, or eukaryotic cell; and synthetic promoters or enhancers that are not “naturally occurring,” i.e., comprise different elements of different transcriptional regulatory regions, and / or mutations that alter expression through methods of genetic engineering that are known in the art. In addition to producing nucleic acid sequences of promoters and enhancers synthetically, promoter sequences can be produced using recombinant cloning and / or nucleic acid amplification technology, including PCR, in connection with the synthetic biological circuits and modules disclosed herein (see, e.g., U.S. Pat. No. 4,683,202, U.S. Pat. No. 5,928,906, each incorporated herein by reference). Furthermore, it is contemplated that control sequences that direct transcription and / or expression of sequences within non-nuclear organelles such as mitochondria, chloroplasts, and the like, can be employed as well.

[0091] As described herein, an “inducible promoter” is one that is characterized by initiating or enhancing transcriptional activity when in the presence of, influenced by, or contacted by an inducer or inducing agent. An “inducer” or “inducing agent,” as defined herein, can be endogenous, or a normally exogenous compound or protein that is administered in such a way as to be active in inducing transcriptional activity from the inducible promoter. In some embodiments, the inducer or inducing agent, i.e., a chemical, a compound or a protein, can itself be the result of transcription or expression of a nucleic acid sequence {i.e., an inducer can be an inducer protein expressed by another component or module), which itself can be under the control or an inducible promoter. In some embodiments, an inducible promoter is induced in the absence of certain agents, such as a repressor. Examples of inducible promoters include but are not limited to, tetracycline, metallothionine, ecdysone, mammalian viruses ( e.g ., the adenovirus late promoter; and the mouse mammary tumor virus long terminal repeat (MMTV-LTR)) and other steroid-responsive promoters, rapamycin responsive promoters and the like.

[0092] The terms “DNA regulatory sequences,” “control elements,” and “regulatory elements,” used interchangeably herein, refer to transcriptional and translational control sequences, such as promoters, enhancers, polyadenylation signals, terminators, protein degradation signals, and the like, that provide for and / or regulate transcription of a non-coding sequence (e.g., DNA-targeting RNA) or a coding sequence (e.g., site-directed modifying polypeptide, or Cas9 / Csnl polypeptide) and / or regulate translation of an encoded polypeptide.

[0093] The term “open reading frame (ORF)” as used herein is meant to refer to a sequence of several nucleotide triplets which may be translated into a peptide or protein. An open reading frame preferably contains a start codon, i.e. a combination of three subsequent nucleotides coding usually for the amino acid methionine (ATG), at its 5’-end and a subsequent region which usually exhibits a length which is a multiple of 3 nucleotides. An ORF is preferably terminated by a stop-codon (e.g., TAA, TAG, TGA). Typically, this is the only stop-codon of the open reading frame. Thus, an open reading frame in the context of the present invention is preferably a nucleotide sequence, consisting of a number of nucleotides that may be divided by three, which starts with a start codon (e.g. ATG) and which preferably terminates with a stop codon (e.g., TAA, TGA, or TAG). The open reading frame may be isolated or it may be incorporated in a longer nucleic acid sequence, for example in a ceDNA vector as described herein.

[0094] “Operably linked” refers to a juxtaposition wherein the components so described are in a relationship permitting them to function in their intended manner. For instance, a promoter is operably linked to a coding sequence if the promoter affects its transcription or expression. An “expression cassette” includes a DNA sequence that is operably linked to a promoter or other regulatory sequence sufficient to direct transcription of the transgene in the ceDNA vector. Suitable promoters include, for example, tissue specific promoters. Promoters can also be of AAV origin.

[0095] The term “subject” as used herein refers to a human or animal, to whom treatment, including prophylactic treatment, with the ceDNA vector according to the present disclosure, isprovided. Usually, the animal is a vertebrate such as, but not limited to a primate, rodent, domestic animal or game animal. Primates include but are not limited to, chimpanzees, cynomologous monkeys, spider monkeys, and macaques, e.g., Rhesus. Rodents include mice, rats, woodchucks, ferrets, rabbits and hamsters. Domestic and game animals include, but are not limited to, cows, horses, pigs, deer, bison, buffalo, feline species, e.g., domestic cat, canine species, e.g., dog, fox, wolf, avian species, e.g., chicken, emu, ostrich, and fish, e.g., trout, catfish and salmon. In certain embodiments of the aspects described herein, the subject is a mammal, e.g., a primate or a human. A subject can be male or female. Additionally, a subject can be an infant or a child. In some embodiments, the subject can be a neonate or an unborn subject, e.g., the subject is in utero. Preferably, the subject is a mammal. The mammal can be a human, non-human primate, mouse, rat, dog, cat, horse, or cow, but is not limited to these examples. Mammals other than humans can be advantageously used as subjects that represent animal models of diseases and disorders. In addition, the methods and compositions described herein can be used for domesticated animals and / or pets. A human subject can be of any age, gender, race or ethnic group, e.g., Caucasian (white), Asian, African, black, African American, African European, Hispanic, Mideastern, etc. In some embodiments, the subject can be a patient or other subject in a clinical setting. In some embodiments, the subject is already undergoing treatment. In some embodiments, the subject is an embryo, a fetus, neonate, infant, child, adolescent, or adult. In some embodiments, the subject is a human fetus, human neonate, human infant, human child, human adolescent, or human adult. In some embodiments, the subject is an animal embryo, or non-human embryo or non-human primate embryo. In some embodiments, the subject is a human embryo.

[0096] As used herein, the term “host cell”, includes any cell type that is susceptible to transformation, transfection, transduction, and the like with a nucleic acid construct or ceDNA expression vector of the present disclosure. As non-limiting examples, a host cell can be an isolated primary cell, pluripotent stem cells, CD34+cells), induced pluripotent stem cells, or any of a number of immortalized cell lines (e.g., HepG2 cells). Alternatively, a host cell can be an in situ or in vivo cell in a tissue, organ or organism.

[0097] The term “exogenous” refers to a substance present in a cell other than its native source. The term “exogenous” when used herein can refer to a nucleic acid (e.g., a nucleic acid encoding a polypeptide) or a polypeptide that has been introduced by a process involving the hand of man into a biological system such as a cell or organism in which it is not normally found and one wishes to introduce the nucleic acid or polypeptide into such a cell or organism. Alternatively, “exogenous” can refer to a nucleic acid or a polypeptide that has been introduced by a process involving the hand of man into a biological system such as a cell or organism in which it is found in relatively low amounts and one wishes to increase the amount of the nucleic acid or polypeptide in the cell or organism, e.g., to create ectopic expression or levels. In contrast, the term “endogenous” refers to a substance that is native to the biological system or cell.

[0098] The term “sequence identity” refers to the relatedness between two nucleotide sequences. For purposes of the present disclosure, the degree of sequence identity between two deoxyribonucleotide sequences is determined using the Needleman-Wunsch algorithm (Needleman and Wunsch, 1970, supra) as implemented in the Needle program of the EMBOSS package (EMBOSS: The European Molecular Biology Open Software Suite, Rice et al., 2000, supra), preferably version 3.0.0 or later. The optional parameters used are gap open penalty of 10, gap extension penalty of 0.5, and the EDNAFULL (EMBOSS version of NCBI NUC4.4) substitution matrix. The output of Needle labeled “longest identity” (obtained using the -nobrief option) is used as the percent identity and is calculated as follows: (Identical Deoxyribonucleotides.times.100) / (Length of Alignment-Total Number of Gaps in Alignment). The length of the alignment is preferably at least 10 nucleotides, preferably at least 25 nucleotides more preferred at least 50 nucleotides and most preferred at least 100 nucleotides.

[0099] The term “homology” or “homologous” as used herein is defined as the percentage of nucleotide residues that are identical to the nucleotide residues in the corresponding sequence on the target chromosome, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity. Alignment for purposes of determining percent nucleotide sequence homology can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN, ClustalW2 or Megalign (DNASTAR) software. Those skilled in the art can determine appropriate parameters for aligning sequences, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared. In some embodiments, a nucleic acid sequence (e.g., DNA sequence), for example of a homology arm, is considered “homologous” when the sequence is 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 more, identical to the corresponding native or unedited nucleic acid sequence (e.g., genomic sequence) of the host cell.

[0100] The term “heterologous,” as used herein, means a nucleotide or polypeptide sequence that is not found in the native nucleic acid or protein, respectively. A heterologous nucleic acid sequence may be linked to a naturally-occurring nucleic acid sequence (or a variant thereof) (e.g., by genetic engineering) to generate a chimeric nucleotide sequence encoding a chimeric polypeptide. A heterologous nucleic acid sequence may be linked to a variant polypeptide (e.g., by genetic engineering) to generate a nucleic acid sequence encoding a fusion variant polypeptide. Alternatively, the term “heterologous” may refer to a nucleic acid sequence which is not naturally present in a cell or subject.

[0101] A “vector” or “expression vector” is a replicon, such as plasmid, bacmid, phage, virus, virion, or cosmid, to which another DNA segment, i.e., an “insert”, may be attached so as to bring about the replication of the attached segment in a cell. A vector can be a nucleic acid construct designed for delivery to a host cell or for transfer between different host cells. As used herein, a vector can be viral or non-viral in origin and / or in final form, however for the purpose of the presentdisclosure, a “vector” generally refers to a ceDNA vector, as that term is used herein. The term “vector” encompasses any genetic element that is capable of replication when associated with the proper control elements and that can transfer gene sequences to cells. In some embodiments, a vector can be an expression vector or recombinant vector.

[0102] As used herein, the term “expression vector” refers to a vector that directs expression of an RNA or polypeptide from sequences linked to transcriptional regulatory sequences on the vector. The sequences expressed will often, but not necessarily, be heterologous to the cell. An expression vector may comprise additional elements, for example, the expression vector may have two replication systems, thus allowing it to be maintained in two organisms, for example in human cells for expression and in a prokaryotic host for cloning and amplification. The term “expression” refers to the cellular processes involved in producing RNA and proteins and as appropriate, secreting proteins, including where applicable, but not limited to, for example, transcription, transcript processing, translation and protein folding, modification and processing. “Expression products” include RNA transcribed from a gene, and polypeptides obtained by translation of mRNA transcribed from a gene. The term “gene” means the nucleic acid sequence which is transcribed (DNA) to RNA in vitro or in vivo when operably linked to appropriate regulatory sequences. The gene may or may not include regions preceding and following the coding region, e.g., 5’ untranslated (5’UTR) or “leader” sequences and 3’ UTR or “trailer” sequences, as well as intervening sequences (introns) between individual coding segments (exons).

[0103] By “recombinant vector” is meant a vector that includes a heterologous nucleic acid sequence, or “transgene” that is capable of expression in vivo. It should be understood that the vectors described herein can, in some embodiments, be combined with other suitable compositions and therapies. In some embodiments, the vector is episomal. The use of a suitable episomal vector provides a means of maintaining the nucleotide of interest in the subject in high copy number extra chromosomal DNA thereby eliminating potential effects of chromosomal integration.

[0104] The phrase “genetic disease” as used herein refers to a disease, partially or completely, directly or indirectly, caused by one or more abnormalities in the genome, especially a condition that is present from birth. The abnormality may be a mutation, an insertion or a deletion. The abnormality may affect the coding sequence of the gene or its regulatory sequence. According to some embodiments, the genetic disease is a result of a mutation in an FIX gene. According to some embodiments, the genetic disease is a result of decreased FIX protein expression. According to some embodiments, the genetic disease is hemophilia. According to some embodiments, the hemophilia is hemophilia B.

[0105] As used herein, “Clotting Factor IX (fIX; FIX)” is meant to refer to a vitamin K-dependent protein required for the efficient clotting of blood, which functions in coagulation as an activator of factor X. A concentration of about 1-5 pg / ml of fIX in the blood is considered in the normal range. Deficiency of FIX is associated with hemophilia B, and severe cases result when the concentration ofFIX is less than about 1% of the normal concentration of FIX (i.e. less than about 0.01-0.05 mg FIX per ml of blood).

[0106] As used herein, the terms, “administration,” “administering” and variants thereof refers to introducing a composition or agent (e.g., a ceDNA as described herein) into a subject and includes concurrent and sequential introduction of one or more compositions or agents. “Administration” can refer, e.g., to therapeutic, pharmacokinetic, diagnostic, research, placebo, and experimental methods. “Administration” also encompasses in vitro and ex vivo treatments. The introduction of a composition or agent into a subject is by any suitable route, including orally, pulmonarily, intranasally, parenterally (intravenously, intramuscularly, intraperitoneally, or subcutaneously), rectally, intralymphatically, intratumorally, or topically. Administration includes self-administration and the administration by another. Administration can be carried out by any suitable route. A suitable route of administration allows the composition or the agent to perform its intended function. For example, if a suitable route is intravenous, the composition is administered by introducing the composition or agent into a vein of the subject.

[0107] As used herein, the phrases “nucleic acid therapeutic”, “therapeutic nucleic acid” and “TNA” are used interchangeably and refer to any modality of therapeutic using nucleic acids as an active component of therapeutic agent to treat a disease or disorder. As used herein, these phrases refer to RNA-based therapeutics and DNA-based therapeutics. Non-limiting examples of RNA-based therapeutics include mRNA, antisense RNA and oligonucleotides, ribozymes, aptamers, interfering RNAs (RNAi), Dicer-substrate dsRNA, small hairpin RNA (shRNA), asymmetrical interfering RNA (aiRNA), microRNA (miRNA). Non-limiting examples of DNA-based therapeutics include minicircle DNA, minigene, viral DNA (e.g., Lentiviral or AAV genome) or non-viral synthetic DNA vectors, closed-ended linear duplex DNA (ceDNA / CELiD), plasmids, bacmids, doggybone™ DNA vectors, minimalistic immunological-defined gene expression (MIDGE) -vector, nonviral ministring DNA vector (linear-covalently closed DNA vector), or dumbbell-shaped DNA minimal vector (“dumbbell DNA”). According to some embodiments, the therapeutic nucleic acid is a ceDNA.

[0108] As used herein, the term “immunosuppressant” refers to a group of small molecules, monoclonal antibodies or polypeptide antagonists that inhibits protein kinases, such as tyrosine kinases.

[0109] As used herein the term “therapeutic effect” refers to a consequence of treatment, the results of which are judged to be desirable and beneficial. A therapeutic effect can include, directly or indirectly, the arrest, reduction, or elimination of a disease manifestation. A therapeutic effect can also include, directly or indirectly, the arrest reduction or elimination of the progression of a disease manifestation.

[0110] For any therapeutic agent described herein therapeutically effective amount may be initially determined from preliminary in vitro studies and / or animal models. A therapeutically effective dosemay also be determined from human data. The applied dose may be adjusted based on the relative bioavailability and potency of the administered compound. Adjusting the dose to achieve maximal efficacy based on the methods described above and other well-known methods is within the capabilities of the ordinarily skilled artisan. General principles for determining therapeutic effectiveness, which may be found in Chapter 1 of Goodman and Gilman's The Pharmacological Basis of Therapeutics, 10th Edition, McGraw-Hill (New York) (2001), incorporated herein by reference, are summarized below.

[0111] Pharmacokinetic principles provide a basis for modifying a dosage regimen to obtain a desired degree of therapeutic efficacy with a minimum of unacceptable adverse effects. In situations where the drug's plasma concentration can be measured and related to therapeutic window, additional guidance for dosage modification can be obtained.

[0112] As used herein, the terms “treat,” “treating,” and / or “treatment” include abrogating, substantially inhibiting, slowing or reversing the progression of a condition, substantially ameliorating clinical symptoms of a condition, or substantially preventing the appearance of clinical symptoms of a condition, obtaining beneficial or desired clinical results. Treating further refers to accomplishing one or more of the following: (a) reducing the severity of the disorder; (b) limiting development of symptoms characteristic of the disorder(s) being treated; (c) limiting worsening of symptoms characteristic of the disorder(s) being treated; (d) limiting recurrence of the disorder(s) in patients that have previously had the disorder(s); and (e) limiting recurrence of symptoms in patients that were previously asymptomatic for the disorder(s).

[0113] Beneficial or desired clinical results, such as pharmacologic and / or physiologic effects include, but are not limited to, preventing the disease, disorder or condition from occurring in a subject that may be predisposed to the disease, disorder or condition but does not yet experience or exhibit symptoms of the disease (prophylactic treatment), alleviation of symptoms of the disease, disorder or condition, diminishment of extent of the disease, disorder or condition, stabilization (i.e., not worsening) of the disease, disorder or condition, preventing spread of the disease, disorder or condition, delaying or slowing of the disease, disorder or condition progression, amelioration or palliation of the disease, disorder or condition, and combinations thereof, as well as prolonging survival as compared to expected survival if not receiving treatment.

[0114] As used herein, the term “increase,” “enhance,” “raise” (and like terms) generally refers to the act of increasing, either directly or indirectly, a concentration, level, function, activity, or behavior relative to the natural, expected, or average, or relative to a control condition.

[0115] As used herein, the term “suppress,” “decrease,” “interfere,” “inhibit” and / or “reduce” (and like terms) generally refers to the act of reducing, either directly or indirectly, a concentration, level, function, activity, or behavior relative to the natural, expected, or average, or relative to a control condition.

[0116] As used herein, a “control” is meant to refer to a reference standard. In some embodiments, the control is a negative control sample obtained from a healthy patient. In other embodiments, the control is a positive control sample obtained from a patient diagnosed with hemophilia. In still other embodiments, the control is a historical control or standard reference value or range of values (such as a previously tested control sample, such as a group of hemophilia A patients with known prognosis or outcome, or group of samples that represent baseline or normal values). A difference between a test sample and a control can be an increase or conversely a decrease. The difference can be a qualitative difference or a quantitative difference, for example a statistically significant difference. In some examples, a difference is an increase or decrease, relative to a control, of at least about 5%, such as at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 100%, at least about 150%, at least about 200%, at least about 250%, at least about 300%, at least about 350%, at least about 400%, at least about 500%, or greater than 500%.

[0117] As used herein the term "comprising" or "comprises" is used in reference to compositions, methods, and respective component(s) thereof, that are essential to the method or composition, yet open to the inclusion of unspecified elements, whether essential or not.

[0118] As used herein the term "consisting essentially of" refers to those elements required for a given embodiment. The term permits the presence of elements that do not materially affect the basic and novel or functional characteristic(s) of that embodiment. The use of “comprising” indicates inclusion rather than limitation.

[0119] The term "consisting of" refers to compositions, methods, and respective components thereof as described herein, which are exclusive of any element not recited in that description of the embodiment.

[0120] As used in this specification and the appended claims, the singular forms “a,” “an,” and “the” include plural references unless the context clearly dictates otherwise. Thus, for example, references to "the method" includes one or more methods, and / or steps of the type described herein and / or which will become apparent to those persons skilled in the art upon reading this disclosure and so forth. Similarly, the word “or” is intended to include “and” unless the context clearly indicates otherwise. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of this disclosure, suitable methods and materials are described below. The abbreviation, “e.g.” is derived from the Latin exempli gratia, and is used herein to indicate a non limiting example. Thus, the abbreviation “e.g.” is synonymous with the term “for example.”

[0121] Other than in the operating examples, or where otherwise indicated, all numbers expressing quantities of ingredients or reaction conditions used herein should be understood as modified in all instances by the term “about.” The term “about” when used in connection with percentages can mean ±1%. The present disclosure is further explained in detail by the following examples, but the scope of the disclosure should not be limited thereto.

[0122] Groupings of alternative elements or embodiments of the disclosure disclosed herein are not to be construed as limitations. Each group member can be referred to and claimed individually or in any combination with other members of the group or other elements found herein. One or more members of a group can be included in, or deleted from, a group for reasons of convenience and / or patentability. When any such inclusion or deletion occurs, the specification is herein deemed to contain the group as modified thus fulfilling the written description of all Markush groups used in the appended claims.

[0123] In some embodiments of any of the aspects, the disclosure described herein does not concern a process for cloning human beings, processes for modifying the germ line genetic identity of human beings, uses of human embryos for industrial or commercial purposes or processes for modifying the genetic identity of animals which are likely to cause them suffering without any substantial medical benefit to man or animal, and also animals resulting from such processes.

[0124] Other terms are defined herein within the description of the various aspects of the disclosure.

[0125] All patents and other publications; including literature references, issued patents, published patent applications, and co-pending patent applications; cited throughout this application are expressly incorporated herein by reference for the purpose of describing and disclosing, for example, the methodologies described in such publications that might be used in connection with the technology described herein. These publications are provided solely for their disclosure prior to the filing date of the present application. Nothing in this regard should be construed as an admission that the inventors are not entitled to antedate such disclosure by virtue of prior disclosure or for any other reason. Ah statements as to the date or representation as to the contents of these documents is based on the information available to the applicants and does not constitute any admission as to the correctness of the dates or contents of these documents.

[0126] The description of embodiments of the disclosure is not intended to be exhaustive or to limit the disclosure to the precise form disclosed. While specific embodiments of, and examples for, the disclosure are described herein for illustrative purposes, various equivalent modifications are possible within the scope of the disclosure, as those skilled in the relevant art will recognize. For example, while method steps or functions are presented in a given order, alternative embodiments may perform functions in a different order, or functions may be performed substantially concurrently. The teachings of the disclosure provided herein can be applied to other procedures or methods as appropriate. The various embodiments described herein can be combined to provide further embodiments. Aspects of the disclosure can be modified, if necessary, to employ the compositions, functions and concepts of the above references and application to provide yet further embodiments of the disclosure. Moreover, due to biological functional equivalency considerations, some changes can be made in protein structure without affecting the biological or chemical action in kind or amount.These and other changes can be made to the disclosure in light of the detailed description. All such modifications are intended to be included within the scope of the appended claims.

[0127] Specific elements of any of the foregoing embodiments can be combined or substituted for elements in other embodiments. Furthermore, while advantages associated with certain embodiments of the disclosure have been described in the context of these embodiments, other embodiments may also exhibit such advantages, and not all embodiments need necessarily exhibit such advantages to fall within the scope of the disclosure.

[0128] The technology described herein is further illustrated by the following examples which in no way should be construed as being further limiting. It should be understood that this disclosure is not limited to the particular methodology, protocols, and reagents, etc., described herein and as such can vary. The terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present disclosure, which is defined solely by the claims.II. Expression of a FIX Protein from a ceDNA vector

[0129] The technology described herein is directed in general to the expression and / or production of FIX protein in a cell from a non-viral DNA vector, e.g. , a ceDNA vector as described herein. ceDNA vectors for expression of FIX protein are described herein in the section entitled “ceDNA vectors in general”. In particular, ceDNA vectors for expression of FIX protein comprise a pair of ITRs (e.g., symmetric or asymetric as described herein) and between the ITR pair, a nucleic acid encoding an FIX protein, as described herein, operatively linked to a promoter or regulatory sequence. A distinct advantage of ceDNA vectors for expression of FIX protein over traditional AAV vectors, and even lenti viral vectors, is that there is no size constraint for the nucleic acid sequences encoding a desired protein. Thus, even a full length 6.8kb FIX protein can be expressed from a single ceDNA vector. Thus, the ceDNA vectors described herein can be used to express a therapeutic FIX protein in a subject in need thereof, e.g., a subject with hemophilia B.

[0130] As one will appreciate, the ceDNA vector technologies described herein can be adapted to any level of complexity or can be used in a modular fashion, where expression of different components of a FIX protein can be controlled in an independent manner. For example, it is specifically contemplated that the ceDNA vector technologies designed herein can be as simple as using a single ceDNA vector to express a single gene sequence (e.g., a FIX protein) or can be as complex as using multiple ceDNA vectors, where each vector expresses multiple FIX proteins or associated co-factors or accessory proteins that are each independently controlled by different promoters. The following embodiments are specifically contemplated herein and can adapted by one of skill in the art as desired.

[0131] In one embodiment, a single ceDNA vector can be used to express a single component of a FIX protein. Alternatively, a single ceDNA vector can be used to express multiple components (e.g., at least 2) of a FIX protein under the control of a single promoter (e.g., a strong promoter), optionally using an IRES sequence(s) to ensure appropriate expression of each of the components, e.g., co-factors or accessory proteins.

[0132] Also contemplated herein, in another embodiment, is a single ceDNA vector comprising at least two inserts (e.g., expressing a heavy chain or light chain), where the expression of each insert is under the control of its own promoter. The promoters can include multiple copies of the same promoter, multiple different promoters, or any combination thereof. As one of skill in the art will appreciate, it is often desirable to express components of a FIX protein at different expression levels, thus controlling the stoichiometry of the individual components expressed to ensure efficient a FIX protein folding and combination in the cell.

[0133] Additional variations of ceDNA vector technologies can be envisioned by one of skill in the art or can be adapted from protein production methods using conventional vectors.A. Factor IX (FIX) expression

[0134] In some embodiments, a transgene encoding the FIX protein can also encode a secretory sequence so that the a FIX protein is directed to the Golgi Apparatus and Endoplasmic Reticulum whence a FIX protein will be folded into the correct conformation by chaperone molecules as it passes through the ER and out of the cell. Exemplary secretory sequences include, but are not limited to VH- 02 (SEQ ID NO: 88) and VK-A26 (SEQ ID NO: 89) and IgK signal sequence (SEQ ID NO: 126), as well as a Glue secretory signal that allows the tagged protein to be secreted out of the cytosol (SEQ ID NO: 188), TMD-ST secretory sequence, that directs the tagged protein to the golgi (SEQ ID NO: 189).

[0135] Regulatory switches can also be used to fine tune the expression of the FIX protein so that the FIX protein is expressed as desired, including but not limited to expression of the FIX protein at a desired expression level or amount, or alternatively, when there is the presence or absence of particular signal, including a cellular signaling event. For instance, as described herein, expression of the FIX protein from the ceDNA vector can be turned on or turned off when a particular condition occurs, as described herein in the section entitled Regulatory Switches.

[0136] For example, and for illustration purposes only, FIX proteins can be used to turn off undesired reaction, such as too high a level of production of the FIX protein. The FIX gene can contain a signal peptide marker to bring the FIX protein to the desired cell. However, in either situation it can be desirable to regulate the expression of the FIX protein. ceDNA vectors readily accommodate the use of regulatory switches.

[0137] A distinct advantage of ceDNA vectors over traditional AAV vectors, and even lentiviral vectors, is that there is no size constraint for the nucleic acid sequences encoding the FIX protein.Thus, even a full-length FIX, as well as optionally any co-factors or assessor proteins can be expressed from a single ceDNA vector. In addition, depending on the necessary stiochemistry one can express multiple segments of the same FIX protein, and can use same or different promoters, and can also use regulatory switches to fine tune expression of each region. For example, as shown in the Examples, a ceDNA vector that comprises a dual promoter system can be used, so that a different promoter is used for each domain of the FIX protein. Use of a ceDNA plasmid to produce the FIX protein can include a unique combination of promoters for expression of the domains of the FIX protein that results in theproper ratios of each domain for the formation of functional FIX protein. Accordingly, in some embodiments, a ceDNA vector can be used to express different regions of FIX protein separately (e.g., under control of a different promoter).

[0138] In another embodiment, the FIX protein expressed from the ceDNA vectors further comprises an additional functionality, such as fluorescence, enzyme activity, secretion signal or immune cell activator.

[0139] In some embodiments, the ceDNA encoding the FIX protein can further comprise a linker domain, for example. As used herein “linker domain” refers to an oligo- or polypeptide region from about 2 to 100 amino acids in length, which links together any of the domains / regions of the FIX protein as described herein. In some embodiment, linkers can include or be composed of flexible residues such as glycine and serine so that the adjacent protein domains are free to move relative to one another. Longer linkers may be used when it is desirable to ensure that two adjacent domains do not sterically interfere with one another. Linkers may be cleavable or non-cleavable. Examples of cleavable linkers include 2 A linkers (for example T2A), 2A-like linkers or functional equivalents thereof and combinations thereof. The linker can be a linker region is T2A derived from Thosea asigna virus.

[0140] It is well within the abilities of one of skill in the art to take a known and / or publically available protein sequence of e.g., the FIX etc., and reverse engineer a cDNA sequence to encode such a protein. The cDNA can then be codon optimized to match the intended host cell and inserted into a ceDNA vector as described herein.B. ceDNA vectors expressing FIX Protein

[0141] A ceDNA vector for expression of FIX protein having one or more sequences encoding a desired FIX can comprise regulatory sequences such as promoters, secretion signals, polyA regions, and enhancers. At a minimum, a ceDNA vector comprises one or more nucleic acid sequences encoding a FIX protein.

[0142] In order to achieve highly efficient and accurate FIX protein assembly, it is specifically contemplated in some embodiments that the FIX protein comprise an endoplasmic reticulum ER leader sequence to direct it to the ER, where protein folding occurs. For example, a sequence that directs the expressed protein(s) to the ER for folding.

[0143] In some embodiments, a cellular or extracellular localization signal (e.g., secretory signal, nuclear localization signal, mitochondrial localization signal etc.) is comprised in the ceDNA vector to direct the secretion or desired subcellular localization of FIX such that the FIX protein can bind to intracellular target(s) (e.g., an intrabody) or extracellular target(s).

[0144] In some embodiments, a ceDNA vector for expression of FIX protein as described herein permits the assembly and expression of any desired FIX protein in a modular fashion. As used herein, the term “modular” refers to elements in a ceDNA expressing plasmid that can be readily removed from the construct. For example, modular elements in a ceDNA-generating plasmid comprise uniquepairs of restriction sites flanking each element within the construct, enabling the exclusive manipulation of individual elements (see e.g., FIGs. 1A-1G). Thus, the ceDNA vector platform can permit the expression and assembly of any desired FIX protein configuration. Provided herein in various embodiments are ceDNA plasmid vectors that can reduce and / or minimize the amount of manipulation required to assemble a desired ceDNA vector encoding FIX protein.C. Exemplary FIX Proteins expressed by ceDNA vectors

[0145] In particular, a ceDNA vector for expression of FIX protein as disclosed herein can encode, for example, but is not limited to, FIX proteins, as well as variants, and / or active fragments thereof, for use in the treatment, prophylaxis, and / or amelioration of one or more symptoms of hemophilia B. In one aspect, the hemophilia B is a human hemophilia B.(i) FIX therapeutic proteins and fragments thereof

[0146] Essentially any version of the FIX therapeutic protein or fragment thereof (e.g., functional fragment) can be encoded by and expressed in and from a ceDNA vector as described herein. One of skill in the art will understand that an FIX therapeutic protein includes all splice variants and orthologs of the FIX protein. A FIX therapeutic protein includes intact molecules as well as fragments (e.g., functional fragments) thereof.Factor IX (FIX)

[0147] Factor IX (or Christmas factor) (EC 3.4.21.22) is one of the serine proteases of the coagulation system; it belongs to peptidase family SI. Deficiency of this protein causes hemophilia B. Factor IX is produced as a zymogen, an inactive precursor. It is processed to remove the signal peptide, glycosylated and then cleaved by factor XIa (of the contact pathway) or factor Vila (of the tissue factor pathway) to produce a two-chain form where the chains are linked by a disulfide bridge. When activated into factor IXa, in the presence of Ca2+, membrane phospholipids, and a Factor VIII cofactor, it hydrolyses one arginine-isoleucine bond in factor X to form factor Xa. Factor IX is Vitamin-K dependent. Factor IX is inhibited by antithrombin.

[0148] The Factor IX gene or protein can also be referred to as F9, Coagulation Factor IX, Plasma Thromboplastin Component, Plasma Thromboplastic Component, Christmas Factor, EC 3.4.21.22, PTC, Christmas Disease, Factor IX F9, Hemophilia B, Factor IX, EC 3.4.21, Factor 9, F9 P22, THPH8, HEMB, FIX, or P19.

[0149] The gene of human FIX lies in the X chromosome, has 8 exons, and spans 33.5 Kb. Factor IX is produced in the liver, and the inactive precursor protein is processed in the endoplasmic reticulum and Golgi, where it undergoes multiple post-translational modifications and is secreted into the bloodstream upon proteolytic cleavage of the propeptide.

[0150] Expression of Factor IX mRNA occurs primarily in the liver. Additional tissues can express Factor IX mRNA, including bone marrow, whole blood, lymph nodes, thymus, brain, cerebral cortex, cerebellum, retina, spinal cord, tibial nerve, heart, artery, smooth muscle, skeletal muscle, smallintestine, colon, adipocytes, kidney, lung, spleen, stomach, esophagus, bladder, pancreas, thyroid, salivary gland, adrenal gland, pituitary gland, breast, skin, ovary, uterus, placenta, prostate, and testis.

[0151] Factor IX protein is predominately expressed in the serum, plasma, and monocytes. Factor IX protein expression can also be detected tissues throughout the body, including but not limited to the tonsil, bone marrow mesenchymal stem cells, spinal cord, heart, colon muscle, oral epithelium, esophagus, stomach, cardia, colon, rectum, liver, fetal liver, kidney, spleen, synovial fluid, vitreous humor, salivary gland, thyroid gland, adrenal gland, breast, pancreas, islet of Langerhans, gallbladder, prostate, urine, urinary bladder, skin, placenta, uterus, cervix, ovary, testis, and seminal vesicle.

[0152] There are at least two known mRNA variants each encoding one protein isoform of Factor IX. Variant 1 represents the longer transcript and encodes the longer isoform 1. Variant 2 lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. It encodes isoform 2, which is shorter than isoform 1. Isoform 2 may undergo proteolytic processing similar to isoform 1. Representative sequence identifiers for mRNA variants 1 and 2 and protein isoforms 1 and 2 are shown below:Homo sapiens coagulation factor IX (F9), transcript variant 1, mRNA (NCBI Reference Sequence: NM_000133.3) 1386 bp (SEQ ID NO: 377)Homo sapiens coagulation factor IX isoform 1 preproprotein (NCBI Reference Sequence: NP_000124.1) 461 amino acids (SEQ ID NO: 378)Homo sapiens coagulation factor IX (F9), transcript variant 2, mRNA (NCBI Reference Sequence: NM_001313913.1) 2688 bp (SEQ ID NO: 379)Homo sapiens coagulation factor IX isoform 2 precursor (NCBI Reference Sequence: NP_001300842.1) 423 amino acids (SEQ ID NO: 380)

[0153] A distinct advantage of ceDNA vectors over traditional AAV vectors, and even lentiviral vectors, is that there is no size constraint for the nucleic acid sequences encoding a desired protein. Thus, multiple full length FIX therapeutic proteins can be expressed from a single ceDNA vector.

[0154] Expression of FIX therapeutic protein or fragment thereof from a ceDNA vector can be achieved both spatially and temporally using one or more inducible or repressible promoters, as known in the art or described herein, including regulatory switches as described herein.

[0155] In one embodiment, FIX therapeutic protein is an “therapeutic protein variant,” which refers to the FIX therapeutic protein having an altered amino acid sequence, composition or structure as compared to its corresponding native FIX therapeutic protein. In one embodiment, FIX is a functional version ( e.g ., wild type). It may also be useful to express a mutant version of FIX protein such as a point mutation or deletion mutation that leads to hemophilia B, e.g., for an animal model of the disease and / or for assessing drugs for hemophilia B. Delivery of mutant or modified FIX proteins to a cell or animal model system can be done in order to generate a disease model. Such a cellular or animal model can be used for research and / or drug screening. FIX therapeutic protein expressed from the ceDNA vectorsmay further comprise a sequence / moiety that confers an additional functionality, such as fluorescence, enzyme activity, or secretion signal. In one embodiment, an FIX therapeutic protein variant comprises a non-native tag sequence for identification (e.g., an immunotag) to allow it to be distinguished from endogenous FIX therapeutic protein in a recipient host cell.

[0156] It is well within the abilities of one of skill in the art to take a known and / or publically available protein sequence of e.g., FIX therapeutic protein and reverse engineer a cDNA sequence to encode such a protein. The cDNA can then be codon optimized to match the intended host cell and inserted into a ceDNA vector as described herein.

[0157] In one embodiment, the FIX therapeutic protein encoding sequence can be derived from an existing host cell or cell line, for example, by reverse transcribing mRNA obtained from the host and amplifying the sequence using PCR.( ii ) FIX therapeutic protein expressing ceDNA vectors

[0158] A ceDNA vector having one or more sequences encoding a desired FIX therapeutic protein can comprise regulatory sequences such as promoters {e.g., see Table 7), secretion signals, poly A regions {e.g., see Table 10), and enhancers {e.g., see Table8). At a minimum, a ceDNA vector comprises one or more nucleic acid sequences encoding the FIX therapeutic protein or functional fragment thereof. Exemplary cassette inserts for generating ceDNA vectors encoding the FIX therapeutic proteins are depicted in Figures 1A-1G. In one embodiment, the ceDNA vector comprises an FIX sequence listed in Table 1 herein.

[0159] Table 1: Exemplary FIX sequences for treatment of hemophilia B(iii) FIX therapeutic proteins and uses thereof for the treatment of hemophilia B

[0160] The ceDNA vectors described herein can be used to deliver therapeutic FIX proteins for treatment of hemophilia B associated with inappropriate expression of the FIX protein and / or mutations within the FIX proteins.

[0161] ceDNA vectors as described herein can be used to express any desired FIX therapeutic protein. Exemplary therapeutic FIX therapeutic proteins include, but are not limited to any FIX protein expressed by the sequences as set forth in Table 1 herein.

[0162] In one embodiment, the expressed FIX therapeutic protein is functional for the treatment of a Hemophilia B. In some embodiments, FIX therapeutic protein does not cause an immune system reaction.

[0163] In another embodiment, the ceDNA vectors encoding FIX therapeutic protein or fragment thereof (e.g., functional fragment) can be used to generate a chimeric protein. Thus, it is specifically contemplated herein that a ceDNA vector expressing a chimeric protein can be administered to e.g., to any one or more tissues selected from: liver, kidneys, gallbladder, prostate, adrenal gland. In some embodiments, when a ceDNA vector expressing FIX is administerd to an infant, or administered to a subject in utero, one can administer a ceDNA vector expressing FIX to any one or more tissues selected from: liver, adrenal gland, heart, intestine, lung, and stomach, or to a liver stem cell precursor thereof for the in vivo or ex vivo treatment of hemophilia B.

[0164] Hemophilia B

[0165] Hemophilia B is a blood clotting disorder that causes easy bruising and bleeding due to an inherited mutation of the gene for factor IX, and resulting in a deficiency of factor IX. Hemophilia B is inherited as an X-linked recessive trait. Current treatments to prevent bleeding in people with hemophilia B involves intravenous infusion of factor IX and / or blood transfusions.

[0166] There are many complications related to treatment of hemophilia B. In children, an easily accessible intravenous port can be inserted to minimize frequent traumatic intravenous cannuiation. However, these ports are associated with high infection rate and a risk of clots forming at the tip of the catheter, rendering it useless. Viral infections can be common in hemophiliacs due to frequent blood transfusions which put patients at risk of acquiring blood borne infections, such as HIV, hepatitis B and hepatitis C. Prion infections can also be transmitted by blood transfusions.

[0167] In some cases, mutations in the promoter region of the FIX gene result in the less severe hemophilia B Leiden, characterized as a nearly complete absence of FIX in childhood and steady increase in the level of endogenous FIX during puberty to the near-normal values.

[0168] Coagulation Cascade

[0169] Coagulation, also known as clotting, is the process by which blood changes from a liquid to a gel, forming a blood clot. It potentially results in hemostasis, the cessation of blood loss from a damaged vessel, followed by repair. The mechanism of coagulation involves activation, adhesion and aggregation of platelets along with deposition and maturation of fibrin. Disorders of coagulation are disease states which can result in bleeding (hemorrhage or bruising) or obstructive clotting (thrombosis).

[0170] Coagulation begins almost instantly after an injury to the blood vessel has damaged the endothelium lining the blood vessel. Exposure of blood to the subendothelial space initiates two processes: changes in platelets, and the exposure of subendothelial tissue factor to plasma Factor VII, which ultimately leads to fibrin formation. Platelets immediately form a plug at the site of injury; this is called primary hemostasis. Secondary hemostasis occurs simultaneously: additional coagulation factors or clotting factors beyond Factor VII (including Factor VIII) respond in a complex cascade to form fibrin strands, which strengthen the platelet plug.

[0171] The coagulation cascade of secondary hemostasis has two initial pathways which lead to fibrin formation. These are the contact activation pathway (also known as the intrinsic pathway), and the tissue factor pathway (also known as the extrinsic pathway), which both lead to the same fundamental reactions that produce fibrin. The primary pathway for the initiation of blood coagulation is the tissue factor (extrinsic) pathway. The pathways are a series of reactions, in which a zymogen (inactive enzyme precursor) of a serine protease and its glycoprotein co-factor are activated to become active components that then catalyze the next reaction in the cascade, ultimately resulting in cross- linked fibrin. Coagulation factors are generally indicated by Roman numerals, with a lowercase a appended to indicate an active form.

[0172] The coagulation factors are generally serine proteases (enzymes), which act by cleaving downstream proteins. The exceptions are tissue factor, FV, FVIII, FXIII. Tissue factor, FV and FVTTT are glycoproteins, and Factor XIII is a transglutaminase. The coagulation factors circulate as inactive zymogens. The coagulation cascade is therefore classically divided into three pathways. The tissuefactor and contact activation pathways both activate the "final common pathway" of factor X, thrombin and fibrin.

[0173] The main role of the tissue factor (extrinsic) pathway is to generate a "thrombin burst", a process by which thrombin, the most important constituent of the coagulation cascade in terms of its feedback activation roles, is released very rapidly. FVIIa circulates in a higher amount than any other activated coagulation factor. The process includes the following steps:

[0174] Step 1 : Following damage to the blood vessel, FVII leaves the circulation and comes into contact with tissue factor (TF) expressed on tissue-factor-bearing cells (stromal fibroblasts and leukocytes), forming an activated complex (TF-FVIIa).

[0175] Step 2: TF-FVIIa activates FIX and FX.

[0176] Step 3: FVII is itself activated by thrombin, FXIa, FXII and FXa.

[0177] Step 4: The activation of FX (to form FXa) by TF-FVIIa is almost immediately inhibited by tissue factor pathway inhibitor (TFPI).

[0178] Step 5: FXa and its co-factor FVa form the prothrombinase complex, which activates prothrombin to thrombin.

[0179] Step 6: Thrombin then activates other components of the coagulation cascade, including FV and FVIII (which forms a complex with FIX), and activates and releases FVIII from being bound to von Willebrand factor (vWF).

[0180] Step 7: FVIIIa is the co-factor of FIXa, and together they form the “tenase” complex, which activates FX; and so the cycle continues.

[0181] The contact activation (intrinsic) pathway begins with formation of the primary complex on collagen by high-molecular- weight kininogen (HMWK), prekallikrein, and FXII (Hageman factor). Prekallikrein is converted to kallikrein and FXII becomes FXIIa. FXIIa converts FXI into FXIa. Factor XIa activates FIX, which with its co-factor FVIIIa form the tenase complex, which activates FX to FXa. The minor role that the contact activation pathway has in initiating clot formation can be illustrated by the fact that patients with severe deficiencies of FXII, HMWK, and prekallikrein do not have a bleeding disorder. Instead, contact activation system is more involved in inflammation, and innate immunity.

[0182] The final common pathway shared by the intrinsic and extrinsic coagulation pathways involves the conversion of prothrombin into thrombin and fibrinogen into fibrin. Thrombin has a large array of functions, not only the conversion of fibrinogen to fibrin, the building block of a hemostatic plug. In addition, it is the most important platelet activator and on top of that it activates Factors VIIIand V and their inhibitor protein C (in the presence of thrombomodulin), and it activates Factor XIII, which forms covalent bonds that crosslink the fibrin polymers that form from activated monomers.

[0183] Following activation by the contact factor or tissue factor pathways, the coagulation cascade is maintained in a prothrombotic state by the continued activation of FVIII and FIX to form the tenase complex, until it is down-regulated by the anticoagulant pathways.

[0184] The methods comprise administering to the subject an effective amount of a composition comprising a ceDNA vector encoding the FIX therapeutic protein or fragment thereof (e.g., functional fragment) as described herein. As will be appreciated by a skilled practitioner, the term “effective amount” refers to the amount of the ceDNA composition administered that results in expression of the protein in a “therapeutically effective amount” for the treatment of a disease or disorder.

[0185] The dosage ranges for the composition comprising a ceDNA vector encoding the FIX therapeutic protein or fragment thereof (e.g., functional fragment) depends upon the potency (e.g., efficiency of the promoter), and includes amounts large enough to produce the desired effect, e.g., expression of the desired FIX therapeutic protein, for the treatment of hemophilia B. The dosage should not be so large as to cause unacceptable adverse side effects. Generally, the dosage will vary with the particular characteristics of the ceDNA vector, expression efficiency and with the age, condition, and sex of the patient. The dosage can be determined by one of skill in the art and, unlike traditional AAV vectors, can also be adjusted by the individual physician in the event of any complication because ceDNA vectors do not comprise immune activating capsid proteins that prevent repeat dosing.

[0186] Administration of the ceDNA compositions described herein can be repeated for a limited period of time. In some embodiments, the doses are given periodically or by pulsed administration. In a preferred embodiment, the doses recited above are administered over several months. The duration of treatment depends upon the subject’s clinical progress and responsiveness to therapy. Booster treatments over time are contemplated. Further, the level of expression can be titrated as the subject grows.

[0187] An FIX therapeutic protein can be expressed in a subject for at least 1 week, at least 2 weeks, at least 1 month, at least 2 months, at least 6 months, at least 12 months / one year, at least 2 years, at least 5 years, at least 10 years, at least 15 years, at least 20 years, at least 30 years, at least 40 years, at least 50 years or more. Long-term expression can be achieved by repeated administration of the ceDNA vectors described herein at predetermined or desired intervals.

[0188] As used herein, the term “therapeutically effective amount” is an amount of an expressed FIX therapeutic protein, or functional fragment thereof that is sufficient to produce a statistically significant, measurable change in expression of a disease biomarker or reduction in a given disease symptom (see “Efficacy Measurement" below). Such effective amounts can be gauged in clinical trials as well as animal studies for a given ceDNA composition.

[0189] Precise amounts of the ceDNA vector required to be administered depend on the judgment of the practitioner and are particular to each individual. Suitable regimes for administration are also variable, but are typified by an initial administration followed by repeated doses at one or more intervals by a subsequent injection or other administration. Alternatively, continuous intravenous infusion sufficient to maintain concentrations in the blood in the ranges specified for in vivo therapies are contemplated, particularly for the treatment of acute diseases / disorders.

[0190] Agents useful in the methods and compositions described herein can be administered topically, intravenously (by bolus or continuous infusion), intracellular injection, intratissue injection, orally, by inhalation, intraperitoneally, intramuscularly, subcutaneously, intracavity, and can be delivered by peristaltic means, if desired, or by other means known by those skilled in the art. The agent can be administered systemically, if so desired. It can also be administered in utero.

[0191] The efficacy of a given treatment for hemophilia B, can be determined by the skilled clinician. However, a treatment is considered “effective treatment," as the term is used herein, if any one or all of the signs or symptoms of the disease or disorder is / are altered in a beneficial manner, or other clinically accepted symptoms or markers of disease are improved, or ameliorated, e.g., by at least 10% following treatment with a ceDNA vector encoding FIX, or a functional fragment thereof. Efficacy can also be measured by failure of an individual to worsen as assessed by stabilization of the disease, or the need for medical interventions (i.e., progression of the disease is halted or at least slowed). Methods of measuring these indicators are known to those of skill in the art and / or described herein. Treatment includes any treatment of a disease in an individual or an animal (some non-limiting examples include a human, or a mammal) and includes: (1) inhibiting the disease, e.g., arresting, or slowing progression of the disease or disorder; or (2) relieving the disease, e.g., causing regression of symptoms; and (3) preventing or reducing the likelihood of the development of the disease, or preventing secondary diseases / disorders associated with the disease, such as liver or kidney failure. An effective amount for the treatment of a disease means that amount which, when administered to a mammal in need thereof, is sufficient to result in effective treatment as that term is defined herein, for that disease.

[0192] Efficacy of an agent can be determined by assessing physical indicators that are particular to hemophilia B. Standard methods of analysis of hemophilia B indicators are known in the art.

[0193] In some embodiments, a ceDNA vector for expression of FIX protein as disclosed herein can also encode co-factors or other polypeptides, sense or antisense oligonucleotides, or RNAs (coding or non-coding; e.g., siRNAs, shRNAs, micro-RNAs, and their antisense counterparts (e.g., antagoMiR)) that can be used in conjunction with the FIX protein expressed from the ceDNA. Additionally, expression cassettes comprising sequence encoding an FIX protein can also include an exogenous sequence that encodes a reporter protein to be used for experimental or diagnostic purposes, such as b-lactamase, b -galactosidase (FacZ), alkaline phosphatase, thymidine kinase, green fluorescent protein (GFP), chloramphenicol acetyltransferase (CAT), luciferase, and others well known in the art.

[0194] In one embodiment, the ceDNA vector comprises a nucleic acid sequence to express the FIX protein that is functional for the treatment of hemophilia B. In a preferred embodiment, the therapeutic FIX protein does not cause an immune system reaction, unless so desired.III. ceDNA vector in general for use in production of FIX therapeutic proteins

[0195] Embodiments of the disclosure are based on methods and compositions comprising close ended linear duplexed (ceDNA) vectors that can express the FIX transgene. In some embodiments, the transgene is a sequence encoding an FIX protein. The ceDNA vectors for expression of FIX protein as described herein are not limited by size, thereby permitting, for example, expression of ah of the components necessary for expression of a transgene from a single vector. The ceDNA vector for expression of FIX protein is preferably duplex, e.g. self-complementary, over at least a portion of the molecule, such as the expression cassette (e.g. ceDNA is not a double stranded circular molecule).The ceDNA vector has covalently closed ends, and thus is resistant to exonuclease digestion (e.g. exonuclease I or exonuclease III), e.g. for over an hour at 37°C.

[0196] In general, a ceDNA vector for expression of FIX protein as disclosed herein, comprises in the 5’ to 3’ direction: a first adeno-associated virus (AAV) inverted terminal repeat (ITR), a nucleic acid sequence of interest (for example an expression cassette as described herein) and a second AAV ITR. The ITR sequences selected from any of: (i) at least one WT ITR and at least one modified AAV inverted terminal repeat (mod-ITR) (e.g., asymmetric modified ITRs); (ii) two modified ITRs where the mod-ITR pair have a different three-dimensional spatial organization with respect to each other (e.g., asymmetric modified ITRs), or (iii) symmetrical or substantially symmetrical WT-WT ITR pair, where each WT-ITR has the same three-dimensional spatial organization, or (iv) symmetrical or substantially symmetrical modified ITR pair, where each mod-ITR has the same three-dimensional spatial organization.

[0197] Encompassed herein are methods and compositions comprising the ceDNA vector for FIX protein production, which may further include a delivery system, such as but not limited to, a liposome nanoparticle delivery system. Non-limiting exemplary liposome nanoparticle systems encompassed for use are disclosed herein. In some aspects, the disclosure provides for a lipid nanoparticle comprising ceDNA and an ionizable lipid. For example, a lipid nanoparticle formulation that is made and loaded with a ceDNA vector obtained by the process is disclosed in International Application PCT / US2018 / 050042, filed on September 7, 2018, which is incorporated herein.

[0198] The ceDNA vectors for expression of FIX protein as disclosed herein have no packaging constraints imposed by the limiting space within the viral capsid. ceDNA vectors represent a viable eukaryoticahy-produced alternative to prokaryote-produced plasmid DNA vectors, as opposed to encapsulated AAV genomes. This permits the insertion of control elements, e.g., regulatory switches as disclosed herein, large transgenes, multiple transgenes etc.

[0199] FIG. 1A-1E show schematics of non-limiting, exemplary ceDNA vectors for expression of FIX protein, or the corresponding sequence of ceDNA plasmids. ceDNA vectors for expression ofFIX protein are capsid-free and can be obtained from a plasmid encoding in this order: a first ITR, an expression cassette comprising a transgene and a second ITR. The expression cassette may include one or more regulatory sequences that allows and / or controls the expression of the transgene, e.g., where the expression cassette can comprise one or more of, in this order: an enhancer / promoter, an ORF reporter (transgene), a post-transcription regulatory element (e.g., WPRE), and a polyadenylation and termination signal (e.g., BGH poly A).

[0200] The expression cassette can also comprise an internal ribosome entry site (IRES) and / or a 2A element. The cis-regulatory elements include, but are not limited to, a promoter, a riboswitch, an insulator, a mir-regulatable element, a post-transcriptional regulatory element, a tissue- and cell type- specific promoter and an enhancer. In some embodiments the ITR can act as the promoter for the transgene, e.g., FIX protein. In some embodiments, the ceDNA vector comprises additional components to regulate expression of the transgene, for example, a regulatory switch, which are described herein in the section entitled “Regulatory Switches” for controlling and regulating the expression of the FIX protein, and can include if desired, a regulatory switch which is a kill switch to enable controlled cell death of a cell comprising a ceDNA vector.

[0201] The expression cassette can comprise more than 4000 nucleotides, 5000 nucleotides,10,000 nucleotides or 20,000 nucleotides, or 30,000 nucleotides, or 40,000 nucleotides or 50,000 nucleotides, or any range between about 4000-10,000 nucleotides or 10,000-50,000 nucleotides, or more than 50,000 nucleotides. In some embodiments, the expression cassette can comprise a transgene in the range of 500 to 50,000 nucleotides in length. In some embodiments, the expression cassette can comprise a transgene in the range of 500 to 75,000 nucleotides in length. In some embodiments, the expression cassette can comprise a transgene which is in the range of 500 to 10,000 nucleotides in length. In some embodiments, the expression cassette can comprise a transgene which is in the range of 1000 to 10,000 nucleotides in length. In some embodiments, the expression cassette can comprise a transgene which is in the range of 500 to 5,000 nucleotides in length. The ceDNA vectors do not have the size limitations of encapsidated AAV vectors, thus enable delivery of a large-size expression cassette to provide efficient transgene expression. In some embodiments, the ceDNA vector is devoid of prokaryote-specific methylation.

[0202] ceDNA expression cassette can include, for example, an expressible exogenous sequence (e.g., open reading frame) or transgene that encodes a protein that is either absent, inactive, or insufficient activity in the recipient subject or a gene that encodes a protein having a desired biological or a therapeutic effect. The transgene can encode a gene product that can function to correct the expression of a defective gene or transcript. In principle, the expression cassette can include any gene that encodes a protein, polypeptide or RNA that is either reduced or absent due to a mutation or which conveys a therapeutic benefit when overexpressed is considered to be within the scope of the disclosure.

[0203] The expression cassette can comprise any transgene (e.g., encoding FIX protein), for example, FIX protein useful for treating hemophilia B in a subject, i.e., a therapeutic FIX protein. A ceDNA vector can be used to deliver and express any FIX protein of interest in the subject, alone or in combination with nucleic acids encoding polypeptides, or non-coding nucleic acids (e.g., RNAi, miRs etc.), as well as exogenous genes and nucleic acid sequences, including virus sequences in a subjects’ genome, e.g., HIV virus sequences and the like. Preferably a ceDNA vector disclosed herein is used for therapeutic purposes (e.g., for medical, diagnostic, or veterinary uses) or immunogenic polypeptides. In certain embodiments, a ceDNA vector is useful to express any gene of interest in the subject, which includes one or more polypeptides, peptides, ribozymes, peptide nucleic acids, siRNAs, RNAis, antisense oligonucleotides, antisense polynucleotides, or RNAs (coding or non-coding; e.g., siRNAs, shRNAs, micro-RNAs, and their antisense counterparts (e.g., antagoMiR)), antibodies, fusion proteins, or any combination thereof.

[0204] The expression cassette can also encode polypeptides, sense or antisense oligonucleotides, or RNAs (coding or non-coding; e.g., siRNAs, shRNAs, micro-RNAs, and their antisense counterparts (e.g., antagoMiR)). Expression cassettes can include an exogenous sequence that encodes a reporter protein to be used for experimental or diagnostic purposes, such as b-lactamase, b -galactosidase (LacZ), alkaline phosphatase, thymidine kinase, green fluorescent protein (GFP), chloramphenicol acetyltransferase (CAT), luciferase, and others well known in the art.

[0205] Sequences provided in the expression cassette, expression construct of a ceDNA vector for expression of FIX protein described herein can be codon optimized for the target host cell. As used herein, the term “codon optimized” or “codon optimization” refers to the process of modifying a nucleic acid sequence for enhanced expression in the cells of the vertebrate of interest, e.g., mouse or human, by replacing at least one, more than one, or a significant number of codons of the native sequence (e.g., a prokaryotic sequence) with codons that are more frequently or most frequently used in the genes of that vertebrate. Various species exhibit particular bias for certain codons of a particular amino acid. Typically, codon optimization does not alter the amino acid sequence of the original translated protein. Optimized codons can be determined using e.g., Aptagen's GENE FORGE® codon optimization and custom gene synthesis platform (Aptagen, Inc., 2190 Fox Mill Rd. Suite 300, Herndon, Va. 20171) or another publicly available database. In some embodiments, the nucleic acid encoding the FIX protein is optimized for human expression, and / or is a human FIX, or functional fragment thereof, as known in the art.

[0206] A transgene expressed by the ceDNA vector for expression of FIX protein as disclosed herein encodes FIX protein. There are many structural features of ceDNA vectors for expression of FIX protein that differ from plasmid-based expression vectors. ceDNA vectors may possess one or more of the following features: the lack of original (i.e., not inserted) bacterial DNA, the lack of a prokaryotic origin of replication, being self-containing, i.e., they do not require any sequences other than the two ITRs, including the Rep binding and terminal resolution sites (RBS and TRS), and anexogenous sequence between the ITRs, the presence of ITR sequences that form hairpins, and the absence of bacterial-type DNA methylation or indeed any other methylation considered abnormal by a mammalian host. In general, it is preferred for the present vectors not to contain any prokaryotic DNA but it is contemplated that some prokaryotic DNA may be inserted as an exogenous sequence, as a non-limiting example in a promoter or enhancer region. Another important feature distinguishing ceDNA vectors from plasmid expression vectors is that ceDNA vectors are single-strand linear DNA having closed ends, while plasmids are always double-strand DNA.

[0207] ceDNA vectors for expression of FIX protein produced by the methods provided herein preferably have a linear and continuous structure rather than a non-continuous structure, as determined by restriction enzyme digestion assay (FIG. 4D). The linear and continuous structure is believed to be more stable from attack by cellular endonucleases, as well as less likely to be recombined and cause mutagenesis. Thus, a ceDNA vector in the linear and continuous structure is a preferred embodiment. The continuous, linear, single strand intramolecular duplex ceDNA vector can have covalently bound terminal ends, without sequences encoding AAV capsid proteins. These ceDNA vectors are structurally distinct from plasmids (including ceDNA plasmids described herein), which are circular duplex nucleic acid molecules of bacterial origin. The complimentary strands of plasmids may be separated following denaturation to produce two nucleic acid molecules, whereas in contrast, ceDNA vectors, while having complimentary strands, are a single DNA molecule and therefore even if denatured, remain a single molecule. In some embodiments, ceDNA vectors as described herein can be produced without DNA base methylation of prokaryotic type, unlike plasmids. Therefore, the ceDNA vectors and ceDNA-plasmids are different both in term of structure (in particular, linear versus circular) and also in view of the methods used for producing and purifying these different objects (see below), and also in view of their DNA methylation which is of prokaryotic type for ceDNA-plasmids and of eukaryotic type for the ceDNA vector.

[0208] There are several advantages of using a ceDNA vector for expression of FIX protein as described herein over plasmid-based expression vectors, such advantages include, but are not limited to: 1) plasmids contain bacterial DNA sequences and are subjected to prokaryotic-specific methylation, e.g., 6-methyl adenosine and 5-methyl cytosine methylation, whereas capsid-free AAV vector sequences are of eukaryotic origin and do not undergo prokaryotic-specific methylation; as a result, capsid-free AAV vectors are less likely to induce inflammatory and immune responses compared to plasmids; 2) while plasmids require the presence of a resistance gene during the production process, ceDNA vectors do not; 3) while a circular plasmid is not delivered to the nucleus upon introduction into a cell and requires overloading to bypass degradation by cellular nucleases, ceDNA vectors contain viral cis-elements, i.e., ITRs, that confer resistance to nucleases and can be designed to be targeted and delivered to the nucleus. It is hypothesized that the minimal defining elements indispensable for ITR function are a Rep-binding site (RBS; 5'-GCGCGCTCGCTCGCTC-3' (SEQ ID NO: 60) for AAV2) and a terminal resolution site (TRS; 5'-AGTTGG-3' (SEQ ID NO: 64)for AAV2) plus a variable palindromic sequence allowing for hairpin formation; and 4) ceDNA vectors do not have the over-representation of CpG dinucleotides often found in prokaryote -derived plasmids that reportedly binds a member of the Toll-like family of receptors, eliciting a T cell- mediated immune response. In contrast, transductions with capsid-free AAV vectors disclosed herein can efficiently target cell and tissue-types that are difficult to transduce with conventional AAV virions using various delivery reagent.IV. Inverted Terminal Repeats (ITRs)

[0209] As disclosed herein, ceDNA vectors for expression of FIX protein contain a transgene or nucleic acid sequence positioned between two inverted terminal repeat (ITR) sequences, where the ITR sequences can be an asymmetrical ITR pair or a symmetrical- or substantially symmetrical ITR pair, as these terms are defined herein. A ceDNA vector as disclosed herein can comprise ITR sequences that are selected from any of: (i) at least one WT ITR and at least one modified AAV inverted terminal repeat (mod-ITR) (e.g., asymmetric modified ITRs); (ii) two modified ITRs where the mod-ITR pair have a different three-dimensional spatial organization with respect to each other (e.g., asymmetric modified ITRs), or (iii) symmetrical or substantially symmetrical WT-WT ITR pair, where each WT-ITR has the same three-dimensional spatial organization, or (iv) symmetrical or substantially symmetrical modified ITR pair, where each mod-ITR has the same three-dimensional spatial organization, where the methods of the present disclosure may further include a delivery system, such as but not limited to a liposome nanoparticle delivery system.

[0210] In some embodiments, the ITR sequence can be from viruses of the Parvoviridae family, which includes two subfamilies: Parvovirinae, which infect vertebrates, and Densovirinae, which infect insects. The subfamily Parvovirinae (referred to as the parvoviruses) includes the genus Dependovirus , the members of which, under most conditions, require coinfection with a helper virus such as adenovirus or herpes virus for productive infection. The genus Dependovirus includes adeno- associated virus (AAV), which normally infects humans (e.g., serotypes 2, 3A, 3B, 5, and 6) or primates (e.g., serotypes 1 and 4), and related viruses that infect other warm-blooded animals (e.g., bovine, canine, equine, and ovine adeno-associated viruses). The parvoviruses and other members of the Parvoviridae family are generally described in Kenneth I. Berns, “Parvoviridae: The Viruses and Their Replication,” Chapter 69 in FIELDS VIROLOGY (3d Ed. 1996).

[0211] While ITRs exemplified in the specification and Examples herein are AAV2 WT-ITRs, one of ordinary skill in the art is aware that one can as stated above use ITRs from any known parvovirus, for example a dependovirus such as AAV (e.g., AAV1, AAV2, AAV3, AAV4, AAV5, AAV 5,AAV7, AAV8, AAV9, AAV10, AAV 11, AAV12, AAVrh8, AAVrhlO, AAV-DJ, and AAV-DJ8 genome. E.g., NCBI: NC 002077; NC 001401; NC001729; NC001829; NC006152; NC 006260; NC 006261), chimeric ITRs, or ITRs from any synthetic AAV. In some embodiments, the AAV can infect warm-blooded animals, e.g., avian (AAAV), bovine (BAAV), canine, equine, and ovine adeno- associated viruses. In some embodiments the ITR is from B 19 parvovirus (GenBank Accession No:NC 000883), Minute Virus from Mouse (MVM) (GenBank Accession No. NC 001510); goose parvovirus (GenBank Accession No. NC 001701); snake parvovirus 1 (GenBank Accession No. NC 006148). In some embodiments, the 5’ WT-ITR can be from one serotype and the 3’ WT-ITR from a different serotype, as discussed herein.

[0212] An ordinarily skilled artisan is aware that ITR sequences have a common structure of a double-stranded Holliday junction, which typically is a T-shaped or Y-shaped hairpin structure (see e.g., FIG. 2A and FIG. 3A), where each WT-ITR is formed by two palindromic arms or loops (B-B’ and C-C’) embedded in a larger palindromic arm (A- A’), and a single stranded D sequence, (where the order of these palindromic sequences defines the flip or flop orientation of the ITR). See, for example, structural analysis and sequence comparison of ITRs from different AAV serotypes (AAV1-AAV6) and described in Grimm et al, J. Virology, 2006; 80(1); 426-439; Yan et al., J. Virology, 2005; 364- 379; Duan et al., Virology 1999; 261; 8-14. One of ordinary skill in the art can readily determine WT- ITR sequences from any AAV serotype for use in a ceDNA vector or ceDNA-plasmid based on the exemplary AAV2 ITR sequences provided herein. See, for example, the sequence comparison of ITRs from different AAV serotypes (AAV1-AAV6, and avian AAV (AAAV) and bovine AAV (BAAV)) described in Grimm et al, J. Virology, 2006; 80(1); 426-439; that show the % identity of the left ITR of AAV2 to the left ITR from other serotypes: AAV-1 (84%), AAV-3 (86%), AAV-4 (79%), AAV-5 (58%), AAV-6 (left ITR) (100%) and AAV-6 (right ITR) (82%).A. Symmetrical ITR pairs

[0213] In some embodiments, a ceDNA vector for expression of FIX protein as described herein comprises, in the 5’ to 3’ direction: a first adeno-associated virus (AAV) inverted terminal repeat (ITR), a nucleic acid sequence of interest (for example an expression cassette as described herein) and a second AAV ITR, where the first ITR (5’ ITR) and the second ITR (3’ ITR) are symmetric, or substantially symmetrical with respect to each other - that is, a ceDNA vector can comprise ITR sequences that have a symmetrical three-dimensional spatial organization such that their structure is the same shape in geometrical space, or have the same A, C-C’ and B-B’ loops in 3D space. In such an embodiment, a symmetrical ITR pair, or substantially symmetrical ITR pair can be modified ITRs (e.g., mod-ITRs) that are not wild-type ITRs. A mod-ITR pair can have the same sequence which has one or more modifications from wild-type ITR and are reverse complements (inverted) of each other. In alternative embodiments, a modified ITR pair are substantially symmetrical as defined herein, that is, the modified ITR pair can have a different sequence but have corresponding or the same symmetrical three-dimensional shape.

[0214] ( i ) Wildtype ITRs

[0215] In some embodiments, the symmetrical ITRs, or substantially symmetrical ITRs are wild type (WT-ITRs) as described herein. That is, both ITRs have a wild-type sequence, but do not necessarily have to be WT-ITRs from the same AAV serotype. That is, in some embodiments, one WT-ITR can be from one AAV serotype, and the other WT-ITR can be from a different AAVserotype. In such an embodiment, a WT-ITR pair are substantially symmetrical as defined herein, that is, they can have one or more conservative nucleotide modification while still retaining the symmetrical three-dimensional spatial organization.

[0216] Accordingly, as disclosed herein, ceDNA vectors contain a transgene or nucleic acid sequence positioned between two flanking wild-type inverted terminal repeat (WT-ITR) sequences, that are either the reverse complement (inverted) of each other, or alternatively, are substantially symmetrical relative to each other - that is a WT-ITR pair have symmetrical three-dimensional spatial organization. In some embodiments, a wild-type ITR sequence (e.g. AAV WT-ITR) comprises a functional Rep binding site (RBS; e.g. 5'-GCGCGCTCGCTCGCTC-3' for AAV2, SEQ ID NO: 60) and a functional terminal resolution site (TRS; e.g. 5'-AGTT-3’, SEQ ID NO: 62).

[0217] In one aspect, ceDNA vectors for expression of FIX protein are obtainable from a vector polynucleotide that encodes a nucleic acid operatively positioned between two WT inverted terminal repeat sequences (WT-ITRs) (e.g. AAV WT-ITRs). That is, both ITRs have a wild type sequence, but do not necessarily have to be WT-ITRs from the same AAV serotype. That is, in some embodiments, one WT-ITR can be from one AAV serotype, and the other WT-ITR can be from a different AAV serotype. In such an embodiment, the WT-ITR pair are substantially symmetrical as defined herein, that is, they can have one or more conservative nucleotide modification while still retaining the symmetrical three-dimensional spatial organization. In some embodiments, the 5’ WT-ITR is from one AAV serotype, and the 3’ WT-ITR is from the same or a different AAV serotype. In some embodiments, the 5’ WT-ITR and the 3’WT-ITR are mirror images of each other, that is they are symmetrical. In some embodiments, the 5’ WT-ITR and the 3’ WT-ITR are from the same AAV serotype.

[0218] WT ITRs are well known. In one embodiment the two ITRs are from the same AAV2 serotype. In certain embodiments one can use WT from other serotypes. There are a number of serotypes that are homologous, e.g. AAV2, AAV4, AAV6, AAV8. In one embodiment, closely homologous ITRs (e.g. ITRs with a similar loop structure) can be used. In another embodiment, one can use AAV WT ITRs that are more diverse, e.g., AAV2 and AAV5, and still another embodiment, one can use an ITR that is substantially WT - that is, it has the basic loop structure of the WT but some conservative nucleotide changes that do not alter or affect the properties. When using WT-ITRs from the same viral serotype, one or more regulatory sequences may further be used. In certain embodiments, the regulatory sequence is a regulatory switch that permits modulation of the activity of the ceDNA, e.g., the expression of the encoded FIX protein.

[0219] In some embodiments, one aspect of the technology described herein relates to a ceDNA vector for expression of FIX protein, wherein the ceDNA vector comprises at least one nucleic acid sequence encoding the FIX protein, operably positioned between two wild-type inverted terminal repeat sequences (WT-ITRs), wherein the WT-ITRs can be from the same serotype, different serotypes or substantially symmetrical with respect to each other (i.e., have the symmetrical three-dimensionalspatial organization such that their structure is the same shape in geometrical space, or have the same A, C-C’ and B-B’ loops in 3D space). In some embodiments, the symmetric WT-ITRs comprises a functional terminal resolution site and a Rep binding site. In some embodiments, the nucleic acid sequence encodes a transgene, and wherein the vector is not in a viral capsid.

[0220] In some embodiments, the WT-ITRs are the same but the reverse complement of each other. For example, the sequence AACG in the 5’ ITR may be CGTT (i.e., the reverse complement) in the 3’ ITR at the corresponding site. In one example, the 5’ WT-ITR sense strand comprises the sequence of ATCGATCG and the corresponding 3’ WT-ITR sense strand comprises CGATCGAT (i.e., the reverse complement of ATCGATCG). In some embodiments, the WT-ITRs ceDNA further comprises a terminal resolution site and a replication protein binding site (RPS) (sometimes referred to as a replicative protein binding site), e.g. a Rep binding site.

[0221] Exemplary WT-ITR sequences for use in the ceDNA vectors for expression of FIX protein comprising WT-ITRs are shown in Table 2 herein, which shows pairs of WT-ITRs (5’ WT-ITR and the 3’ WT-ITR).

[0222] As an exemplary example, the present disclosure provides a ceDNA vector for expression of FIX protein comprising a promoter operably linked to a transgene (e.g., nucleic acid sequence), with or without the regulatory switch, where the ceDNA is devoid of capsid proteins and is: (a) produced from a ceDNA-plasmid (e.g., see FIGS. 1F-1G) that encodes WT-ITRs, where each WT-ITR has the same number of intramolecularly duplexed base pairs in its hairpin secondary configuration (preferably excluding deletion of any AAA or TTT terminal loop in this configuration compared to these reference sequences), and (b) is identified as ceDNA using the assay for the identification of ceDNA by agarose gel electrophoresis under native gel and denaturing conditions in Example 1.

[0223] In some embodiments, the flanking WT-ITRs are substantially symmetrical to each other.In this embodiment the 5’ WT-ITR can be from one serotype of AAV, and the 3’ WT-ITR from a different serotype of AAV, such that the WT-ITRs are not identical reverse complements. For example, the 5’ WT-ITR can be from AAV2, and the 3’ WT-ITR from a different serotype (e.g.AAV1, 3, 4, 5, 6, 7, 8, 9, 10, 11, and 12. In some embodiments, WT-ITRs can be selected from two different parvoviruses selected from any to of: AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, AAV12, AAV13, snake parvovirus (e.g., royal python parvovirus), bovine parvovirus, goat parvovirus, avian parvovirus, canine parvovirus, equine parvovirus, shrimp parvovirus, porcine parvovirus, or insect AAV. In some embodiments, such a combination of WT ITRs is the combination of WT-ITRs from AAV2 and AAV6. In one embodiment, the substantially symmetrical WT-ITRs are when one is inverted relative to the other ITR at least 90% identical, at least 95% identical, at least 96%...97%... 98%... 99%....99.5% and all points in between, and has the same symmetrical three-dimensional spatial organization. In some embodiments, a WT-ITR pair are substantially symmetrical as they have symmetrical three-dimensional spatial organization, e.g., have the same 3D organization of the A, C-C’. B-B’ and D arms. In one embodiment, a substantiallysymmetrical WT-ITR pair are inverted relative to the other, and are at least 95% identical, at least 96%...97%... 98%... 99%....99.5% and all points in between, to each other, and one WT-ITR retains the Rep-binding site (RBS) of 5 '-GCGCGCT CGCTCGCT C-3 ' (SEQ ID NO: 60) and a terminal resolution site (trs). In some embodiments, a substantially symmetrical WT-ITR pair are inverted relative to each other, and are at least 95% identical, at least 96%...97%... 98%... 99%....99.5% and all points in between, to each other, and one WT-ITR retains the Rep-binding site (RBS) of 5'- G C G C G C T C G C TC G C T C - 3 ' (SEQ ID NO: 60) and a terminal resolution site (trs) and in addition to a variable palindromic sequence allowing for hairpin secondary structure formation. Homology can be determined by standard means well known in the art such as BLAST (Basic Local Alignment Search Tool), BLASTN at default setting.

[0224] In some embodiments, the structural element of the ITR can be any structural element that is involved in the functional interaction of the ITR with a large Rep protein (e.g., Rep 78 or Rep 68).In certain embodiments, the structural element provides selectivity to the interaction of an ITR with a large Rep protein, i.e., determines at least in part which Rep protein functionally interacts with the ITR. In other embodiments, the structural element physically interacts with a large Rep protein when the Rep protein is bound to the ITR. Each structural element can be, e.g., a secondary structure of the ITR, a nucleic acid sequence of the ITR, a spacing between two or more elements, or a combination of any of the above. In one embodiment, the structural elements are selected from the group consisting of an A and an A’ arm, a B and a B’ arm, a C and a C’ arm, a D arm, a Rep binding site (RBE) and an RBE’ (i.e., complementary RBE sequence), and a terminal resolution sire (trs).

[0225] By way of example only, Table 2 indicates exemplary combinations of WT-ITRs.

[0226] Table 2: Exemplary combinations of WT-ITRs from the same serotype or different serotypes, or different parvoviruses. The order shown is not indicative of the ITR position, for example, “AAV1, AAV2” demonstrates that the ceDNA can comprise a WT-AAV1 ITR in the 5’ position, and a WT-AAV2 ITR in the 3’ position, or vice versa, a WT-AAV2 ITR the 5’ position, and a WT-AAV1 ITR in the 3’ position. Abbreviations: AAV serotype 1 (AAV1), AAV serotype 2 (AAV2), AAV serotype 3 (AAV3), AAV serotype 4 (AAV4), AAV serotype 5 (AAV5), AAV serotype 6 (AAV6), AAV serotype 7 (AAV7), AAV serotype 8 (AAV8), AAV serotype 9 (AAV9), AAV serotype 10 (AAV10), AAV serotype 11 (AAV11), or AAV serotype 12 (AAV12); AAVrh8, AAVrhlO, AAV-DJ, and AAV-DJ8 genome (E.g., NCBI: NC 002077; NC 001401; NC001729; NC001829; NC006152; NC 006260; NC 006261), ITRs from warm-blooded animals (avian AAV (AAAV), bovine AAV (BAAV), canine, equine, and ovine AAV), ITRs from B 19 Parvovirus (GenBank Accession No: NC 000883), Minute Virus from Mouse (MVM) (GenBank Accession No. NC 001510); Goose: goose parvovirus (GenBank Accession No. NC 001701); snake: snake parvovirus 1 (GenBank Accession No. NC 006148).Table 2: Exemplary combinations of WT-ITRs

[0227] By way of example only, Table 3 shows the sequences of exemplary WT-ITRs from some different AAV serotypes.Table 3: Exemplary WT-ITRs

[0228] In some embodiments, the nucleic acid sequence of the WT-ITR sequence can be modified (e.g., by modifying 1, 2, 3, 4 or 5, or more nucleotides or any range therein), whereby the modification is a substitution for a complementary nucleotide, e.g., G for a C, and vice versa, and T for an A, and vice versa.

[0229] In certain embodiments of the present disclosure, the ceDNA vector for expression of FIX protein does not have a WT-ITR consisting of the nucleic acid sequence selected from any of: SEQ ID NOs: 1, 2, 5-14. In alternative embodiments of the present disclosure, if a ceDNA vector has a WT- ITR comprising the nucleic acid sequence selected from any of: SEQ ID NOs: 1, 2, 5-14, then the flanking ITR is also WT and the ceDNA vector comprises a regulatory switch, e.g., as disclosed herein and in International application PCT / US 18 / 49996 (e.g., see Table 11 of PCT / US 18 / 49996, incorporated by reference in its entirety herein). In some embodiments, the ceDNA vector for expression of FIX protein comprises a regulatory switch as disclosed herein and a WT-ITR selected having the nucleic acid sequence selected from any of the group consisting of: SEQ ID NO: 1, 2, 5-14.

[0230] The ceDNA vector for expression of FIX protein as described herein can include WT-ITR structures that retains an operable RBE, trs and RBE' portion. FIG. 2A and FIG. 2B, using wild-type ITRs for exemplary purposes, show one possible mechanism for the operation of a trs site within a wild type ITR structure portion of a ceDNA vector. In some embodiments, the ceDNA vector for expression of FIX protein contains one or more functional WT-ITR polynucleotide sequences that comprise a Rep-binding site (RBS; 5'-GCGCGCTCGCTCGCTC-3' (SEQ ID NO: 60) for AAV2) and a terminal resolution site (TRS; 5'-AGTT (SEQ ID NO: 62)). In some embodiments, at least one WT- ITR is functional. In alternative embodiments, where a ceDNA vector for expression of FIX protein comprises two WT-ITRs that are substantially symmetrical to each other, at least one WT-ITR is functional and at least one WT-ITR is non-functional.B. Modified ITRs (mod-ITRs) in general for ceDNA vectors comprising asymmetric ITR pairs or symmetric ITR pairs

[0231] As discussed herein, a ceDNA vector for expression of FIX protein can comprise a symmetrical ITR pair or an asymmetrical ITR pair. In both instances, one or both of the ITRs can bemodified ITRs - the difference being that in the first instance (i.e., symmetric mod-ITRs), the mod- ITRs have the same three-dimensional spatial organization (i.e., have the same A-A’, C-C’ and B-B’ arm configurations), whereas in the second instance (i.e., asymmetric mod-ITRs), the mod-ITRs have a different three-dimensional spatial organization (i.e., have a different configuration of A-A’, C-C’ and B-B’ arms).

[0232] In some embodiments, a modified ITR is an ITRs that is modified by deletion, insertion, and / or substitution as compared to a wild-type ITR sequence (e.g. AAV ITR). In some embodiments, at least one of the ITRs in the ceDNA vector comprises a functional Rep binding site (RBS; e.g. 5'- GCGCGCTCGCTCGCTC-3' for AAV2, SEQ ID NO: 60) and a functional terminal resolution site (TRS; e.g. 5'-AGTT-3’, SEQ ID NO: 62.) In one embodiment, at least one of the ITRs is a non functional ITR. In one embodiment, the different or modified ITRs are not each wild type ITRs from different serotypes.

[0233] Specific alterations and mutations in the ITRs are described in detail herein, but in the context of ITRs, “altered” or “mutated” or “modified”, it indicates that nucleotides have been inserted, deleted, and / or substituted relative to the wild-type, reference, or original ITR sequence. The altered or mutated ITR can be an engineered ITR. As used herein, “engineered" refers to the aspect of having been manipulated by the hand of man. For example, a polypeptide is considered to be “engineered" when at least one aspect of the polypeptide, e.g., its sequence, has been manipulated by the hand of man to differ from the aspect as it exists in nature.

[0234] In some embodiments, a mod-ITR may be synthetic. In one embodiment, a synthetic ITR is based on ITR sequences from more than one AAV serotype. In another embodiment, a synthetic ITR includes no AAV-based sequence. In yet another embodiment, a synthetic ITR preserves the ITR structure described above although having only some or no AAV-sourced sequence. In some aspects, a synthetic ITR may interact preferentially with a wild type Rep or a Rep of a specific serotype, or in some instances will not be recognized by a wild-type Rep and be recognized only by a mutated Rep.

[0235] The skilled artisan can determine the corresponding sequence in other serotypes by known means. For example, determining if the change is in the A, A’, B, B’, C, C’ or D region and determine the corresponding region in another serotype. One can use BLAST® (Basic Local Alignment Search Tool) or other homology alignment programs at default status to determine the corresponding sequence. The disclosure further provides populations and pluralities of ceDNA vectors comprising mod-ITRs from a combination of different AAV serotypes - that is, one mod-ITR can be from one AAV serotype and the other mod-ITR can be from a different serotype. Without wishing to be bound by theory, in one embodiment one ITR can be from or based on an AAV2 ITR sequence and the other ITR of the ceDNA vector can be from or be based on any one or more ITR sequence of AAV serotype 1 (AAV1), AAV serotype 4 (AAV4), AAV serotype 5 (AAV5), AAV serotype 6 (AAV6), AAV serotype 7 (AAV7), AAV serotype 8 (AAV8), AAV serotype 9 (AAV9), AAV serotype 10 (AAV 10), AAV serotype 11 (AAV 11), or AAV serotype 12 (AAV 12).

[0236] Any parvovirus ITR can be used as an ITR or as a base ITR for modification. Preferably, the parvovirus is a dependovirus. More preferably AAV. The serotype chosen can be based upon the tissue tropism of the serotype. AAV2 has a broad tissue tropism, AAV1 preferentially targets to neuronal and skeletal muscle, and AAV5 preferentially targets neuronal, retinal pigmented epithelia, and photoreceptors. AAV6 preferentially targets skeletal muscle and lung. AAV8 preferentially targets liver, skeletal muscle, heart, and pancreatic tissues. AAV9 preferentially targets liver, skeletal and lung tissue. In one embodiment, the modified ITR is based on an AAV2 ITR.

[0237] More specifically, the ability of a structural element to functionally interact with a particular large Rep protein can be altered by modifying the structural element. For example, the nucleic acid sequence of the structural element can be modified as compared to the wild-type sequence of the ITR. In one embodiment, the structural element (e.g., A arm, A’ arm, B arm, B’ arm, C arm, C’ arm, D arm, RBE, RBE’, and trs) of an ITR can be removed and replaced with a wild-type structural element from a different parvovirus. For example, the replacement structure can be from AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, AAV12, AAV13, snake parvovirus (e.g., royal python parvovirus), bovine parvovirus, goat parvovirus, avian parvovirus, canine parvovirus, equine parvovirus, shrimp parvovirus, porcine parvovirus, or insect AAV. For example, the ITR can be an AAV2 ITR and the A or A’ arm or RBE can be replaced with a structural element from AAV5. In another example, the ITR can be an AAV5 ITR and the C or C’ arms, the RBE, and the trs can be replaced with a structural element from AAV2. In another example, the AAV ITR can be an AAV5 ITR with the B and B’ arms replaced with the AAV2 ITR B and B’ arms.

[0238] By way of example only, Table 4 indicates exemplary modifications of at least one nucleotide (e.g., a deletion, insertion and / or substitution) in regions of a modified ITR, where X is indicative of a modification of at least one nucleic acid (e.g., a deletion, insertion and / or substitution) in that section relative to the corresponding wild-type ITR. In some embodiments, any modification of at least one nucleotide (e.g., a deletion, insertion and / or substitution) in any of the regions of C and / or C’ and / or B and / or B’ retains three sequential T nucleotides (i.e., TTT) in at least one terminal loop. For example, if the modification results in any of: a single arm ITR (e.g., single C-C’ arm, or a single B-B’ arm), or a modified C-B’ arm or C’-B arm, or a two arm ITR with at least one truncated arm (e.g., a truncated C-C’ arm and / or truncated B-B’ arm), at least the single arm, or at least one of the arms of a two arm ITR (where one arm can be truncated) retains three sequential T nucleotides (i.e., TTT) in at least one terminal loop. In some embodiments, a truncated C-C’ arm and / or a truncated B- B’ arm has three sequential T nucleotides (i.e., TTT) in the terminal loop.Table 4: Exemplary combinations of modifications of at least one nucleotide (e.g., a deletion, insertion and / or substitution) to different B-B’ and C-C’ regions or arms of ITRs (X indicates a nucleotide modification, e.g., addition, deletion or substitution of at least one nucleotide in the region).

[0239] In some embodiments, mod-ITR for use in a ceDNA vector for expression of FIX protein comprises an asymmetric ITR pair, or a symmetric mod-ITR pair as disclosed herein, can comprise any one of the combinations of modifications shown in Table 4, and also a modification of at least one nucleotide in any one or more of the regions selected from: between A’ and C, between C and C’, between C’ and B, between B and B’ and between B’ and A. In some embodiments, any modification of at least one nucleotide (e.g., a deletion, insertion and / or substitution) in the C or C’ or B or B’ regions, still preserves the terminal loop of the stem-loop. In some embodiments, any modification of at least one nucleotide (e.g., a deletion, insertion and / or substitution) between C and C’ and / or B and B’ retains three sequential T nucleotides (i.e., TTT) in at least one terminal loop. In alternative embodiments, any modification of at least one nucleotide (e.g., a deletion, insertion and / or substitution) between C and C’ and / or B and B’ retains three sequential A nucleotides (i.e., AAA) in at least one terminal loop. In some embodiments, a modified ITR for use herein can comprise any one of the combinations of modifications shown in Table 4, and also a modification of at least one nucleotide (e.g., a deletion, insertion and / or substitution) in any one or more of the regions selected from: A’, A and / or D. For example, in some embodiments, a modified ITR for use herein can comprise any one of the combinations of modifications shown in Table 4, and also a modification of at least one nucleotide (e.g., a deletion, insertion and / or substitution) in the A region. In some embodiments, a modified ITR for use herein can comprise any one of the combinations of modifications shown in Table 4, and also a modification of at least one nucleotide (e.g., a deletion, insertion and / or substitution) in the A’ region. In some embodiments, a modified ITR for use herein can comprise any one of the combinations of modifications shown in Table 4, and also a modification of at least one nucleotide (e.g., a deletion, insertion and / or substitution) in the A and / or A’ region. In some embodiments, a modified ITR for useherein can comprise any one of the combinations of modifications shown in Table 4, and also a modification of at least one nucleotide (e.g., a deletion, insertion and / or substitution) in the D region.

[0240] In one embodiment, the nucleotide sequence of the structural element can be modified (e.g., by modifying 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 or more nucleotides or any range therein) to produce a modified structural element. In one embodiment, the specific modifications to the ITRs are exemplified herein (e.g., SEQ ID NOS: 3, 4, 15-47, 101-116 or 165-187, or shown in FIG. 7A-7B of International Patent Application No. PCT / US2018 / 064242, filed on December 6, 2018 (e.g., SEQ ID Nos 97-98, 101-103, 105-108, 111-112, 117-134, 545-54 inPCT / US2018 / 064242). In some embodiments, an ITR can be modified (e.g., by modifying 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 or more nucleotides or any range therein). In other embodiments, the ITR can have 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 more sequence identity with one of the modified ITRs of SEQ ID NOS: 3, 4, 15-47, 101-116 or 165-187, or the RBE-containing section of the A-A’ arm and C-C’ and B-B’ arms of SEQ ID NO: 3, 4, 15-47, 101-116 or 165-187, or shown in Tables 2-9 (i.e.,SEQ ID NO: 110-112, 115-190, 200-468) of International Patent Application No. PCT / US 18 / 49996, which is incorporated herein in its entirety by reference.

[0241] In some embodiments, a modified ITR can for example, comprise removal or deletion of all of a particular arm, e.g., all or part of the A-A’ arm, or all or part of the B-B’ arm or all or part of the C-C’ arm, or alternatively, the removal of 1, 2, 3, 4, 5, 6, 7, 8, 9 or more base pairs forming the stem of the loop so long as the final loop capping the stem (e.g., single arm) is still present (e.g., see ITR-21 in FIG. 7A of PCT / US2018 / 064242, filed December 6, 2018). In some embodiments, a modified ITR can comprise the removal of 1, 2, 3, 4, 5, 6, 7, 8, 9 or more base pairs from the B-B’ arm. In some embodiments, a modified ITR can comprise the removal of 1, 2, 3, 4, 5, 6, 7, 8, 9 or more base pairs from the C-C’ arm (see, e.g., ITR-1 in FIG. 3B, or ITR-45 in FIG. 7A of International Patent Application No. PCT / US2018 / 064242, filed December 6, 2018). In some embodiments, a modified ITR can comprise the removal of 1, 2, 3, 4, 5, 6, 7, 8, 9 or more base pairs from the C-C’ arm and the removal of 1, 2, 3, 4, 5, 6, 7, 8, 9 or more base pairs from the B-B’ arm. Any combination of removal of base pairs is envisioned, for example, 6 base pairs can be removed in the C-C’ arm and 2 base pairs in the B-B’ arm. As an illustrative example, FIG. 3B shows an exemplary modified ITR with at least 7 base pairs deleted from each of the C portion and the C’ portion, a substitution of a nucleotide in the loop between C and C’ region, and at least one base pair deletion from each of the B region and B’ regions such that the modified ITR comprises two arms where at least one arm (e.g., C-C’) is truncated. In some embodiments, the modified ITR also comprises at least one base pair deletion from each of the B region and B’ regions, such that the B-B’ arm is also truncated relative to WT ITR.

[0242] In some embodiments, a modified ITR can have between 1 and 50 (e.g. 1, 2, 3, 4, 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, 36,37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50) nucleotide deletions relative to a full-lengthwild-type ITR sequence. In some embodiments, a modified ITR can have between 1 and 30 nucleotide deletions relative to a full-length WT ITR sequence. In some embodiments, a modified ITR has between 2 and 20 nucleotide deletions relative to a full-length wild-type ITR sequence.

[0243] In some embodiments, a modified ITR does not contain any nucleotide deletions in the RBE-containing portion of the A or A' regions, so as not to interfere with DNA replication (e.g. binding to an RBE by Rep protein, or nicking at a terminal resolution site). In some embodiments, a modified ITR encompassed for use herein has one or more deletions in the B, B', C, and / or C region as described herein.

[0244] In some embodiments, a ceDNA vector for expression of FIX protein comprising a symmetric ITR pair or asymmetric ITR pair comprises a regulatory switch as disclosed herein and at least one modified ITR selected having the nucleotide sequence selected from any of the group consisting of: SEQ ID NO: 3, 4, 15-47, 101-116 or 165-187.

[0245] In another embodiment, the structure of the structural element can be modified. For example, the structural element a change in the height of the stem and / or the number of nucleotides in the loop. For example, the height of the stem can be about 2, 3, 4, 5, 6, 7, 8, or 9 nucleotides or more or any range therein. In one embodiment, the stem height can be about 5 nucleotides to about 9 nucleotides and functionally interacts with Rep. In another embodiment, the stem height can be about 7 nucleotides and functionally interacts with Rep. In another example, the loop can have 3, 4, 5, 6, 7,8, 9, or 10 nucleotides or more or any range therein.

[0246] In another embodiment, the number of GAGY binding sites or GAGY-related binding sites within the RBE or extended RBE can be increased or decreased. In one example, the RBE or extended RBE, can comprise 1, 2, 3, 4, 5, or 6 or more GAGY binding sites or any range therein. Each GAGY binding site can independently be an exact GAGY sequence or a sequence similar to GAGY as long as the sequence is sufficient to bind a Rep protein.

[0247] In another embodiment, the spacing between two elements (such as but not limited to the RBE and a hairpin) can be altered (e.g., increased or decreased) to alter functional interaction with a large Rep protein. For example, the spacing can be about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21 nucleotides or more or any range therein.

[0248] The ceDNA vector for expression of FIX protein asdescribed herein can include an ITR structure that is modified with respect to the wild type AAV2 ITR structure disclosed herein, but still retains an operable RBE, trs and RBE" portion. FIG. 2A and FIG. 2B show one possible mechanism for the operation of a trs site within a wild type ITR structure portion of a ceDNA vector for expression of FIX protein. In some embodiments, the ceDNA vector for expression of FIX protein contains one or more functional ITR polynucleotide sequences that comprise a Rep-binding site (RBS; 5'-GCGCGCTCGCTCGCTC-3' (SEQ ID NO: 60) for AAV2) and a terminal resolution site (TRS; 5'- AGTT (SEQ ID NO: 62)). In some embodiments, at least one ITR (wt or modified ITR) is functional. In alternative embodiments, where a ceDNA vector for expression of FIX protein comprises twomodified ITRs that are different or asymmetrical to each other, at least one modified ITR is functional and at least one modified ITR is non-functional.

[0249] In some embodiments, the modified ITR (e.g., the left or right ITR) of a ceDNA vector for expression of FIX protein as described herein has modifications within the loop arm, the truncated arm, or the spacer. Exemplary sequences of ITRs having modifications within the loop arm, the truncated arm, or the spacer are listed in Table 2 (i.e., SEQ ID NOS: 135-190, 200-233); Table 3 (e.g., SEQ ID Nos: 234-263); Table 4 (e.g., SEQ ID NOs: 264-293); Table 5 (e.g., SEQ ID Nos: 294-318 herein); Table 6 (e.g., SEQ ID NO: 319-468; and Tables 7-9 (e.g., SEQ ID Nos: 101-110, 111-112, 115-134) or Table 10A or 10B (e.g., SEQ ID Nos: 9, 100, 469-483, 484-499) of International Patent Application No. PCT / US 18 / 49996, which is incorporated herein in its entirety by reference.

[0250] In some embodiments, the modified ITR for use in a ceDNA vector for expression of FIX protein comprising an asymmetric ITR pair, or symmetric mod-ITR pair is selected from any or a combination of those shown in Tables 2, 3, 4, 5, 6, 7, 8, 9 and 10A-10B of International Patent Application No. PCT / US 18 / 49996 which is incorporated herein in its entirety by reference.

[0251] Additional exemplary modified ITRs for use in a ceDNA vector for expression of FIX protein comprising an asymmetric ITR pair, or symmetric mod-ITR pair in each of the above classes are provided in Tables 5A and 5B. The predicted secondary structure of the Right modified ITRs in Table 5A are shown in FIG. 7A of International Patent Application No. PCT / US2018 / 064242, filed December 6, 2018, and the predicted secondary structure of the Left modified ITRs in Table 5B are shown in FIG. 7B of International Patent Application No. PCT / US2018 / 064242, filed December 6, 2018, which is incorporated herein in its entirety by reference.

[0252] Table 5A and Table 5B list the SEQ ID NOs of exemplary right and left modified ITRs. Table 5A: Exemplary modified right ITRs. These exemplary modified right ITRs can comprise the RBE of GCGCGCTCGCTCGCTC-3' (SEQ ID NO: 60), spacer of ACTGAGGC (SEQ ID NO: 69), the spacer complement GCCTCAGT (SEQ ID NO: 70) and RBE’ (i.e., complement to RBE) of GAGCGAGCGAGCGCGC (SEQ ID NO: 71).TABLE 5B: Exemplary modified left ITRs. These exemplary modified left ITRs can comprise the RBE of GCGCGCTCGCTCGCTC-3' (SEQ ID NO: 60), spacer of ACTGAGGC (SEQ ID NO: 69), the spacer complement GCCTCAGT (SEQ ID NO: 70) and RBE complement (RBE’) of GAGCGAGCGAGCGCGC (SEQ ID NO: 71).

[0253] In one embodiment, a ceDNA vector for expression of FIX protein comprises, in the 5’ to 3’ direction: a first adeno-associated virus (AAV) inverted terminal repeat (ITR), a nucleic acid sequence of interest (for example an expression cassette as described herein) and a second AAV ITR, where the first ITR (5’ ITR) and the second ITR (3’ ITR) are asymmetric with respect to each other - that is, they have a different 3D-spatial configuration from one another. As an exemplary embodiment, the first ITR can be a wild-type ITR and the second ITR can be a mutated or modified ITR, or vice versa, where the first ITR can be a mutated or modified ITR and the second ITR a wild-type ITR. In some embodiment, the first ITR and the second ITR are both mod-ITRs, but have different sequences, or have different modifications, and thus are not the same modified ITRs, and have different 3D spatial configurations. Stated differently, a ceDNA vector with asymmetric ITRs comprises ITRs where any changes in one ITR relative to the WT-ITR are not reflected in the other ITR; or alternatively, where the asymmetric ITRs have a modified asymmetric ITR pair can have a different sequence and different three-dimensional shape with respect to each other. Exemplary asymmetric ITRs in the ceDNA vectorfor expression of FIX protein and for use to generate a ceDNA-pIasmid are shown in Table 5A and 5B.

[0254] In an alternative embodiment, a ceDNA vector for expression of FIX protein comprises two symmetrical mod-ITRs - that is, both ITRs have the same sequence, but are reverse complements (inverted) of each other. In some embodiments, a symmetrical mod-ITR pair comprises at least one or any combination of a deletion, insertion, or substitution relative to wild type ITR sequence from the same AAV serotype. The additions, deletions, or substitutions in the symmetrical ITR are the same but the reverse complement of each other. For example, an insertion of 3 nucleotides in the C region of the 5’ ITR would be reflected in the insertion of 3 reverse complement nucleotides in the corresponding section in the C’ region of the 3’ ITR. Solely for illustration purposes only, if the addition is AACG in the 5’ ITR, the addition is CGTT in the 3’ ITR at the corresponding site. For example, if the 5’ ITR sense strand is ATCGATCG with an addition of AACG between the G and A to result in the sequence ATCGAACGATCG (SEQ ID NO: 51). The corresponding 3’ ITR sense strand is CGATCGAT (the reverse complement of ATCGATCG) with an addition of CGTT ( i.e . the reverse complement of AACG) between the T and C to result in the sequence CG AT CG7TCG AT (SEQ ID NO: 49) (the reverse complement of ATCGAACGATCG) (SEQ ID NO: 51).

[0255] In alternative embodiments, the modified ITR pair are substantially symmetrical as defined herein - that is, the modified ITR pair can have a different sequence but have corresponding or the same symmetrical three-dimensional shape. For example, one modified ITR can be from one serotype and the other modified ITR be from a different serotype, but they have the same mutation (e.g., nucleotide insertion, deletion or substitution) in the same region. Stated differently, for illustrative purposes only, a 5’ mod-ITR can be from AAV2 and have a deletion in the C region, and the 3’ mod- ITR can be from AAV5 and have the corresponding deletion in the C’ region, and provided the 5’mod- ITR and the 3’ mod-ITR have the same or symmetrical three-dimensional spatial organization, they are encompassed for use herein as a modified ITR pair.

[0256] In some embodiments, a substantially symmetrical mod-ITR pair has the same A, C-C’ and B-B’ loops in 3D space, e.g., if a modified ITR in a substantially symmetrical mod-ITR pair has a deletion of a C-C’ arm, then the cognate mod-ITR has the corresponding deletion of the C-C’ loop and also has a similar 3D structure of the remaining A and B-B’ loops in the same shape in geometric space of its cognate mod-ITR. By way of example only, substantially symmetrical ITRs can have a symmetrical spatial organization such that their structure is the same shape in geometrical space. This can occur, e.g., when a G-C pair is modified, for example, to a C-G pair or vice versa, or A-T pair is modified to a T-A pair, or vice versa. Therefore, using the exemplary example above of modified 5’ ITR as a ATCGAACGATCG (SEQ ID NO: 51), and modified 3’ ITR as CGAT CG7TCGAT (SEQ ID NO: 49) (i.e., the reverse complement of ATCGAACGATCG (SEQ ID NO: 51)), these modified ITRs would still be symmetrical if, for example, the 5’ ITR had the sequence of ATCGAACCATCG (SEQ ID NO: 50), where G in the addition is modified to C, and the substantially symmetrical 3’ ITR has thesequence of CGATCG7TCGAT (SEQ ID NO: 49), without the corresponding modification of the T in the addition to a. In some embodiments, such a modified ITR pair are substantially symmetrical as the modified ITR pair has symmetrical stereochemistry.

[0257] Table 6 shows exemplary symmetric modified ITR pairs (i.e., a left modified ITRs and the symmetric right modified ITR) for use in a ceDNA vector for expression of FIX protein. The bold (red) portion of the sequences identify partial ITR sequences (i.e., sequences of A-A’, C-C’ and B-B’ loops), also shown in FIGS 31A-46B. These exemplary modified ITRs can comprise the RBE of GCGCGCTCGCTCGCTC-3' (SEQ ID NO: 60), spacer of ACTGAGGC (SEQ ID NO: 69), the spacer complement GCCTCAGT (SEQ ID NO: 70) and RBE’ (i.e., complement to RBE) of GAGCGAGCGAGCGCGC (SEQ ID NO: 71).Table 6: Exemplary symmetric modified ITR pairs in a ceDNA vector for expression of FIX protein

[0258] In some embodiments, a ceDNA vector for expression of FIX protein comprising an asymmetric ITR pair can comprise an ITR with a modification corresponding to any of the modifications in ITR sequences or ITR partial sequences shown in any one or more of Tables 5A-5B herein, or the sequences shown in FIG. 7A-7B of International Patent Application No.PCT / US2018 / 064242, filed December 6, 2018, which is incorporated herein in its entirety, or disclosed in Tables 2, 3, 4, 5, 6, 7, 8, 9 or 10A-10B of International Patent Application No.PCT / US 18 / 49996 filed September 7, 2018 which is incorporated herein in its entirety by reference.V. Exemplary ceDNA vectors

[0259] As described above, the present disclosure relates to recombinant ceDNA expression vectors and ceDNA vectors that encode FIX protein, comprising any one of: an asymmetrical ITR pair, a symmetrical ITR pair, or substantially symmetrical ITR pair as described above. In certainembodiments, the disclosure relates to recombinant ceDNA vectors for expression of FIX protein having flanking ITR sequences and a transgene, where the ITR sequences are asymmetrical, symmetrical or substantially symmetrical relative to each other as defined herein, and the ceDNA further comprises a nucleic acid sequence of interest (for example an expression cassette comprising the nucleic acid of a transgene) located between the flanking ITRs, wherein said nucleic acid molecule is devoid of viral capsid protein coding sequences.

[0260] The ceDNA expression vector for expression of FIX protein may be any ceDNA vector that can be conveniently subjected to recombinant DNA procedures including nucleic acid sequence(s) as described herein, provided at least one ITR is altered. The ceDNA vectors for expression of FIX protein of the present disclosure are compatible with the host cell into which the ceDNA vector is to be introduced. In certain embodiments, the ceDNA vectors may be linear. In certain embodiments, the ceDNA vectors may exist as an extrachromosomal entity. In certain embodiments, the ceDNA vectors of the present disclosure may contain an element(s) that permits integration of a donor sequence into the host cell's genome. As used herein “transgene” , “nucleic acid sequence” and “heterologous nucleic acid sequence” are synonymous, and encode FIX protein, as described herein.

[0261] Referring now to FIGS 1A-1G, schematics of the functional components of two non limiting plasmids useful in making a ceDNA vector for expression of FIX protein are shown. FIG.1A, IB, ID, IF show the construct of ceDNA vectors or the corresponding sequences of ceDNA plasmids for expression of FIX protein. ceDNA vectors are capsid-free and can be obtained from a plasmid encoding in this order: a first ITR, an expressible transgene cassette and a second ITR, where the first and second ITR sequences are asymmetrical, symmetrical or substantially symmetrical relative to each other as defined herein. ceDNA vectors for expression of FIX protein are capsid-free and can be obtained from a plasmid encoding in this order: a first ITR, an expressible transgene (protein or nucleic acid) and a second ITR, where the first and second ITR sequences are asymmetrical, symmetrical or substantially symmetrical relative to each other as defined herein. In some embodiments, the expressible transgene cassette includes, as needed: an enhancer / promoter, one or more homology arms, a donor sequence, a post-transcription regulatory element (e.g., WPRE, e.g., SEQ ID NO: 67)), and a polyadenylation and termination signal (e.g., BGF1 polyA, e.g., SEQ ID NO: 68).

[0262] FIG. 5 is a gel confirming the production of ceDNA from multiple plasmid constructs using the method described in the Examples. The ceDNA is confirmed by a characteristic band pattern in the gel, as discussed with respect to FIG. 4A above and in the Examples.A. Regulatory elements.

[0263] The ceDNA vectors for expression of FIX protein as described herein comprising an asymmetric ITR pair or symmetric ITR pair as defined herein, can further comprise a specific combination of cis-regulatory elements. The cis-regulatory elements include, but are not limited to, a promoter, a riboswitch, an insulator, a mir-regulatable element, a post-transcriptional regulatoryelement, a tissue- and cell type-specific promoter and an enhancer. Exemplary promoters are listed in Table 7. Exemplary enhancers are listed in Table 8. In some embodiments, the ITR can act as the promoter for the transgene, e.g., FIX protein. In some embodiments, the ceDNA vector for expression of FIX protein as described herein comprises additional components to regulate expression of the transgene, for example, regulatory switches as described herein, to regulate the expression of the transgene, or a kill switch, which can kill a cell comprising the ceDNA vector encoding FIX protein thereof. Regulatory elements, including Regulatory Switches that can be used in the present disclosure are more fully discussed in International Patent Application No. PCT / US 18 / 49996, which is incorporated herein in its entirety by reference.

[0264] In embodiments, the second nucleic acid sequence includes a regulatory sequence, and a nucleic acid sequence encoding a nuclease. In certain embodiments the gene regulatory sequence is operably linked to the nucleic acid sequence encoding the nuclease. In certain embodiments, the regulatory sequence is suitable for controlling the expression of the nuclease in a host cell. In certain embodiments, the regulatory sequence includes a suitable promoter sequence, being able to direct transcription of a gene operably linked to the promoter sequence, such as a nucleic acid sequence encoding the nuclease(s) of the present disclosure. In certain embodiments, the second nucleic acid sequence includes an intron sequence linked to the 5' terminus of the nucleic acid sequence encoding the nuclease. In certain embodiments, an enhancer sequence is provided upstream of the promoter to increase the efficacy of the promoter. In certain embodiments, the regulatory sequence includes an enhancer and a promoter, wherein the second nucleic acid sequence includes an intron sequence upstream of the nucleic acid sequence encoding a nuclease, wherein the intron includes one or more nuclease cleavage site(s), and wherein the promoter is operably linked to the nucleic acid sequence encoding the nuclease.

[0265] The ceDNA vectors for expression of FIX protein produced synthetically, or using a cell- based production method as described herein in the Examples, can further comprise a specific combination of cis-regulatory elements such as WHP posttranscriptional regulatory element (WPRE) (e.g., SEQ ID NO: 67) and BGH polyA (SEQ ID NO: 68). Suitable expression cassettes for use in expression constructs are not limited by the packaging constraint imposed by the viral capsid.(i). Promoters:

[0266] It will be appreciated by one of ordinary skill in the art that promoters used in the ceDNA vectors for expression of FIX protein as disclosed herein should be tailored as appropriate for the specific sequences they are promoting. Sequnce identifiers of exemplary promoters operatively linked to a transgene (e.g., FIX) useful in a ceDNA vector are disclosed in Table 7, herein.Table 7: Exemplary promoters

[0267] Expression cassettes of the ceDNA vector for expression of FIX protein can include a promoter, e.g., any of the promoter selected from Table 7, which can influence overall expression levels as well as cell-specificity. For transgene expression, e.g., expression of FIX protein, they can include a highly active virus-derived immediate early promoter. Expression cassettes can contain tissue-specific eukaryotic promoters to limit transgene expression to specific cell types and reduce toxic effects and immune responses resulting from unregulated, ectopic expression. In some embodiments, an expression cassette can contain a promoter or synthetic regulatory element, such as a CAG promoter (SEQ ID NO: 72). The CAG promoter comprises (i) the cytomegalovirus (CMV) early enhancer element, (ii) the promoter, the first exon and the first intron of chicken beta-actin gene, and (iii) the splice acceptor of the rabbit beta-globin gene. Alternatively, an expression cassette can contain an Alpha- 1 -antitrypsin (AAT) promoter (SEQ ID NO: 73 or SEQ ID NO: 74), a liver specific (LP1) promoter (SEQ ID NO: 75 or SEQ ID NO: 76), or a Human elongation factor-1 alpha (EFla) promoter (e.g., SEQ ID NO: 77 or SEQ ID NO: 78). In some embodiments, the expression cassette includes one or more constitutive promoters, for example, a retroviral Rous sarcoma virus (RSV) LTR promoter (optionally with the RSV enhancer), or a cytomegalovirus (CMV) immediate early promoter (optionally with the CMV enhancer, e.g., SEQ ID NO: 79). Alternatively, an inducible promoter, a native promoter for a transgene, a tissue-specific promoter, or various promoters known in the art can be used.

[0268] Suitable promoters, including those described in Table 7 and above, can be derived from viruses and can therefore be referred to as viral promoters, or they can be derived from any organism, including prokaryotic or eukaryotic organisms. Suitable promoters can be used to drive expression by any RNA polymerase (e.g., pol I, pol II, pol III). Exemplary promoters include, but are not limited to the SV40 early promoter, mouse mammary tumor virus long terminal repeat (LTR) promoter; adenovirus major late promoter (Ad MLP); a herpes simplex virus (HSV) promoter, a cytomegalovirus (CMV) promoter such as the CMV immediate early promoter region (CMVIE), a rous sarcoma virus (RSV) promoter, a human U6 small nuclear promoter (U6, e.g., SEQ ID NO: 80) (Miyagishi et al.,Nature Biotechnology 20, 497-500 (2002)), an enhanced U6 promoter (e.g., Xia et al., Nucleic Acids Res. 2003 Sep. 1; 31(17)), a human HI promoter (HI) (e.g., SEQ ID NO: 81 or SEQ ID NO: 155), a CAG promoter, a human alpha 1-antitypsin (HAAT) promoter (e.g., SEQ ID NO: 82), and the like. In certain embodiments, these promoters are altered at their downstream intron containing end to include one or more nuclease cleavage sites. In certain embodiments, the DNA containing the nuclease cleavage site(s) is foreign to the promoter DNA.

[0269] In one embodiment, the promoter used is the native promoter of the gene encoding the therapeutic protein. The promoters and other regulatory sequences for the respective genes encoding the therapeutic proteins are known and have been characterized. The promoter region used may further include one or more additional regulatory sequences (e.g., native), e.g., enhancers, (e.g. SEQ ID NO: 79 and SEQ ID NO: 83), including a SV40 enhancer (SEQ ID NO: 126).

[0270] In some embodiments, a promoter may also be a promoter from a human gene such as human ubiquitin C (hUbC), human actin, human myosin, human hemoglobin, human muscle creatine, or human metallothionein. The promoter may also be a tissue specific promoter, such as a liver specific promoter, such as human alpha 1-antitypsin (HAAT), natural or synthetic. In one embodiment, delivery to the liver can be achieved using endogenous ApoE specific targeting of the composition comprising a ceDNA vector to hepatocytes via the low density lipoprotein (LDL) receptor present on the surface of the hepatocyte.

[0271] Non-limiting examples of suitable promoters for use in accordance with the present disclosure include any of the promoters listed in Table 7, or any of the following: the CAG promoter of, for example (SEQ ID NO: 72), the HAAT promoter (SEQ ID NO: 82), the human EFl-a promoter (SEQ ID NO: 77) or a fragment of the EFla promoter (SEQ ID NO: 78), IE2 promoter (e.g., SEQ ID NO: 84) and the rat EFl-a promoter (SEQ ID NO: 85), mEFl promoter (SEQ ID NO: 59), or 1E1 promoter fragment (SEQ ID NO: 125).

[0272] ( ii ) Enhancers

[0273] In some embodiments, a ceDNA expressing FIX comprises one or more enhancers. In some embodiments, an enhancer sequence is located 5’ of the promoter sequence. In some embodiments, the enhancer sequence is located 3’ of the promoter sequence. Sequence identifiers of exemplary enhancers are listed in Table 8 herein.Table 8: Exemplary enhancer sequences(iii) 5’ UTR sequences and intron sequences

[0274] In some embodiments, a ceDNA vector comprises a 5’ UTR sequence and / or an intron sequence that located 3’ of the 5’ ITR sequence. In some embodiments, the 5’ UTR is located 5’ of the transgene, e.g., sequence encoding the FIX protein. Sequence identifers of exemplary 5’ UTR sequences listed in Table 9A.Table 9A: Exemplary 5’ UTR sequences and intron sequences

[0275] (iv) 3’ UTR sequences

[0276] In some embodiments, a ceDNA vector comprises a 3’ UTR sequence that located 5’ of the 3’ ITR sequence. In some embodiments, the 3’ UTR is located 3’ of the transgene, e.g., sequence encoding the FIX protein. Sequence identifiers of exemplary 3’ UTR sequences listed in Table 9B.Table 9B: Exemplary 3’ UTR sequences and intron sequences(v). Polyadenylation Sequences:

[0277] A sequence encoding a polyadenylation sequence can be included in the ceDNA vector for expression of FIX protein to stabilize an mRNA expressed from the ceDNA vector, and to aid in nuclear export and translation. In one embodiment, the ceDNA vector does not include a polyadenylation sequence. In other embodiments, the ceDNA vector for expression of FIX protein includes at least 1, at least 2, at least 3, at least 4, at least 5, at least 10, at least 15, at least 20, at least 25, at least 30, at least 40, least 45, at least 50 or more adenine dinucleotides. In some embodiments, the polyadenylation sequence comprises about 43 nucleotides, about 40-50 nucleotides, about 40-55 nucleotides, about 45-50 nucleotides, about 35-50 nucleotides, or any range there between.

[0278] The expression cassettes can include any poly-adenylation sequence known in the art or a variation thereof. In some embodiments, a poly-adenylation (poly A) sequence is selected from any of those listed in Table 10. Other polyA sequences commonly known in the art can also be used, e.g., including but not limited to, naturally occurring sequence isolated from bovine BGHpA (e.g., SEQ ID NO: 68) or a virus SV40pA (e.g., SEQ ID NO: 86), or a synthetic sequence (e.g., SEQ ID NO: 87). Some expression cassettes can also include SV40 late polyA signal upstream enhancer (USE)sequence. In some embodiments, a USE sequence can be used in combination with SV40pA or heterologous poly-A signal. PolyA sequences are located 3’ of the transgene encoding the FIX protein.

[0279] The expression cassettes can also include a post-transcriptional element to increase the expression of a transgene. In some embodiments, Woodchuck Hepatitis Virus (WHP) posttranscriptional regulatory element (WPRE) (e.g., SEQ ID NO: 67) is used to increase the expression of a transgene. Other posttranscriptional processing elements such as the post transcriptional element from the thymidine kinase gene of herpes simplex virus, or hepatitis B virus(HBV) can be used. Secretory sequences can be linked to the transgenes, e.g., VH-02 and VK-A26 sequences, e.g., SEQ ID NO: 88 and SEQ ID NO: 89.Table 10: Sequence identifiers of exemplary polyA sequences( vi ). Nuclear Localization Sequences

[0280] In some embodiments, the ceDNA vector for expression of FIX protein comprises one or more nuclear localization sequences (NLSs), for example, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more NLSs. In some embodiments, the one or more NLSs are located at or near the amino-terminus, at or near the carboxy-terminus, or a combination of these (e.g., one or more NLS at the amino-terminus and / or one or more NLS at the carboxy terminus). When more than one NLS is present, each can be selected independently of the others, such that a single NLS is present in more than one copy and / or in combination with one or more other NLSs present in one or more copies. Sequence identifiers of non limiting examples of NLSs are shown in Table 11.Table 11: Nuclear Localization SequenceB. Additional Components of ceDNA vectors

[0281] The ceDNA vectors for expression of FIX protein of the present disclosure may contain nucleotides that encode other components for gene expression. For example, to select for specific gene targeting events, a protective shRNA may be embedded in a microRNA and inserted into a recombinant ceDNA vector designed to integrate site-specifically into the highly active locus, such as an albumin locus. Such embodiments may provide a system for in vivo selection and expansion of gene-modified hepatocytes in any genetic background such as described in Nygaard et al., A universal system to select gene-modified hepatocytes in vivo, Gene Therapy, June 8, 2016. The ceDNA vectors of the present disclosure may contain one or more selectable markers that permit selection of transformed, transfected, transduced, or the like cells. A selectable marker is a gene the product ofwhich provides for biocide or viral resistance, resistance to heavy metals, prototrophy to auxotrophs, NeoR, and the like. In certain embodiments, positive selection markers are incorporated into the donor sequences such as NeoR. Negative selections markers may be incorporated downstream the donor sequences, for example a nucleic acid sequence HSV-tk encoding a negative selection marker may be incorporated into a nucleic acid construct downstream the donor sequence.C. Regulatory Switches

[0282] A molecular regulatory switch is one which generates a measurable change in state in response to a signal. Such regulatory switches can be usefully combined with the ceDNA vectors for expression of FIX protein as described herein to control the output of expression of FIX protein from the ceDNA vector. In some embodiments, the ceDNA vector for expression of FIX protein comprises a regulatory switch that serves to fine tune expression of the FIX protein. For example, it can serve as a biocontainment function of the ceDNA vector. In some embodiments, the switch is an “ON / OFF” switch that is designed to start or stop (i.e., shut down) expression of FIX protein in the ceDNA vector in a controllable and regulatable fashion. In some embodiments, the switch can include a “kill switch” that can instruct the cell comprising the ceDNA vector to undergo cell programmed death once the switch is activated. Exemplary regulatory switches encompassed for use in a ceDNA vector for expression of FIX protein can be used to regulate the expression of a transgene, and are more fully discussed in International application PCT / US 18 / 49996, which is incorporated herein in its entirety by reference( i ) Binary Regulatory Switches

[0283] In some embodiments, the ceDNA vector for expression of FIX protein comprises a regulatory switch that can serve to controllably modulate expression of FIX protein. For example, the expression cassette located between the ITRs of the ceDNA vector may additionally comprise a regulatory region, e.g., a promoter, cis-element, repressor, enhancer etc., that is operatively linked to the nucleic acid sequence encoding FIX protein, where the regulatory region is regulated by one or more cofactors or exogenous agents. By way of example only, regulatory regions can be modulated by small molecule switches or inducible or repressible promoters. Non-limiting examples of inducible promoters are hormone -inducible or metal-inducible promoters. Other exemplary inducible promoters / enhancer elements include, but are not limited to, an RU486-inducible promoter, an ecdysone -inducible promoter, a rapamycin-inducible promoter, and a metallothionein promoter.( ii ) Small molecule Regulatory Switches

[0284] A variety of art-known small-molecule based regulatory switches are known in the art and can be combined with the ceDNA vectors for expression of FIX protein as disclosed herein to form a regulatory-switch controlled ceDNA vector. In some embodiments, the regulatory switch can be selected from any one or a combination of: an orthogonal ligand / nuclear receptor pair, for example retinoid receptor variant / LG335 and GRQCIMFI, along with an artificial promoter controlling expression of the operatively linked transgene, such as that as disclosed in Taylor, et al. BMCBiotechnology 10 (2010): 15; engineered steroid receptors, e.g., modified progesterone receptor with a C-terminal truncation that cannot bind progesterone but binds RU486 (mifepristone) (US Patent No. 5,364,791); an ecdysone receptor from Drosophila and their ecdysteroid ligands (Saez, et al., PNAS, 97(26)(2000), 14512-14517; or a switch controlled by the antibiotic trimethoprim (TMP), as disclosed in Sando R 3rd; Nat Methods. 2013, 10( 11) : 1085-8. In some embodiments, the regulatory switch to control the transgene or expressed by the ceDNA vector is a pro-drug activation switch, such as that disclosed in US patents 8,771,679, and 6,339,070.( iii ) “Passcode ” Regulatory Switches

[0285] In some embodiments the regulatory switch can be a “passcode switch” or “passcode circuit”. Passcode switches allow fine tuning of the control of the expression of the transgene from the ceDNA vector when specific conditions occur - that is, a combination of conditions need to be present for transgene expression and / or repression to occur. For example, for expression of a transgene to occur at least conditions A and B must occur. A passcode regulatory switch can be any number of conditions, e.g., at least 2, or at least 3, or at least 4, or at least 5, or at least 6 or at least 7 or more conditions to be present for transgene expression to occur. In some embodiments, at least 2 conditions (e.g., A, B conditions) need to occur, and in some embodiments, at least 3 conditions need to occur (e.g., A, B and C, or A, B and D). By way of an example only, for gene expression from a ceDNA to occur that has a passcode “ABC” regulatory switch, conditions A, B and C must be present.Conditions A, B and C could be as follows; condition A is the presence of a condition or disease, condition B is a hormonal response, and condition C is a response to the transgene expression. For example, if the transgene edits a defective EPO gene, Condition A is the presence of Chronic Kidney Disease (CKD), Condition B occurs if the subject has hypoxic conditions in the kidney, Condition C is that Erythropoietin-producing cells (EPC) recruitment in the kidney is impaired; or alternatively, HIF- 2 activation is impaired. Once the oxygen levels increase or the desired level of EPO is reached, the transgene turns off again until 3 conditions occur, turning it back on.

[0286] In some embodiments, a passcode regulatory switch or “Passcode circuit” encompassed for use in the ceDNA vector comprises hybrid transcription factors (TFs) to expand the range and complexity of environmental signals used to define biocontainment conditions. As opposed to a deadman switch which triggers cell death in the presence of a predetermined condition, the “passcode circuit” allows cell survival or transgene expression in the presence of a particular “passcode”, and can be easily reprogrammed to allow transgene expression and / or cell survival only when the predetermined environmental condition or passcode is present.

[0287] Any and all combinations of regulatory switches disclosed herein, e.g., small molecule switches, nucleic acid-based switches, small molecule -nucleic acid hybrid switches, post- transcriptional transgene regulation switches, post-translational regulation, radiation-controlled switches, hypoxia-mediated switches and other regulatory switches known by persons of ordinary skill in the art as disclosed herein can be used in a passcode regulatory switch as disclosed herein.Regulatory switches encompassed for use are also discussed in the review article Kis et al., J R Soc Interface. 12: 20141000 (2015), and summarized in Table 1 of Kis. In some embodiments, a regulatory switch for use in a passcode system can be selected from any or a combination of the switches disclosed in Table 11 of Internatioanl Patent Application PCT / US 18 / 49996, which is incorporated herein in its entirety by reference.(iv). Nucleic acid-based regulatory switches to control transgene expression

[0288] In some embodiments, the regulatory switch to control the expression of FIX protein by the ceDNA is based on a nucleic-acid based control mechanism. Exemplary nucleic acid control mechanisms are known in the art and are envisioned for use. For example, such mechanisms include riboswitches, such as those disclosed in, e.g., US2009 / 0305253, US2008 / 0269258, US2017 / 0204477, WO2018026762A1, US patent 9,222,093 and EP application EP288071, and also disclosed in the review by Villa JK et al., Microbiol Spectr. 2018 May;6(3). Also included are metabolite -responsive transcription biosensors, such as those disclosed in WO2018 / 075486 and WO2017 / 147585. Other art- known mechanisms envisioned for use include silencing of the transgene with an siRNA or RNAi molecule (e.g., miR, shRNA). For example, the ceDNA vector can comprise a regulatory switch that encodes a RNAi molecule that is complementary to the to part of the transgene expressed by the ceDNA vector. When such RNAi is expressed even if the transgene (e.g., FIX protein) is expressed by the ceDNA vector, it will be silenced by the complementary RNAi molecule, and when the RNAi is not expressed when the transgene is expressed by the ceDNA vector the transgene (e.g., FIX protein) is not silenced by the RNAi.

[0289] In some embodiments, the regulatory switch is a tissue-specific self-inactivating regulatory switch, for example as disclosed in US2002 / 0022018, whereby the regulatory switch deliberately switches transgene (e.g., FIX protein) off at a site where transgene expression might otherwise be disadvantageous. In some embodiments, the regulatory switch is a recombinase reversible gene expression system, for example as disclosed in US2014 / 0127162 and US Patent 8,324,436.(v). Post-transcriptional and post-translational regulatory switches.

[0290] In some embodiments, the regulatory switch to control the expression of FIX protein by the ceDNA vector is a post-transcriptional modification system. For example, such a regulatory switch can be an aptazyme ribos witch that is sensitive to tetracycline or theophylline, as disclosed in US2018 / 0119156, GB201107768, W02001 / 064956A3, EP Patent 2707487 and Beilstein et al., ACS Synth. Biol., 2015, 4 (5), pp 526-534; Zhong et al., Elife. 2016 Nov 2;5. pii: el8858. In some embodiments, it is envisioned that a person of ordinary skill in the art could encode both the transgene and an inhibitory siRNA which contains a ligand sensitive (OFF-switch) aptamer, the net result being a ligand sensitive ON-switch.( vi ). Other exemplary regulatory switches

[0291] Any known regulatory switch can be used in the ceDNA vector to control the expression of FIX protein by the ceDNA vector, including those triggered by environmental changes. Additionalexamples include, but are not limited to; the BOC method of Suzuki et al., Scientific Reports 8; 10051 (2018); genetic code expansion and a non-physiologic amino acid; radiation-controlled or ultra-sound controlled on / off switches (see, e.g., Scott S et al., Gene Ther. 2000 Jul;7(13): 1121-5; US patents 5,612,318; 5,571,797; 5,770,581; 5,817,636; and WO1999 / 025385A1. In some embodiments, the regulatory switch is controlled by an implantable system, e.g., as disclosed in US patent 7,840,263; US2007 / 0190028A1 where gene expression is controlled by one or more forms of energy, including electromagnetic energy, that activates promoters operatively linked to the transgene in the ceDNA vector.

[0292] In some embodiments, a regulatory switch envisioned for use in the ceDNA vector is a hypoxia-mediated or stress-activated switch, e.g., such as those disclosed in WO 1999060142 A2, US patent 5,834,306; 6,218,179; 6,709,858; US2015 / 0322410; Greco et al., (2004) Targeted Cancer Therapies 9, S368, as well as FROG, TOAD and NRSE elements and conditionally inducible silence elements, including hypoxia response elements (HREs), inflammatory response elements (IREs) and shear-stress activated elements (SSAEs), e.g., as disclosed in U.S. Patent 9,394,526. Such an embodiment is useful for turning on expression of the transgene from the ceDNA vector after ischemia or in ischemic tissues, and / or tumors.( vii ). Kill Switches

[0293] Other embodiments described herein relate to a ceDNA vector for expression of FIX protein as described herein comprising a kill switch. A kill switch as disclosed herein enables a cell comprising the ceDNA vector to be killed or undergo programmed cell death as a means to permanently remove an introduced ceDNA vector from the subject’s system. It will be appreciated by one of ordinary skill in the art that use of kill switches in the ceDNA vectors for expression of FIX protein would be typically coupled with targeting of the ceDNA vector to a limited number of cells that the subject can acceptably lose or to a cell type where apoptosis is desirable (e.g., cancer cells). In all aspects, a “kill switch” as disclosed herein is designed to provide rapid and robust cell killing of the cell comprising the ceDNA vector in the absence of an input survival signal or other specified condition. Stated another way, a kill switch encoded by a ceDNA vector for expression of FIX protein as described herein can restrict cell survival of a cell comprising a ceDNA vector to an environment defined by specific input signals. Such kill switches serve as a biological biocontainment function should it be desirable to remove the ceDNA vector e expression of FIX protein in a subject or to ensure that it will not express the encoded FIX protein.

[0294] Other kill switches known to a person of ordinary skill in the art are encompassed for use in the ceDNA vector for expression of FIX protein as disclosed herein, e.g., as disclosed in US2010 / 0175141; US2013 / 0009799; US2011 / 0172826; US2013 / 0109568, as well as kill switches disclosed in Jusiak et al, Reviews in Cell Biology and molecular Medicine; 2014; 1-56; Kobayashi et al., PNAS, 2004; 101; 8419-9; Marchisio et al., Int. Journal of Biochem and Cell Biol., 2011; 43; 310- 319; and in Reinshagen et al., Science Translational Medicine, 2018, 11.

[0295] Accordingly, in some embodiments, the ceDNA vector for expression of FIX protein can comprise a kill switch nucleic acid construct, which comprises the nucleic acid encoding an effector toxin or reporter protein, where the expression of the effector toxin (e.g., a death protein) or reporter protein is controlled by a predetermined condition. For example, a predetermined condition can be the presence of an environmental agent, such as, e.g., an exogenous agent, without which the cell will default to expression of the effector toxin (e.g., a death protein) and be killed. In alternative embodiments, a predetermined condition is the presence of two or more environmental agents, e.g., the cell will only survive when two or more necessary exogenous agents are supplied, and without either of which, the cell comprising the ceDNA vector is killed.

[0296] In some embodiments, the ceDNA vector for expression of FIX protein is modified to incorporate a kill-switch to destroy the cells comprising the ceDNA vector to effectively terminate the in vivo expression of the transgene being expressed by the ceDNA vector (e.g., expression of FIX protein). Specifically, the ceDNA vector is further genetically engineered to express a switch-protein that is not functional in mammalian cells under normal physiological conditions. Only upon administration of a drug or environmental condition that specifically targets this switch-protein, the cells expressing the switch-protein will be destroyed thereby terminating the expression of the therapeutic protein or peptide. For instance, it was reported that cells expressing FISV-thymidine kinase can be killed upon administration of drugs, such as ganciclovir and cytosine deaminase. See, for example, Dey and Evans, Suicide Gene Therapy by Flerpes Simplex Virus-1 Thymidine Kinase (HSV- TK), in Targets in Gene Therapy, edited by You (2011); and Beltinger et al., Proc. Natl. Acad. Sci. USA 96(15):8699-8704 (1999). In some embodiments the ceDNA vector can comprise a siRNA kill switch referred to as DISE (Death Induced by Survival gene Elimination) (Murmann et al., Oncotarget. 2017; 8:84643-84658. Induction of DISE in ovarian cancer cells in vivo).D. Exemplary ceDNA-FIX vectors

[0297] According to some embodiments, an exemplary ceDNA-FIX vector is selected from a ceDNA-FIX vector shown below in Table 12. According to some embodiments, the disclosure provides a capsid-free close-ended DNA (ceDNA) vector comprising at least one nucleic acid sequence between flanking inverted terminal repeats (ITRs), wherein at least one nucleic acid sequence encodes at least one FIX protein, and wherein the ceDNA vector is selected from a ceDNA- FIX vector shown in Table 12.Table 12: ceDNA-FIX constructs

[0298] According to some embodiments, the exemplary ceDNA vector is ceDNA-FIXvl, comprising SEQ ID NO: 404. According to some embodiments, the ceDNA vector is at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 404.

[0299] According to some embodiments, the exemplary ceDNA vector is ceDNA-FIX2109, comprising SEQ ID NO: 405. According to some embodiments, the ceDNA vector is at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 405.

[0300] According to some embodiments, the exemplary ceDNA vector is ceDNA-FIX2112, comprising SEQ ID NO: 406. According to some embodiments, the ceDNA vector is at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 406.

[0301] According to some embodiments, the exemplary ceDNA vector is ceDNA-FIX2113, comprising SEQ ID NO: 407. According to some embodiments, the ceDNA vector is at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 407.

[0302] According to some embodiments, the exemplary ceDNA vector is ceDNA-FIX2114, comprising SEQ ID NO: 408. According to some embodiments, the ceDNA vector is at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 408.

[0303] According to some embodiments, the exemplary ceDNA vector is ceDNA-FIX2115, comprising SEQ ID NO: 409. According to some embodiments, the ceDNA vector is at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 409.

[0304] According to some embodiments, the exemplary ceDNA vector is ceDNA-FIX2116, comprising SEQ ID NO: 410. According to some embodiments, the ceDNA vector is at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 410.

[0305] According to some embodiments, the disclosure provides a capsid-free close-ended DNA (ceDNA) vector comprising at least one nucleic acid sequence between flanking inverted terminalrepeats (ITRs), wherein at least one nucleic acid sequence encodes at least one FIX protein, and wherein the ceDNA vector comprises SEQ ID NO: 404. According to some embodiments, the ceDNA vector is at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 404.

[0306] According to some embodiments, the disclosure provides a capsid-free close-ended DNA (ceDNA) vector comprising at least one nucleic acid sequence between flanking inverted terminal repeats (ITRs), wherein at least one nucleic acid sequence encodes at least one FIX protein, and wherein the ceDNA vector comprises SEQ ID NO: 405. According to some embodiments, the ceDNA vector is at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 405.

[0307] According to some embodiments, the disclosure provides a capsid-free close-ended DNA (ceDNA) vector comprising at least one nucleic acid sequence between flanking inverted terminal repeats (ITRs), wherein at least one nucleic acid sequence encodes at least one FIX protein, and wherein the ceDNA vector comprises SEQ ID NO: 406. According to some embodiments, the ceDNA vector is at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 406.

[0308] According to some embodiments, SEQ ID NO: 404 comprises the following components, where the numbers indicate nucleic acid residues:1..141 =left-ITR_v 1142..194 = spacer_left-ITR_vl195..524 = Enhancer525..921 =Promoter922..950 = 5pUTR951..1034 = hFIX Signal Peptide951..1037 = CDS951..3774 = Exon Intron_ORF1039..2476 = Intron2476-3774 = CDS “Translation 2476-3774"3538..3540 = R338L Padua Mutation3775-3862 = 3p UTR3863-4090 = poly A4091-4151 = spacer right-ITR4152..4281 = right-ITR

[0309] According to some embodiments, SEQ ID NO: 405 comprises the following components, where the numbers indicate nucleic acid residues:1..141 = left-ITR142..183 = spacer_left-ITR_v.2.1184..255 = SerpinEnhancer184..837 = 3x Serpin-TTRe_PromoterSet257..328 = Serpin Enhancer330..401 = Serpin Enhancer562..745 = Mouse TTR 5pUTR714..745 = 5pUTR 746-836 = MVM intron 838-845 = Pmel_site 846-854 = Consensus Kozak 855-2240 = FIX-cDNA-691_2 224E.2248 = Pad site 2249-2829 = WPRE_3pUTR 2830-3054 = bGH 3055-3115 = spacer_right-ITR_vl 3116-3245 = right-ITR_vl

[0310] According to some embodiments, SEQ ID NO: 406 comprises the following components, where the numbers indicate nucleic acid residues:1..141 = left-ITR_vl142..183 = spacer_left-ITR_v2.1184..255 = SerpinEnhancer184..837 = 3x Serpin-TTRe_PromoterSet 257-328 = Serpin Enhancer330-401 =Serpin Enhancer562-745 = Mouse TTR 5pUTR (NM_013697.5)714..745 = 5pUTR 746-836 = MVM Intron 838-845 = Pmel_site 846-854 = Consensus_Kozak 855-2240 =FIX-cDNA-691_16 2241-2248 =PacI_site 2249-2829 = WPRE_3pUTR 2830-3054 = bGH 3055-3115 = spacer_right-ITR_vl 3116-3245 = right-ITR_vlVI. Detailed method of Production of a ceDNA Vector A. Production in General

[0311] Certain methods for the production of a ceDNA vector for expression of FIX protein comprising an asymmetrical ITR pair or symmetrical ITR pair as defined herein is described in section IV of International application PCT / US 18 / 49996 filed September 7, 2018, which is incorporated herein in its entirety by reference. In some embodiments, a ceDNA vector for expression of FIX protein as disclosed herein can be produced using insect cells, as described herein. In alternative embodiments, a ceDNA vector for expression of FIX protein as disclosed herein can be produced synthetically and in some embodiments, in a cell-free method, as disclosed on International Application PCT / US19 / 14122, filed January 18, 2019, which is incorporated herein in its entirety by reference.

[0312] As described herein, in one embodiment, a ceDNA vector for expression of FIX protein can be obtained, for example, by the process comprising the steps of: a) incubating a population of host cells (e.g. insect cells) harboring the polynucleotide expression construct template (e.g., a ceDNA- plasmid, a ceDNA-Bacmid, and / or a ceDNA-baculovirus), which is devoid of viral capsid coding sequences, in the presence of a Rep protein under conditions effective and for a time sufficient to induce production of the ceDNA vector within the host cells, and wherein the host cells do not comprise viral capsid coding sequences; and b) harvesting and isolating the ceDNA vector from the host cells. The presence of Rep protein induces replication of the vector polynucleotide with a modified ITR to produce the ceDNA vector in a host cell. However, no viral particles (e.g. AAV virions) are expressed. Thus, there is no size limitation such as that naturally imposed in AAV or other viral-based vectors.

[0313] The presence of the ceDNA vector isolated from the host cells can be confirmed by digesting DNA isolated from the host cell with a restriction enzyme having a single recognition site onthe ceDNA vector and analyzing the digested DNA material on a non-denaturing gel to confirm the presence of characteristic bands of linear and continuous DNA as compared to linear and non- continuous DNA.

[0314] In yet another aspect, the disclosure provides for use of host cell lines that have stably integrated the DNA vector polynucleotide expression template (ceDNA template) into their own genome in production of the non-viral DNA vector, e.g. as described in Lee, L. et al. (2013) Plos One 8(8): e69879. Preferably, Rep is added to host cells at an MOI of about 3. When the host cell line is a mammalian cell line, e.g., HEK293 cells, the cell lines can have polynucleotide vector template stably integrated, and a second vector such as herpes virus can be used to introduce Rep protein into cells, allowing for the excision and amplification of ceDNA in the presence of Rep and helper virus.

[0315] In one embodiment, the host cells used to make the ceDNA vectors for expression of FIX protein as described herein are insect cells, and baculovirus is used to deliver both the polynucleotide that encodes Rep protein and the non-viral DNA vector polynucleotide expression construct template for ceDNA, e.g., as described in FIGS. 4A-4C and Example 1. In some embodiments, the host cell is engineered to express Rep protein.

[0316] The ceDNA vector is then harvested and isolated from the host cells. The time for harvesting and collecting ceDNA vectors described herein from the cells can be selected and optimized to achieve a high-yield production of the ceDNA vectors. For example, the harvest time can be selected in view of cell viability, cell morphology, cell growth, etc. In one embodiment, cells are grown and harvested a sufficient time after baculoviral infection to produce ceDNA vectors but before most cells start to die due to the baculoviral toxicity. The DNA vectors can be isolated using plasmid purification kits such as Qiagen Endo-Free Plasmid kits. Other methods developed for plasmid isolation can be also adapted for DNA vectors. Generally, any nucleic acid purification methods can be adopted.

[0317] The DNA vectors can be purified by any means known to those of skill in the art for purification of DNA. In one embodiment, ceDNA vectors are purified as DNA molecules. In another embodiment, the ceDNA vectors are purified as exosomes or microparticles.

[0318] The presence of the ceDNA vector for expression of FIX protein can be confirmed by digesting the vector DNA isolated from the cells with a restriction enzyme having a single recognition site on the DNA vector and analyzing both digested and undigested DNA material using gel electrophoresis to confirm the presence of characteristic bands of linear and continuous DNA as compared to linear and non-continuous DNA. FIG. 4C and FIG. 4D illustrate one embodiment for identifying the presence of the closed ended ceDNA vectors produced by the processes herein.

[0319] According to some embodiments, the ceDNA is synthetically produced in a cell-free environment.B. ceDNA Plasmid

[0320] A ceDNA-plasmid is a plasmid used for later production of a ceDNA vector for expression of FIX protein. In some embodiments, a ceDNA-plasmid can be constructed using known techniques to provide at least the following as operatively linked components in the direction of transcription: (1) a modified 5’ ITR sequence; (2) an expression cassette containing a r / ,s -regulatory element, for example, a promoter, inducible promoter, regulatory switch, enhancers and the like; and (3) a modified 3’ ITR sequence, where the 3’ ITR sequence is symmetric relative to the 5’ ITR sequence. In some embodiments, the expression cassette flanked by the ITRs comprises a cloning site for introducing an exogenous sequence. The expression cassette replaces the rep and cap coding regions of the AAV genomes.

[0321] In one aspect, a ceDNA vector for expression of FIX protein is obtained from a plasmid, referred to herein as a “ceDNA-plasmid” encoding in this order: a first adeno-associated virus (AAV) inverted terminal repeat (ITR), an expression cassette comprising a transgene, and a mutated or modified AAV ITR, wherein said ceDNA-plasmid is devoid of AAV capsid protein coding sequences. In alternative embodiments, the ceDNA-plasmid encodes in this order: a first (or 5’) modified or mutated AAV ITR, an expression cassette comprising a transgene, and a second (or 3’) modified AAV ITR, wherein said ceDNA-plasmid is devoid of AAV capsid protein coding sequences, and wherein the 5’ and 3’ ITRs are symmetric relative to each other. In alternative embodiments, the ceDNA- plasmid encodes in this order: a first (or 5’) modified or mutated AAV ITR, an expression cassette comprising a transgene, and a second (or 3’) mutated or modified AAV ITR, wherein said ceDNA- plasmid is devoid of AAV capsid protein coding sequences, and wherein the 5’ and 3’ modified ITRs have the same modifications (i.e., they are inverse complement or symmetric relative to each other).

[0322] In a further embodiment, the ceDNA-plasmid system is devoid of viral capsid protein coding sequences (i.e. it is devoid of AAV capsid genes but also of capsid genes of other viruses). In addition, in a particular embodiment, the ceDNA-plasmid is also devoid of AAV Rep protein coding sequences. Accordingly, in a preferred embodiment, ceDNA-plasmid is devoid of functional AAV cap and AAV rep genes GG-3' for AAV2) plus a variable palindromic sequence allowing for hairpin formation.

[0323] A ceDNA-plasmid of the present disclosure can be generated using natural nucleic acid sequences of the genomes of any AAV serotypes well known in the art. In one embodiment, the ceDNA-plasmid backbone is derived from the AAV1, AAV2, AAV3, AAV4, AAV5, AAV 5, AAV7, AAV8, AAV9, AAV10, AAV 11, AAV12, AAVrh8, AAVrhlO, AAV-DJ, and AAV-DJ8 genome. E.g., NCBI: NC 002077; NC 001401; NC001729; NC001829; NC006152; NC 006260; NC 006261; Kotin and Smith, The Springer Index of Viruses, available at the URL maintained by Springer (at www web address: oesys.springer.de / viruses / database / mkchapter.asp?virID=42.04.)(note -references to a URL or database refer to the contents of the URL or database as of the effective filing date of this application) In a particular embodiment, the ceDNA-plasmid backbone is derived from the AAV2genome. In another particular embodiment, the ceDNA-pIasmid backbone is a synthetic backbone genetically engineered to include at its 5’ and 3’ ITRs derived from one of these AAV genomes.

[0324] A ceDNA-pIasmid can optionally include a selectable or selection marker for use in the establishment of a ceDNA vector-producing cell line. In one embodiment, the selection marker can be inserted downstream (i.e., 3’) of the 3’ ITR sequence. In another embodiment, the selection marker can be inserted upstream (i.e., 5’) of the 5’ ITR sequence. Appropriate selection markers include, for example, those that confer drug resistance. Selection markers can be, for example, a blasticidin S- resistance gene, kanamycin, geneticin, and the like. In a preferred embodiment, the drug selection marker is a blasticidin S-resistance gene.

[0325] An exemplary ceDNA ( e.g ., rAAVO) vector for expression of FIX protein is produced from an rAAV plasmid. A method for the production of a rAAV vector, can comprise: (a) providing a host cell with a rAAV plasmid as described above, wherein both the host cell and the plasmid are devoid of capsid protein encoding genes, (b) culturing the host cell under conditions allowing production of an ceDNA genome, and (c) harvesting the cells and isolating the AAV genome produced from said cells.C. Exemplary method of making the ceDNA vectors from ceDNA plasmids

[0326] Methods for making capsid-less ceDNA vectors for expression of FIX protein are also provided herein, notably a method with a sufficiently high yield to provide sufficient vector for in vivo experiments.

[0327] In some embodiments, a method for the production of a ceDNA vector for expression of FIX protein comprises the steps of: (1) introducing the nucleic acid construct comprising an expression cassette and two symmetric ITR sequences into a host cell (e.g., Sf9 cells), (2) optionally, establishing a clonal cell line, for example, by using a selection marker present on the plasmid, (3) introducing a Rep coding gene (either by transfection or infection with a baculovirus carrying said gene) into said insect cell, and (4) harvesting the cell and purifying the ceDNA vector. The nucleic acid construct comprising an expression cassette and two ITR sequences described above for the production of ceDNA vector can be in the form of a ceDNA plasmid, or Bacmid or Baculovirus generated with the ceDNA plasmid as described below. The nucleic acid construct can be introduced into a host cell by transfection, viral transduction, stable integration, or other methods known in the art.D. Cell lines

[0328] Host cell lines used in the production of a ceDNA vector for expression of FIX protein can include insect cell lines derived from Spodoptera frugiperda, such as Sf9 Sf21, or Trichoplusia ni cell, or other invertebrate, vertebrate, or other eukaryotic cell lines including mammalian cells. Other cell lines known to an ordinarily skilled artisan can also be used, such as HEK293, Huh-7, HeLa, HepG2, HeplA, 911, CHO, COS, MeWo, NIH3T3, A549, HT1 180, monocytes, and mature and immature dendritic cells. Host cell lines can be transfected for stable expression of the ceDNA-plasmid for high yield ceDNA vector production.

[0329] CeDNA-plasmids can be introduced into Sf9 cells by transient transfection using reagents ( e.g ., liposomal, calcium phosphate) or physical means (e.g., electroporation) known in the art. Alternatively, stable Sf9 cell lines which have stably integrated the ceDNA-plasmid into their genomes can be established. Such stable cell lines can be established by incorporating a selection marker into the ceDNA -plasmid as described above. If the ceDNA -plasmid used to transfect the cell line includes a selection marker, such as an antibiotic, cells that have been transfected with the ceDNA-plasmid and integrated the ceDNA-plasmid DNA into their genome can be selected for by addition of the antibiotic to the cell growth media. Resistant clones of the cells can then be isolated by single-cell dilution or colony transfer techniques and propagated.E. Isolating and Purifying ceDNA vectors

[0330] Examples of the process for obtaining and isolating ceDNA vectors are described in FIGS. 4A-4E and the specific examples below. ceDNA-vectors for expression of FIX protein disclosed herein can be obtained from a producer cell expressing AAV Rep protein(s), further transformed with a ceDNA-plasmid, ceDNA-bacmid, or ceDNA-baculovirus. Plasmids useful for the production of ceDNA vectors include plasmids that encode FIX protein, or plamids encoding one or more REP proteins.

[0331] In one aspect, a polynucleotide encodes the AAV Rep protein (Rep 78 or 68) delivered to a producer cell in a plasmid (Rep-plasmid), a bacmid (Rep-bacmid), or a baculovirus (Rep-baculovirus). The Rep-plasmid, Rep-bacmid, and Rep-baculovirus can be generated by methods described above.

[0332] Methods to produce a ceDNA vector for expression of FIX protein are described herein. Expression constructs used for generating a ceDNA vector for expression of FIX protein as described herein can be a plasmid (e.g., ceDNA-plasmids), a Bacmid (e.g., ceDNA-bacmid), and / or a baculovirus (e.g., ceDNA-baculovirus). By way of an example only, a ceDNA-vector can be generated from the cells co-infected with ceDNA-baculovirus and Rep-baculovirus. Rep proteins produced from the Rep-baculovirus can replicate the ceDNA-baculovirus to generate ceDNA-vectors. Alternatively, ceDNA vectors for expression of FIX protein can be generated from the cells stably transfected with a construct comprising a sequence encoding the AAV Rep protein (Rep78 / 52) delivered in Rep-plasmids, Rep-bacmids, or Rep-baculovirus. CeDNA-Baculo virus can be transiently transfected to the cells, be replicated by Rep protein and produce ceDNA vectors.

[0333] The bacmid (e.g., ceDNA-bacmid) can be transfected into permissive insect cells such as Sf9, Sf21, Tni (Trichoplusia ni) cell, High Five cell, and generate ceDNA-baculovirus, which is a recombinant baculovirus including the sequences comprising the symmetric ITRs and the expression cassette. ceDNA-baculovirus can be again infected into the insect cells to obtain a next generation of the recombinant baculovirus. Optionally, the step can be repeated once or multiple times to produce the recombinant baculovirus in a larger quantity.

[0334] The time for harvesting and collecting ceDNA vectors for expression of FIX protein as described herein from the cells can be selected and optimized to achieve a high-yield production of theceDNA vectors. For example, the harvest time can be selected in view of cell viability, cell morphology, cell growth, etc. Usually, cells can be harvested after sufficient time after baculoviral infection to produce ceDNA vectors (e.g., ceDNA vectors) but before majority of cells start to die because of the viral toxicity. The ceDNA-vectors can be isolated from the Sf9 cells using plasmid purification kits such as Qiagen ENDO-FREE PLASMID®kits. Other methods developed for plasmid isolation can be also adapted for ceDNA vectors. Generally, any art-known nucleic acid purification methods can be adopted, as well as commercially available DNA extraction kits.

[0335] Alternatively, purification can be implemented by subjecting a cell pellet to an alkaline lysis process, centrifuging the resulting lysate and performing chromatographic separation. As one non-limiting example, the process can be performed by loading the supernatant on an ion exchange column (e.g. SARTOBIND Q®) which retains nucleic acids, and then eluting (e.g. with a 1.2 M NaCl solution) and performing a further chromatographic purification on a gel filtration column (e.g. 6 fast flow GE). The capsid-free AAV vector is then recovered by, e.g., precipitation.

[0336] In some embodiments, ceDNA vectors for expression of FIX protein can also be purified in the form of exosomes, or microparticles. It is known in the art that many cell types release not only soluble proteins, but also complex protein / nucleic acid cargoes via membrane microvesicle shedding (Cocucci et al, 2009; EP 10306226.1) Such vesicles include microvesicles (also referred to as microparticles) and exosomes (also referred to as nanovesicles), both of which comprise proteins and RNA as cargo. Microvesicles are generated from the direct budding of the plasma membrane, and exosomes are released into the extracellular environment upon fusion of multivesicular endosomes with the plasma membrane. Thus, ceDNA vector-containing microvesicles and / or exosomes can be isolated from cells that have been transduced with the ceDNA-plasmid or a bacmid or baculovirus generated with the ceDNA-plasmid.

[0337] Micro vesicles can be isolated by subjecting culture medium to filtration or ultracentrifugation at 20,000 x g, and exosomes at 100,000 x g. The optimal duration of ultracentrifugation can be experimentally-determined and will depend on the particular cell type from which the vesicles are isolated. Preferably, the culture medium is first cleared by low-speed centrifugation (e.g., at 2000 x g for 5-20 minutes) and subjected to spin concentration using, e.g., an AMICON® spin column (Millipore, Watford, UK). Microvesicles and exosomes can be further purified via FACS or MACS by using specific antibodies that recognize specific surface antigens present on the microvesicles and exosomes. Other microvesicle and exosome purification methods include, but are not limited to, immunoprecipitation, affinity chromatography, filtration, and magnetic beads coated with specific antibodies or aptamers. Upon purification, vesicles are washed with, e.g., phosphate-buffered saline. One advantage of using microvesicles or exosome to deliver ceDNA- containing vesicles is that these vesicles can be targeted to various cell types by including on their membranes proteins recognized by specific receptors on the respective cell types. (See also EP 10306226)

[0338] Another aspect of the disclosure herein relates to methods of purifying ceDNA vectors from host cell lines that have stably integrated a ceDNA construct into their own genome. In one embodiment, ceDNA vectors are purified as DNA molecules. In another embodiment, the ceDNA vectors are purified as exosomes or microparticles.

[0339] FIG. 5 of International application PCT / US 18 / 49996 shows a gel confirming the production of ceDNA from multiple ceDNA-plasmid constructs using the method described in the Examples. The ceDNA is confirmed by a characteristic band pattern in the gel, as discussed with respect to FIG. 4D in the Examples.VII. Pharmaceutical Compositions

[0340] In another aspect, pharmaceutical compositions are provided. The pharmaceutical composition comprises a ceDNA vector for expression of FIX protein as described herein and a pharmaceutically acceptable carrier or diluent.

[0341] The ceDNA vectors for expression of FIX protein as disclosed herein can be incorporated into pharmaceutical compositions suitable for administration to a subject for in vivo delivery to cells, tissues, or organs of the subject. Typically, the pharmaceutical composition comprises a ceDNA-vector as disclosed herein and a pharmaceutically acceptable carrier. For example, the ceDNA vectors for expression of FIX protein as described herein can be incorporated into a pharmaceutical composition suitable for a desired route of therapeutic administration ( e.g ., parenteral administration). Passive tissue transduction via high pressure intravenous or intra-arterial infusion, as well as intracellular injection, such as intranuclear microinjection or intracytoplasmic injection, are also contemplated. Pharmaceutical compositions for therapeutic purposes can be formulated as a solution, microemulsion, dispersion, liposomes, or other ordered structure suitable to high ceDNA vector concentration. Sterile injectable solutions can be prepared by incorporating the ceDNA vector compound in the required amount in an appropriate buffer with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization including a ceDNA vector can be formulated to deliver a transgene in the nucleic acid to the cells of a recipient, resulting in the therapeutic expression of the transgene or donor sequence therein. The composition can also include a pharmaceutically acceptable carrier.

[0342] Pharmaceutically active compositions comprising a ceDNA vector for expression of FIX protein can be formulated to deliver a transgene for various purposes to the cell, e.g., cells of a subject.

[0343] Pharmaceutical compositions for therapeutic purposes typically must be sterile and stable under the conditions of manufacture and storage. The composition can be formulated as a solution, microemulsion, dispersion, liposomes, or other ordered structure suitable to high ceDNA vector concentration. Sterile injectable solutions can be prepared by incorporating the ceDNA vector compound in the required amount in an appropriate buffer with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization.

[0344] A ceDNA vector for expression of FIX protein as disclosed herein can be incorporated into a pharmaceutical composition suitable for topical, systemic, intra-amniotic, intrathecal, intracranial, intra-arterial, intravenous, intralymphatic, intraperitoneal, subcutaneous, tracheal, intra-tissue (e.g., intramuscular, intracardiac, intrahepatic, intrarenal, intracerebral), intrathecal, intravesical, conjunctival (e.g., extra-orbital, intraorbital, retroorbital, intraretinal, subretinal, choroidal, sub- choroidal, intrastromal, intracameral and intravitreal), intracochlear, and mucosal (e.g., oral, rectal, nasal) administration. Passive tissue transduction via high pressure intravenous or intraarterial infusion, as well as intracellular injection, such as intranuclear microinjection or intracytoplasmic injection, are also contemplated.

[0345] In some aspects, the methods provided herein comprise delivering one or more ceDNA vectors for expression of FIX protein as disclosed herein to a host cell. Also provided herein are cells produced by such methods, and organisms (such as animals, plants, or fungi) comprising or produced from such cells. Methods of delivery of nucleic acids can include lipofection, nucleofection, microinjection, biolistics, liposomes, immunoliposomes, polycation or lipid ucleic acid conjugates, naked DNA, and agent-enhanced uptake of DNA. Lipofection is described in e.g., U.S. Pat. Nos. 5,049,386, 4,946,787; and 4,897,355) and lipofection reagents are sold commercially (e.g., Transfectam™ and Lipofectin™). Delivery can be to cells (e.g., in vitro or ex vivo administration) or target tissues (e.g., in vivo administration).

[0346] Various techniques and methods are known in the art for delivering nucleic acids to cells. For example, nucleic acids, such as ceDNA for expression of FIX protein can be formulated into lipid nanoparticles (LNPs), lipidoids, liposomes, lipid nanoparticles, lipoplexes, or core-shell nanoparticles. Typically, LNPs are composed of nucleic acid (e.g., ceDNA) molecules, one or more ionizable or cationic lipids (or salts thereof), one or more non-ionic or neutral lipids (e.g., a phospholipid), a molecule that prevents aggregation (e.g., PEG or a PEG-lipid conjugate), and optionally a sterol (e.g., cholesterol).

[0347] Another method for delivering nucleic acids, such as ceDNA for expression of FIX protein to a cell is by conjugating the nucleic acid with a ligand that is internalized by the cell. For example, the ligand can bind a receptor on the cell surface and internalized via endocytosis. The ligand can be covalently linked to a nucleotide in the nucleic acid. Exemplary conjugates for delivering nucleic acids into a cell are described, example, in W02015 / 006740, WO2014 / 025805, WO2012 / 037254, W02009 / 082606, W02009 / 073809, W02009 / 018332, W02006 / 112872, W02004 / 090108, W02004 / 091515 and WO2017 / 177326.

[0348] Nucleic acids, such as ceDNA vectors for expression of FIX protein can also be delivered to a cell by transfection. Useful transfection methods include, but are not limited to, lipid-mediated transfection, cationic polymer-mediated transfection, or calcium phosphate precipitation. Transfection reagents are well known in the art and include, but are not limited to, TurboFect Transfection Reagent (Thermo Fisher Scientific), Pro-Ject Reagent (Thermo Fisher Scientific), TRANSPASS™ P ProteinTransfection Reagent (New England Biolabs), CHARIOT™ Protein Delivery Reagent (Active Motif), PROTEOJUICE™ Protein Transfection Reagent (EMD Millipore), 293fectin, LIPOFECT AMINE™ 2000, LIPOFECT AMINE™ 3000 (Thermo Fisher Scientific), LIPOFECT AMINE™ (Thermo Fisher Scientific), LIPOFECTIN™ (Thermo Fisher Scientific), DMRIE-C, CELLFECTIN™ (Thermo Fisher Scientific), OLIGOFECT AMINE™ (Thermo Fisher Scientific), LIPOFECTACE™, FUGENE™ (Roche, Basel, Switzerland), FUGENE™ HD (Roche), TRANSFECT AM™(Transfectam, Promega, Madison, Wis.), TFX-10™ (Promega), TFX-20™ (Promega), TFX-50™ (Promega), TRANSFECTIN™ (BioRad, Hercules, Calif.), SILENTFECT™ (Bio-Rad), Effectene™ (Qiagen, Valencia, Calif.), DC-chol (Avanti Polar Lipids), GENEPORTER™ (Gene Therapy Systems, San Diego, Calif.), DHARMAFECT 1™ (Dharmacon, Lafayette, Colo.), DHARMAFECT 2™ (Dharmacon), DHARMAFECT 3™ (Dharmacon), DHARMAFECT 4™ (Dharmacon), ESCORT™ III (Sigma, St. Louis, Mo.), and ESCORT™ IV (Sigma Chemical Co.). Nucleic acids, such as ceDNA, can also be delivered to a cell via microfluidics methods known to those of skill in the art.

[0349] ceDNA vectors for expression of FIX protein as described herein can also be administered directly to an organism for transduction of cells in vivo. Administration is by any of the routes normally used for introducing a molecule into ultimate contact with blood or tissue cells including, but not limited to, injection, infusion, topical application and electroporation. Suitable methods of administering such nucleic acids are available and well known to those of skill in the art, and, although more than one route can be used to administer a particular composition, a particular route can often provide a more immediate and more effective reaction than another route.

[0350] Methods for introduction of a nucleic acid vector ceDNA vector for expression of FIX protein as disclosed herein can be delivered into hematopoietic stem cells, for example, by the methods as described, for example, in U.S. Pat. No. 5,928,638.

[0351] The ceDNA vectors for expression of FIX protein in accordance with the present disclosure can be added to liposomes for delivery to a cell or target organ in a subject. Liposomes are vesicles that possess at least one lipid bilayer. Liposomes are typical used as carriers for drug / therapeutic delivery in the context of pharmaceutical development. They work by fusing with a cellular membrane and repositioning its lipid structure to deliver a drug or active pharmaceutical ingredient (API). Liposome compositions for such delivery are composed of phospholipids, especially compounds having a phosphatidylcholine group, however these compositions may also include other lipids. Exemplary liposomes and liposome formulations, including but not limited to polyethylene glycol (PEG)-functional group containing compounds are disclosed in International Application PCT / US2018 / 050042, filed on September 7, 2018 and in International application PCT / US2018 / 064242, filed on December 6, 2018, e.g., see the section entitled “Pharmaceutical Formulations”.

[0352] Various delivery methods known in the art or modification thereof can be used to deliver ceDNA vectors in vitro or in vivo. For example, in some embodiments, ceDNA vectors for expressionof FIX protein are delivered by making transient penetration in cell membrane by mechanical, electrical, ultrasonic, hydrodynamic, or laser-based energy so that DNA entrance into the targeted cells is facilitated. For example, a ceDNA vector can be delivered by transiently disrupting cell membrane by squeezing the cell through a size-restricted channel or by other means known in the art. In some cases, a ceDNA vector alone is directly injected as naked DNA into any one of: any one or more tissues selected from: liver, kidneys, gallbladder, prostate, adrenal gland, heart, intestine, lung, and stomach, skin, thymus, cardiac muscle or skeletal muscle. In some cases, a ceDNA vector is delivered by gene gun. Gold or tungsten spherical particles (1-3 pm diameter) coated with capsid-free AAV vectors can be accelerated to high speed by pressurized gas to penetrate into target tissue cells.

[0353] Compositions comprising a ceDNA vector for expression of FIX protein and a pharmaceutically acceptable carrier are specifically contemplated herein. In some embodiments, the ceDNA vector is formulated with a lipid delivery system, for example, liposomes as described herein. In some embodiments, such compositions are administered by any route desired by a skilled practitioner. The compositions may be administered to a subject by different routes including orally, parenterally, sublingually, transdermally, rectally, transmucosally, topically, via inhalation, via buccal administration, intrapleurally, intravenous, intra-arterial, intraperitoneal, subcutaneous, intramuscular, intranasal intrathecal, and intraarticular or combinations thereof. For veterinary use, the composition may be administered as a suitably acceptable formulation in accordance with normal veterinary practice. The veterinarian may readily determine the dosing regimen and route of administration that is most appropriate for a particular animal. The compositions may be administered by traditional syringes, needleless injection devices, “microprojectile bombardment gene guns”, or other physical methods such as electroporation (“EP”), hydrodynamic methods, or ultrasound.

[0354] In some cases, a ceDNA vector for expression of FIX protein is delivered by hydrodynamic injection, which is a simple and highly efficient method for direct intracellular delivery of any water- soluble compounds and particles into internal organs and skeletal muscle in an entire limb.

[0355] In some cases, ceDNA vectors for expression of FIX protein are delivered by ultrasound by making nanoscopic pores in membrane to facilitate intracellular delivery of DNA particles into cells of internal organs or tumors, so the size and concentration of plasmid DNA have great role in efficiency of the system. In some cases, ceDNA vectors are delivered by magnetofection by using magnetic fields to concentrate particles containing nucleic acid into the target cells.

[0356] In some cases, chemical delivery systems can be used, for example, by using nanomeric complexes, which include compaction of negatively charged nucleic acid by polycationic nanomeric particles, belonging to cationic liposome / micelle or cationic polymers. Cationic lipids used for the delivery method includes, but not limited to monovalent cationic lipids, polyvalent cationic lipids, guanidine containing compounds, cholesterol derivative compounds, cationic polymers, (e.g., poly(ethylenimine), poly-L -lysine, protamine, other cationic polymers), and lipid-polymer hybrid.A. Exosomes:

[0357] In some embodiments, a ceDNA vector for expression of FIX protein as disclosed herein is delivered by being packaged in an exosome. Exosomes are small membrane vesicles of endocytic origin that are released into the extracellular environment following fusion of multivesicular bodies with the plasma membrane. Their surface consists of a lipid bilayer from the donor cell's cell membrane, they contain cytosol from the cell that produced the exosome, and exhibit membrane proteins from the parental cell on the surface. Exosomes are produced by various cell types including epithelial cells, B and T lymphocytes, mast cells (MC) as well as dendritic cells (DC). Some embodiments, exosomes with a diameter between lOnm and 1 pm, between 20nm and 500nm, between 30nm and 250nm, between 50nm and lOOnm are envisioned for use. Exosomes can be isolated for a delivery to target cells using either their donor cells or by introducing specific nucleic acids into them. Various approaches known in the art can be used to produce exosomes containing capsid-free AAV vectors of the present disclosure.B. Microparticle / Nanoparticles

[0358] In some embodiments, a ceDNA vector for expression of FIX protein as disclosed herein is delivered by a lipid nanoparticle. Generally, lipid nanoparticles comprise an ionizable amino lipid (e.g., heptatriaconta-6,9,28,31-tetraen-19-yl 4-(dimethylamino)butanoate, DLin-MC3-DMA, a phosphatidylcholine (l,2-distearoyl-sn-glycero-3-phosphocholine, DSPC), cholesterol and a coat lipid (polyethylene glycol-dimyristolglycerol, PEG-DMG), for example as disclosed by Tam et al. (2013). Advances in Lipid Nanoparticles for siRNA delivery. Pharmaceuticals 5(3): 498-507.

[0359] In some embodiments, a lipid nanoparticle has a mean diameter between about 10 and about 1000 nm. In some embodiments, a lipid nanoparticle has a diameter that is less than 300 nm. In some embodiments, a lipid nanoparticle has a diameter between about 10 and about 300 nm. In some embodiments, a lipid nanoparticle has a diameter that is less than 200 nm. In some embodiments, a lipid nanoparticle has a diameter between about 25 and about 200 nm. In some embodiments, a lipid nanoparticle preparation (e.g., composition comprising a plurality of lipid nanoparticles) has a size distribution in which the mean size (e.g., diameter) is about 70 nm to about 200 nm, and more typically the mean size is about 100 nm or less.

[0360] Various lipid nanoparticles known in the art can be used to deliver ceDNA vector for expression of FIX protein as disclosed herein. For example, various delivery methods using lipid nanoparticles are described in U.S. Patent Nos. 9,404,127, 9,006,417 and 9,518,272.

[0361] In some embodiments, a ceDNA vector for expression of FIX protein as disclosed herein is delivered by a gold nanoparticle. Generally, a nucleic acid can be covalently bound to a gold nanoparticle or non-covalently bound to a gold nanoparticle (e.g., bound by a charge-charge interaction), for example as described by Ding et al. (2014). Gold Nanoparticles for Nucleic Acid Delivery. Mol. Ther. 22(6); 1075-1083. In some embodiments, gold nanoparticle-nucleic acid conjugates are produced using methods described, for example, in U.S. Patent No. 6,812,334.C. Conjugates

[0362] In some embodiments, a ceDNA vector for expression of FIX protein as disclosed herein is conjugated (e.g., covalently bound to an agent that increases cellular uptake. An “agent that increases cellular uptake” is a molecule that facilitates transport of a nucleic acid across a lipid membrane. For example, a nucleic acid can be conjugated to a lipophilic compound (e.g., cholesterol, tocopherol, etc.), a cell penetrating peptide (CPP) (e.g., penetratin, TAT, SynlB, etc.), and polyamines (e.g., spermine). Further examples of agents that increase cellular uptake are disclosed, for example, in Winkler (2013). Oligonucleotide conjugates for therapeutic applications. Ther. Deliv. 4(7); 791-809.

[0363] In some embodiments, a ceDNA vector for expression of FIX protein as disclosed herein is conjugated to a polymer (e.g., a polymeric molecule) or a folate molecule (e.g., folic acid molecule). Generally, delivery of nucleic acids conjugated to polymers is known in the art, for example as described in W02000 / 34343 and W02008 / 022309. In some embodiments, a ceDNA vector for expression of FIX protein as disclosed herein is conjugated to a poly( amide) polymer, for example as described by U.S. Patent No. 8,987,377. In some embodiments, a nucleic acid described by the disclosure is conjugated to a folic acid molecule as described in U.S. Patent No. 8,507,455.

[0364] In some embodiments, a ceDNA vector for expression of FIX protein as disclosed herein is conjugated to a carbohydrate, for example as described in U.S. Patent No. 8,450,467.D. Nanocapsule

[0365] Alternatively, nanocapsule formulations of a ceDNA vector for expression of FIX protein as disclosed herein can be used. Nanocapsules can generally entrap substances in a stable and reproducible way. To avoid side effects due to intracellular polymeric overloading, such ultrafine particles (sized around 0.1 pm) should be designed using polymers able to be degraded in vivo. Biodegradable polyalkyl-cyanoacrylate nanoparticles that meet these requirements are contemplated for use.E. Liposomes

[0366] The ceDNA vectors for expression of FIX protein in accordance with the present disclosure can be added to liposomes for delivery to a cell or target organ in a subject. Liposomes are vesicles that possess at least one lipid bilayer. Liposomes are typical used as carriers for drug / therapeutic delivery in the context of pharmaceutical development. They work by fusing with a cellular membrane and repositioning its lipid structure to deliver a drug or active pharmaceutical ingredient (API). Liposome compositions for such delivery are composed of phospholipids, especially compounds having a phosphatidylcholine group, however these compositions may also include other lipids.

[0367] The formation and use of liposomes is generally known to those of skill in the art. Liposomes have been developed with improved serum stability and circulation half-times (U.S. Pat.No. 5,741,516). Further, various methods of liposome and liposome like preparations as potential drug carriers have been described (U.S. Pat. Nos. 5,567,434; 5,552,157; 5,565,213; 5,738,868 and 5,795,587).F. Exemplary liposome and Lipid Nanoparticle (LNP) Compositions

[0368] The ceDNA vectors for expression of FIX protein in accordance with the present disclosure can be added to liposomes for delivery to a cell, e.g., a cell in need of expression of the transgene. Liposomes are vesicles that possess at least one lipid bilayer. Liposomes are typical used as carriers for drug / therapeutic delivery in the context of pharmaceutical development. They work by fusing with a cellular membrane and repositioning its lipid structure to deliver a drug or active pharmaceutical ingredient (API). Liposome compositions for such delivery are composed of phospholipids, especially compounds having a phosphatidylcholine group, however these compositions may also include other lipids.

[0369] Lipid nanoparticles (LNPs) comprising ceDNA vectors are disclosed in International Application PCT / US2018 / 050042, filed on September 7, 2018, and International Application PCT / US2018 / 064242, filed on December 6, 2018 which are incorporated herein in their entirety and envisioned for use in the methods and compositions for ceDNA vectors for expression of FIX protein as disclosed herein.

[0370] In some aspects, the disclosure provides for a liposome formulation that includes one or more compounds with a polyethylene glycol (PEG) functional group (so-called “PEG-ylated compounds”) which can reduce the immunogenicity / antigenicity of, provide hydrophilicity and hydrophobicity to the compound(s) and reduce dosage frequency. Or the liposome formulation simply includes polyethylene glycol (PEG) polymer as an additional component. In such aspects, the molecular weight of the PEG or PEG functional group can be from 62 Da to about 5,000 Da.

[0371] In some aspects, the disclosure provides for a liposome formulation that will deliver an API with extended release or controlled release profile over a period of hours to weeks. In some related aspects, the liposome formulation may comprise aqueous chambers that are bound by lipid bilayers. In other related aspects, the liposome formulation encapsulates an API with components that undergo a physical transition at elevated temperature which releases the API over a period of hours to weeks.

[0372] In some aspects, the liposome formulation comprises sphingomyelin and one or more lipids disclosed herein. In some aspects, the liposome formulation comprises optisomes.

[0373] In some aspects, the disclosure provides for a liposome formulation that includes one or more lipids selected from: N-(carbonyl-methoxypolyethylene glycol 2000)-l,2-distearoyl-sn-glycero- 3-phosphoethanolamine sodium salt, (distearoyl-sn-glycero-phosphoethanolamine), MPEG (methoxy polyethylene glycol)-conjugated lipid, HSPC (hydrogenated soy phosphatidylcholine); PEG (polyethylene glycol); DSPE (distearoyl-sn-glycero-phosphoethanolamine); DSPC (distearoylphosphatidylcholine); DOPC (dioleoylphosphatidylcholine); DPPG (dipalmitoylphosphatidylglycerol); EPC (egg phosphatidylcholine); DOPS (dioleoylphosphatidylserine); POPC (palmitoyloleoylphosphatidylcholine); SM (sphingomyelin); MPEG (methoxy polyethylene glycol); DMPC (dimyristoyl phosphatidylcholine); DMPG (dimyristoyl phosphatidylglycerol); DSPG (distearoylphosphatidylglycerol); DEPC(dierucoylphosphatidylcholine); DOPE (dioleoly-sn-glycero-phophoethanolamine). cholesteryl sulphate (CS), dipalmitoylphosphatidylglycerol (DPPG), DOPC (dioleoly-sn-glycero- phosphatidylcholine) or any combination thereof.

[0374] In some aspects, the disclosure provides for a liposome formulation comprising phospholipid, cholesterol and a PEG-ylated lipid in a molar ratio of 56:38:5. In some aspects, the liposome formulation’s overall lipid content is from 2-16 mg / mL. In some aspects, the disclosure provides for a liposome formulation comprising a lipid containing a phosphatidylcholine functional group, a lipid containing an ethanolamine functional group and a PEG-ylated lipid. In some aspects, the disclosure provides for a liposome formulation comprising a lipid containing a phosphatidylcholine functional group, a lipid containing an ethanolamine functional group and a PEG-ylated lipid in a molar ratio of 3:0.015:2 respectively. In some aspects, the disclosure provides for a liposome formulation comprising a lipid containing a phosphatidylcholine functional group, cholesterol and a PEG-ylated lipid. In some aspects, the disclosure provides for a liposome formulation comprising a lipid containing a phosphatidylcholine functional group and cholesterol. In some aspects, the PEG- ylated lipid is PEG-2000-DSPE. In some aspects, the disclosure provides for a liposome formulation comprising DPPG, soy PC, MPEG-DSPE lipid conjugate and cholesterol.

[0375] In some aspects, the disclosure provides for a liposome formulation comprising one or more lipids containing a phosphatidylcholine functional group and one or more lipids containing an ethanolamine functional group. In some aspects, the disclosure provides for a liposome formulation comprising one or more: lipids containing a phosphatidylcholine functional group, lipids containing an ethanolamine functional group, and sterols, e.g. cholesterol. In some aspects, the liposome formulation comprises DOPC / DEPC; and DOPE.

[0376] In some aspects, the disclosure provides for a liposome formulation further comprising one or more pharmaceutical excipients, e.g. sucrose and / or glycine.

[0377] In some aspects, the disclosure provides for a liposome formulation that is either unilamellar or multilamellar in structure. In some aspects, the disclosure provides for a liposome formulation that comprises multi-vesicular particles and / or foam-based particles. In some aspects, the disclosure provides for a liposome formulation that are larger in relative size to common nanoparticles and about 150 to 250 nm in size. In some aspects, the liposome formulation is a lyophilized powder.In some aspects, the disclosure provides for a liposome formulation that is made and loaded with ceDNA vectors disclosed or described herein, by adding a weak base to a mixture having the isolated ceDNA outside the liposome. This addition increases the pH outside the liposomes to approximately 7.3 and drives the API into the liposome. In some aspects, the disclosure provides for a liposome formulation having a pH that is acidic on the inside of the liposome. In such cases the inside of the liposome can be at pH 4-6.9, and more preferably pH 6.5. In other aspects, the disclosure provides for a liposome formulation made by using intra-liposomal drug stabilization technology. In such cases,polymeric or non-polymeric highly charged anions and intra-liposomal trapping agents are utilized, e.g. polyphosphate or sucrose octasulfate.

[0378] In some aspects, the disclosure provides for a lipid nanoparticle comprising ceDNA and an ionizable lipid. For example, a lipid nanoparticle formulation that is made and loaded with ceDNA obtained by the process as disclosed in International Application PCT / US2018 / 050042, filed on September 7, 2018, which is incorporated herein. This can be accomplished by high energy mixing of ethanolic lipids with aqueous ceDNA at low pH which protonates the ionizable lipid and provides favorable energetics for ceDNA / lipid association and nucleation of particles. The particles can be further stabilized through aqueous dilution and removal of the organic solvent. The particles can be concentrated to the desired level.

[0379] Generally, the lipid nanoparticles are prepared at a total lipid to ceDNA (mass or weight) ratio of from about 10:1 to 60:1. In some embodiments, the lipid to ceDNA ratio (mass / mass ratio; w / w ratio) can be in the range of from about 1:1 to about 60:1, from about 1:1 to about 55:1, from about 1:1 to about 50:1, from about 1:1 to about 45:1, from about 1:1 to about 40:1, from about 1:1 to about 35:1, from about 1:1 to about 30:1, from about 1:1 to about 25:1, from about 10:1 to about 14:1, from about 3:1 to about 15:1, from about 4:1 to about 10:1, from about 5:1 to about 9:1, about 6:1 to about 9:1; from about 30:1 to about 60:1. According to some embodiments, the lipid particles (e.g., lipid nanoparticles) are prepared at a ceDNA (mass or weight) to total lipid ratio of about 60:1. According to some embodiments, the lipid particles are prepared at a total lipid to ceDNA (mass or weight) ratio of from about 10:1 to 30:1. In some embodiments, the lipid to ceDNA ratio (mass / mass ratio; w / w ratio) can be in the range of from about 1:1 to about 25:1, from about 10:1 to about 14:1, from about 3:1 to about 15:1, from about 4:1 to about 10:1, from about 5:1 to about 9:1, or about 6:1 to about 9:1. The amounts of lipids and ceDNA can be adjusted to provide a desired N / P ratio, for example, N / P ratio of 3, 4, 5, 6, 7, 8, 9, 10 or higher. Generally, the lipid particle formulation’s overall lipid content can range from about 5 mg / ml to about 30 mg / mL.

[0380] The ionizable lipid is typically employed to condense the nucleic acid cargo, e.g., ceDNA at low pH and to drive membrane association and fusogenicity. Generally, ionizable lipids are lipids comprising at least one amino group that is positively charged or becomes protonated under acidic conditions, for example at pH of 6.5 or lower. Ionizable lipids are also referred to as cationic lipids herein.

[0381] Exemplary ionizable lipids are described in International PCT patent publications W02015 / 095340, WO2015 / 199952, W02018 / 011633, WO2017 / 049245, WO2015 / 061467,WO2012 / 040184, W02012 / 000104, W02015 / 074085, W02016 / 081029, WO2017 / 004143, WO2017 / 075531, WO2017 / 117528, WO2011 / 022460, WO2013 / 148541, WO2013 / 116126,WO2011 / 153120, WO2012 / 044638, WO2012 / 054365, WO2011 / 090965, W02013 / 016058, W02012 / 162210, W02008 / 042973, WO2010 / 129709, W02010 / 144740 , WO2012 / 099755, WO2013 / 049328, WO2013 / 086322, WO2013 / 086373, WO2011 / 071860, W02009 / 132131,W02010 / 048536, W02010 / 088537, W02010 / 054401, W02010 / 054406 , W02010 / 054405,WO20 10 / 054384, W02012 / 016184, W02009 / 086558, W02010 / 042877, WO2011 / 000106,WO2011 / 000107, W02005 / 120152, WO2011 / 141705, WO2013 / 126803, W02006 / 007712,WO2011 / 038160, WO2005 / 121348, WO2011 / 066651, W02009 / 127060, WO2011 / 141704, W02006 / 069782, WO2012 / 031043, W02013 / 006825, WO2013 / 033563, WO2013 / 089151, WO2017 / 099823, WO2015 / 095346, and WO2013 / 086354, and US patent publications US2016 / 0311759, US2015 / 0376115, US2016 / 0151284, US2017 / 0210697, US2015 / 0140070, US2013 / 0178541, US2013 / 0303587, US2015 / 0141678, US2015 / 0239926, US2016 / 0376224,US2017 / 0119904, US2012 / 0149894, US2015 / 0057373, US2013 / 0090372, US2013 / 0274523,US2013 / 0274504, US2013 / 0274504, US2009 / 0023673, US2012 / 0128760, US2010 / 0324120, US2014 / 0200257, US2015 / 0203446, US2018 / 0005363, US2014 / 0308304, US2013 / 0338210, US2012 / 0101148, US2012 / 0027796, US2012 / 0058144, US2013 / 0323269, US2011 / 0117125,US2011 / 0256175, US2012 / 0202871, US2011 / 0076335, US2006 / 0083780, US2013 / 0123338, US2015 / 0064242, US2006 / 0051405, US2013 / 0065939, US2006 / 0008910, US2003 / 0022649, US2010 / 0130588, US2013 / 0116307, US2010 / 0062967, US2013 / 0202684, US2014 / 0141070, US2014 / 0255472, US2014 / 0039032, US2018 / 0028664, US2016 / 0317458, and US2013 / 0195920, the contents of all of which are incorporated herein by reference in their entirety.

[0382] In some embodiments, the ionizable lipid is MC3 (6Z,9Z,28Z,31Z)-heptatriaconta- 6,9,28,31-tetraen-19-yl-4-(dimethylamino) butanoate (DLin-MC3-DMA or MC3) having the following structure:DLi ii-M -C3 - DMA ("MC3")

[0383] The lipid DLin-MC3-DMA is described in Jayaraman et al, Angew. Chem. Int. Ed Engl. (2012), 51(34): 8529-8533, content of which is incorporated herein by reference in its entirety.

[0384] In some embodiments, the ionizable lipid is the lipid ATX-002 as described in W02015 / 074085, content of which is incorporated herein by reference in its entirety.

[0385] In some embodiments, the ionizable lipid is ( 13Z, 16Z)- / V, / V-dimethyl-3-nonyldocosa- 13, 16- dien-l-amine (Compound 32), as described in W02012 / 040184, content of which is incorporated herein by reference in its entirety.

[0386] In some embodiments, the ionizable lipid is Compound 6 or Compound 22 as described in WO2015 / 199952, content of which is incorporated herein by reference in its entirety.

[0387] Without limitations, ionizable lipid can comprise 20-90% (mol) of the total lipid present in the lipid nanoparticle. For example, ionizable lipid molar content can be 20-70% (mol), 30-60% (mol) or 40-50% (mol) of the total lipid present in the lipid nanoparticle. In some embodiments, ionizablelipid comprises from about 50 mol % to about 90 mol % of the total lipid present in the lipid nanoparticle.

[0388] In some aspects, the lipid nanoparticle can further comprise a non-cationic lipid. Non-ionic lipids include amphipathic lipids, neutral lipids and anionic lipids. Accordingly, the non-cationic lipid can be a neutral uncharged, zwitterionic, or anionic lipid. Non-cationic lipids are typically employed to enhance fusogenicity.

[0389] Exemplary non-cationic lipids envisioned for use in the methods and compositions as disclosed herein are described in International Application PCT / US2018 / 050042, filed on September 7, 2018, and PCT / US2018 / 064242, filed on December 6, 2018 which is incorporated herein in its entirety. Exemplary non-cationic lipids are described in International Application Publication WO2017 / 099823 and US patent publication US2018 / 0028664, the contents of both of which are incorporated herein by reference in their entirety.

[0390] The non-cationic lipid can comprise 0-30% (mol) of the total lipid present in the lipid nanoparticle. For example, the non-cationic lipid content is 5-20% (mol) or 10-15% (mol) of the total lipid present in the lipid nanoparticle. In various embodiments, the molar ratio of ionizable lipid to the neutral lipid ranges from about 2:1 to about 8:1.

[0391] In some embodiments, the lipid nanoparticles do not comprise any phospholipids. In some aspects, the lipid nanoparticle can further comprise a component, such as a sterol, to provide membrane integrity.

[0392] One exemplary sterol that can be used in the lipid nanoparticle is cholesterol and derivatives thereof. Exemplary cholesterol derivatives are described in International application W02009 / 127060 and US patent publication US2010 / 0130588, contents of both of which are incorporated herein by reference in their entirety.

[0393] The component providing membrane integrity, such as a sterol, can comprise 0-50% (mol) of the total lipid present in the lipid nanoparticle. In some embodiments, such a component is 20-50% (mol) 30-40% (mol) of the total lipid content of the lipid nanoparticle.

[0394] In some aspects, the lipid nanoparticle can further comprise a polyethylene glycol (PEG) or a conjugated lipid molecule. Generally, these are used to inhibit aggregation of lipid nanoparticles and / or provide steric stabilization. Exemplary conjugated lipids include, but are not limited to, PEG- lipid conjugates, polyoxazoline (POZ)-lipid conjugates, polyamide -lipid conjugates (such as ATTA- lipid conjugates), cationic-polymer lipid (CPL) conjugates, and mixtures thereof. In some embodiments, the conjugated lipid molecule is a PEG-lipid conjugate, for example, a (methoxy polyethylene glycol)-conjugated lipid. Exemplary PEG-lipid conjugates include, but are not limited to, PEG-diacylglycerol (DAG) (such as l-(monomethoxy-poly ethyleneglycol) -2, 3 -dimyristoylglycerol (PEG-DMG)), PEG-dialkyloxypropyl (DAA), PEG-phospholipid, PEG-ceramide (Cer), a pegylated phosphatidylethanoloamine (PEG-PE), PEG succinate diacylglycerol (PEGS-DAG) (such as 4-0- (2',3'-di(tetradecanoyloxy)propyl-l -0-(w-methoxy(polyethoxy)ethyl) butanedioate (PEG-S-DMG)),PEG dialkoxypropylcarbam, N-(carbonyl-methoxypoly ethylene glycol 2000)-l,2-distearoyl-sn- glycero-3-phosphoethanolamine sodium salt, or a mixture thereof. Additional exemplary PEG-lipid conjugates are described, for example, in US5,885,613, US6,287,591,US2003 / 0077829, US2003 / 0077829, US2005 / 0175682, US2008 / 0020058, US2011 / 0117125, US2010 / 0130588, US2016 / 0376224, and US2017 / 0119904, the contents of all of which are incorporated herein by reference in their entirety.

[0395] In some embodiments, a PEG-lipid is a compound as defined in US2018 / 0028664, the content of which is incorporated herein by reference in its entirety. In some embodiments, a PEG-lipid is disclosed in US20150376115 or in US2016 / 0376224, the content of both of which is incorporated herein by reference in its entirety.

[0396] The PEG-DAA conjugate can be, for example, PEG-dilauryloxypropyl, PEG- dimyristyloxypropyl, PEG-dipalmityloxypropyl, or PEG-distearyloxypropyl. The PEG-lipid can be one or more of PEG-DMG, PEG-dilaurylglycerol, PEG-dipalmitoylglycerol, PEG-disterylglycerol, PEG-dilaurylglycamide, PEG-dimyristylglycamide, PEG-dipalmitoylglycamide, PEG- disterylglycamide, PEG-cholesterol (l-[8'-(Cholest-5-en-3[beta]-oxy)carboxamido-3',6'-dioxaoctanyl] carbamoyl- [omega] -methyl -poly(ethylene glycol), PEG-DMB (3,4-Ditetradecoxylbenzyl- [omega] - methyl-poly(ethylene glycol) ether), and l,2-dimyristoyl-sn-glycero-3-phosphoethanolamine-N- [methoxy(polyethylene glycol)-2000]. In some examples, the PEG-lipid can be selected from the group consisting of PEG-DMG, l,2-dimyristoyl-sn-glycero-3-phosphoethanolamine-N- [methoxy(polyethylene glycol)-2000] ,

[0397] Lipids conjugated with a molecule other than a PEG can also be used in place of PEG-lipid. For example, polyoxazoline (POZ)-lipid conjugates, polyamide -lipid conjugates (such as ATTA-lipid conjugates), and cationic-polymer lipid (CPL) conjugates can be used in place of or in addition to the PEG-lipid. Exemplary conjugated lipids, i.e., PEG-lipids, (POZ)-lipid conjugates, ATTA-lipid conjugates and cationic polymer-lipids are described in the International patent application publications WO1996 / 010392, WO1998 / 051278, W02002 / 087541, W02005 / 026372, WO2008 / 147438, W02009 / 086558, W02012 / 000104, WO2017 / 117528, WO2017 / 099823, WO2015 / 199952, WO2017 / 004143, WO2015 / 095346, WO2012 / 000104, W02012 / 000104, and W02010 / 006282, US patent application publications US2003 / 0077829, US2005 / 0175682, US2008 / 0020058, US2011 / 0117125, US2013 / 0303587, US2018 / 0028664, US2015 / 0376115,US2016 / 0376224, US2016 / 0317458, US2013 / 0303587, US2013 / 0303587, and US20110123453, and US patents US5,885,613, US6,287,591, US6,320,017, and US6,586,559, the contents of all of which are incorporated herein by reference in their entirety.

[0398] In some embodiments, the one or more additional compound can be a therapeutic agent. The therapeutic agent can be selected from any class suitable for the therapeutic objective. In other words, the therapeutic agent can be selected from any class suitable for the therapeutic objective. In other words, the therapeutic agent can be selected according to the treatment objectiveand biological action desired. For example, if the ceDNA within the LNP is useful for treating hemophilia B, the additional compound can be an anti-hemophilia B agent (e.g., a chemotherapeutic agent, or other hemophilia B therapy (including, but not limited to, a small molecule or an antibody). In another example, if the LNP containing the ceDNA is useful for treating an infection, the additional compound can be an antimicrobial agent (e.g., an antibiotic or antiviral compound). In yet another example, if the LNP containing the ceDNA is useful for treating an immune disease or disorder, the additional compound can be a compound that modulates an immune response (e.g., an immunosuppressant, immunostimulatory compound, or compound modulating one or more specific immune pathways). In some embodiments, different cocktails of different lipid nanoparticles containing different compounds, such as a ceDNA encoding a different protein or a different compound, such as a therapeutic may be used in the compositions and methods of the disclosure.

[0399] In some embodiments, the additional compound is an immune modulating agent. For example, the additional compound is an immunosuppressant. Immunosuppressants described herein include protein kinase inhibitors (PKIs), such as tyrosine kinase inhibitors (TKIs), which include but are not limited to small molecule compounds, biologies (such as monoclonal antibodies), and large polypeptide molecules that inhibit the activity of, for example, IFN signaling and production pathways, or any other form of antagonists that can decrease expression of a target protein in the immune response pathway. It is to be understood that the present disclosure contemplates use of any modality of therapeutics that can act as an antagonist of, e.g., the IFN signaling and production pathways that modulate immune responses.

[0400] The immunosuppressants are protein kinase inhibitors belonging to a wide class of compounds that inhibits the activity of protein kinases and can be used in conjunction with any nucleic acid therapeutic that triggers immune responses (innate and / or adaptive) in a host cell or a subject suffering from a genetic disorder. Tyrosine kinases regulate a variety of cellular functions including cell growth (e.g., IFN signaling and production and epidermal growth factor (“EGFR” such as ERBB1, ERBB2 / HER2, ERBB3 / HER3, ERBB4 / HER4)). These are the main signal transducers and activators which act downstream of multiple cytokines, growth factors, and hormones, thereby regulating immune responses. For example, upon binding of a specific ligand to its cognate receptor, conformational changes lead to receptor oligomerization and activation of the receptor-associated JAKs. JAKs auto- and trans-phosphorylate one another and phosphorylate receptor chains, providing the docking sites for STAT molecules. STATs then undergo JAK-mediated phosphorylation, dimerize, and translocate to the nucleus, where they regulate the transcription of target genes involving immune responses (e.g., interferon-a, interferon-b, interferon-g, TNFa, IL2, IL-6, IL-18, etc.).

[0401] In some embodiments, the immunosuppressant is an antagonist of Jakl, Jak2, Jak3, Stat, Tyk2, c-MET, EGFR, c-KIT, BTK, ALK, ABL, SRC, ROS1, Syk, MEK, ATM, NRF2, Flt3, fms / CSFlR, FDGFRs, RON, IGF1R, EPHA2, EPHA3, VEGF or VEGFR. In some embodiment, theimmunosuppressant is an antagonist of tyrosine kinase. In one embodiment, the immunosuppressant is an antagonist of Jakl. In another embodiment, the immunosuppressant is an antagonist of Jak2. In one embodiment, the immunosuppressant is an antagonist of Jak3. In yet another embodiment, the immunosuppressant is an antagonist of Tyk2. In yet another embodiment, the immunosuppressant is an antagonist of EGFR. In one embodiment, the immunosuppressant is an antagonist of ALK. In yet another embodiment, the immunosuppressant is an antagonist of Syk.

[0402] In one embodiment, the immunosuppressant is a small molecule antagonist. In another embodiment, the immunosuppressant is an antibody that binds to a protein kinase target. In another embodiment, the immunosuppressant is an antibody that binds to a tyrosine kinase. In another embodiment, the immunosuppressant is a monoclonal antibody against a protein kinase. In another embodiment, the immunosuppressant is a monoclonal antibody against tyrosine kinase. In another embodiment, the immunosuppressant is a monoclonal antibody against a target selected from the group consisting of Jakl, Jak2, Jak3, Stat, Tyk2, c-MET, EGFR, c-KIT, BTK, ALK, ABL, SRC, ROS1, Syk, MEK, ATM, NRF2, Flt3, fms / CSFIR, FDGFRs, RON, IGF1R, EPHA2, EPHA3, VEGF and VEGFR. In yet another embodiment, the immunosuppressant is a polypeptide that has binding affinity to a protein kinase. In yet another embodiment, the immunosuppressant is a nucleic acid, such as RNAi or an anti-sense oligonucleotide, that attenuates expression of Jakl, Jak2, Jak3, Stat, Tyk2, c- MET, EGFR, c-KIT, BTK, ALK, ABL, SRC, ROS1, Syk, MEK, ATM, NRF2, Flt3, fms / CSFIR, FDGFRs, RON, IGF1R, EPHA2, EPHA3, VEGF or VEGFR.

[0403] In some embodiments, inhibition of a protein kinase, e.g., a tyrosine kinase, can be achieved by using small molecules that bind to the ATP pocket of a given protein kinase, blocking it from catalyzing the phosphorylation of target proteins. Hence, in some embodiments, the immunosuppressant can be a small molecule antagonist of protein kinase. Non-limiting examples of immunosuppressant protein kinase antagonist include imatinib mesylate (GLEEVEC®), Nilotinib (TASIGNA®), sorafenib (NEXAVAR®), sunitinib (SUTNET®), dasatinib (SPRCEL®), acalabrutinib, alectinib, axitinib, baricitinib, afatinib, bosutinib, brigatinib, cabozantinib, cerdulatinib, ceritinib, cobimetinib, crizotinib, dacomitinib, dasatinib, erlotinib, imatinib, fostamatinib, gefitinib, AG- 1478, lapatinib, lorlatinib, TAK-659, ruxolitinib, osimertinib, pazopanib, pegaptanib, ponatinib, regorafenib, saracatinib, tofacitinib, BMS- 986165, vandetinib, vemurafenib, or a pharmaceutically acceptable salt thereof.

[0404] In some embodiments, the immunosuppressant can be a small molecule antagonist of tyrosine kinase and is selected from the group consisting of baricitinib, afatinib, brigatinib, cerdulatinib, ceritinib, cobimetinib, dacomitinib, dasatinib, osimertinib, fostamatinib, saracatinib, TAK-659, ruxolitinib, BMS-986165, tofacitinib, and a pharmaceutically acceptable salt thereof.

[0405] In some embodiments, said TKI is selected from the group consisting of sunitinib, imatinib, sorafenib, dasatinib, entoplestinib, fostamatinib, TAK-659, ruxolitinib, baricitinib, BMS-986165, tofacitinib, and a pharmaceutically acceptable salt thereof.

[0406] In some embodiments, the TKI is selected from the group consisting of fostamatinib, ruxolitinib, BMS-986165, and a pharmaceutically acceptable salt thereof.

[0407] In one embodiment, the TKI is ruxolitinib or ruxolitinib phosphate.

[0408] In some embodiments, the TKI may selectively inhibit one or multiple kinases; or target multiple kinases in the same pathway. For example, ruxolitinib and baricitinib can inhibit Jakl and Jak2. Lorlatinib can inhibit ROS1 and ALK. Dasatinib can inhibit Alb, Src and c-Kit. Brigatinib, genfinitinib, erlotinib, AG-1478 and lapatinib can inhibit EGFR. Crizitinib can inhibit both ALK and c-Met. Fostamatinib and cerdulitinib can selectively inhibit Syk. Saracatinib can inhibit Src and Abl.In some embodiments, the TKI is an inhibitor of Jakl. In some embodiments, the TKI is an inhibitor of Jak2. In some embodiments, the TKI is an inhibitor of Jakl and Jak2. In some embodiments, the TKI is an inhibitor of EGFR. In some embodiments, the TKI is an inhibitor of ALK. In some embodiments, the TKI is an inhibitor of Syk.

[0409] Protein kinase activity in immune response pathways may also be inhibited by biologic drugs, such as a monoclonal antibody against a protein kinase. These therapeutics may exert efficacy by preventing receptor protein kinases from activating and are capable of binding cell surface antigens with high specificity. Several monoclonal antibodies target receptor protein kinases that play a role in inhibiting protein kinases involving in DNA sensing immune response signaling pathways. Trastuzumab and bevacizumab are nonlimiting examples of such monoclonal antibodies.

[0410] In some embodiments, the biologic agent that functions to suppress unwanted immune response to a TNA is a monoclonal antibody selected from the group consisting of ado-trastuzumab emtansine, cetuximab, CetuGEX™, cixutumumab, dalotuzumab, duligotumab, ertumaxomab, futuximab, ganitumab, icrucumab, margetuximab, narnatumab, necitumumab, nimotuzumab (h-R3), olaratumab, onartuzumab, panitumumab, pertuzumab, ranibizumab, ramucirumab, seribantumab, tanibirumab, teprotumumab, trasGEX™, trastuzumab, and zatuximab. In one embodiment, the monoclonal antibody is trastuzumab. In another embodiment, the monoclonal antibody is cetuximab.

[0411] In some embodiments, the protein kinase inhibitor is a peptide. The peptide can be polypeptide having a specific affinity binding to target proteins such as Jakl, Jak2, Jak3, ST AT, Tyk2, c-MET, EGFR, c-KIT, BTK, ALK, ABL, SRC, ROS1, Syk, MEK, ATM, NRF2, Flt3, fms / CSFIR, FDGFRs, RON, IGFlr, EPHA2, EPHA3, VEGF or VEGFR. Non-limiting examples of a polypeptide immunosuppressant include aflibercept (VEGF). Binding targets for the peptide can be in a signaling pathway involved in, e.g., IFN response and production pathways.

[0412] In some embodiments, the immunosuppressants of the present disclosure effectively reduce in vitro and in vivo pro-inflammatory cytokine and chemokine levels when the immunosuppressants are present in combination with the nucleic acid therapeutics. The pro-inflammatory cytokine can be selected from any or a combination of interferon-a (IFN-a), interferon-g (IFN-g), tumor necrosis factor-a (TNF-a), interleukin- 1b (IL-Ib), interleukin-6 (IL-6), interleukin-8 (IL-8), interleukin- 10 (IL-10), interleukin- 12 (IL-12), interleukin- 18 (IL-18), vascular endothelial growth factor (VEGF), leukemia inhibitory factor (LIF), matrixmetalloproteinase 2 (MMP2), monocyte chemoattractant protein-1 (MCP-1), RANTES (CCL5), IP-10 (CXCL10), macrophage inflammatory protein-la (MIP-la; CCL3) and / or macrophage inflammatory protein-ΐb (MIR-1b; CCL4).

[0413] In some embodiments, the additional compound is immune stimulatory agent. Also provided herein is a pharmaceutical composition comprising the lipid nanoparticle-encapsulated insect-cell produced, or a synthetically produced ceDNA vector for expression of FIX protein as described herein and a pharmaceutically acceptable carrier or excipient.

[0414] In some aspects, the disclosure provides for a lipid nanoparticle formulation further comprising one or more pharmaceutical excipients. In some embodiments, the lipid nanoparticle formulation further comprises sucrose, tris, trehalose and / or glycine.

[0415] The ceDNA vector can be complexed with the lipid portion of the particle or encapsulated in the lipid position of the lipid nanoparticle. In some embodiments, the ceDNA can be fully encapsulated in the lipid position of the lipid nanoparticle, thereby protecting it from degradation by a nuclease, e.g., in an aqueous solution. In some embodiments, the ceDNA in the lipid nanoparticle is not substantially degraded after exposure of the lipid nanoparticle to a nuclease at 37°C. for at least about 20, 30, 45, or 60 minutes. In some embodiments, the ceDNA in the lipid nanoparticle is not substantially degraded after incubation of the particle in serum at 37°C. for at least about 30, 45, or 60 minutes or at least about 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, or 36 hours.

[0416] In certain embodiments, the lipid nanoparticles are substantially non-toxic to a subject, e.g., to a mammal such as a human. In some aspects, the lipid nanoparticle formulation is a lyophilized powder.

[0417] In some embodiments, lipid nanoparticles are solid core particles that possess at least one lipid bilayer. In other embodiments, the lipid nanoparticles have a non-bilayer structure, i.e., a non- lamehar (i.e., non-bilayer) morphology. Without limitations, the non-bilayer morphology can include, for example, three dimensional tubes, rods, cubic symmetries, etc. For example, the morphology of the lipid nanoparticles (lamellar vs. non-lamehar) can readily be assessed and characterized using, e.g., Cryo-TEM analysis as described in US2010 / 0130588, the content of which is incorporated herein by reference in its entirety.

[0418] In some further embodiments, the lipid nanoparticles having a non-lamehar morphology are electron dense. In some aspects, the disclosure provides for a lipid nanoparticle that is either unilamellar or multilamehar in structure. In some aspects, the disclosure provides for a lipid nanoparticle formulation that comprises multi-vesicular particles and / or foam-based particles.

[0419] By controlling the composition and concentration of the lipid components, one can control the rate at which the lipid conjugate exchanges out of the lipid particle and, in turn, the rate at which the lipid nanoparticle becomes fusogenic. In addition, other variables including, e.g., pH, temperature, or ionic strength, can be used to vary and / or control the rate at which the lipid nanoparticle becomes fusogenic. Other methods which can be used to control the rate at which the lipid nanoparticle becomes fusogenic will be apparent to those of ordinary skill in the art based on this disclosure. It will also be apparent that by controlling the composition and concentration of the lipid conjugate, one can control the lipid particle size.

[0420] The pKa of formulated cationic lipids can be correlated with the effectiveness of the LNPs for delivery of nucleic acids (see Jayaraman et al, Angewandte Chemie, International Edition (2012), 51(34), 8529-8533; Semple et al, Nature Biotechnology 28, 172-176 (2010), both of which are incorporated by reference in their entirety). The p...

Claims

CLAIMSI. A capsid-free closed-ended DNA (ceDNA) vector comprising: at least one nucleic acid sequence between flanking inverted terminal repeats (ITRs), wherein the at least one nucleic acid sequence encodes at least one FIX protein.

2. The ceDNA vector of claim 1, wherein the least one nucleic acid sequence that encodes at least one FIX protein is selected from any of the sequences set forth in Table 1 or any open reading frame (ORF) sequence included in any ceDNA sequence listed in Table 12.

3. The ceDNA vector of claims 1 or 2, wherein the ceDNA vector comprises a promoter sequence selected from any of those in Table 7 operatively linked to the least one nucleic acid sequence that encodes at least one FIX protein.

4. The ceDNA vector of any of claims 1 to 3, wherein the ceDNA vector comprises an enhancer sequence selected from any of those in Table 8.

5. The ceDNA vector of any of claims 1 to 4, wherein the ceDNA vector comprises a 5’ UTR and / or intron sequence selected from any of those in Table 9 A.

6. The ceDNA vector of any of claims 1 to 5, wherein the ceDNA vector comprises a 3’ UTR sequence selected from any of those in Table 9B.

7. The ceDNA vector of any of claims 1 to 6, wherein the ceDNA vector comprises at least one poly A sequence selected from any of those in Table 10.

8. The ceDNA vector of any one of claims 1-7, wherein the ceDNA vector comprises at least one promoter sequence operably linked to at least one nucleic acid sequence.

9. The ceDNA vector of any one of claims 1-8, wherein the at least one nucleic acid sequence is cDNA.

10. The ceDNA vector of any one of claims 1-9, wherein at least one ITR comprises a functional terminal resolution site and a Rep binding site.II. The ceDNA vector of any one of claims 1-10, wherein one or both of the ITRs are from a virus selected from a Parvovirus, a Dependovirus , and an adeno-associated virus (AAV).

12. The ceDNA vector of any one of claims 1-11, wherein the flanking ITRs are symmetric or asymmetric with respect to one another.

13. The ceDNA vector of claim 12, wherein the flanking ITRs are symmetrical or substantially symmetrical.

14. The ceDNA vector of claim 12, wherein the flanking ITRs are asymmetric.

15. The ceDNA vector of any one of claims 1-14, wherein one or both of the ITRs are wild type, or wherein both of the ITRs are wild- type ITRs.

16. The ceDNA vector of any one of claims 1-15, wherein the flanking ITRs are from different viral serotypes.

17. The ceDNA vector of any one of claims 1-16, wherein the flanking ITRs are selected from any pair of viral serotypes shown in Table 2.

18. The ceDNA vector of any one of claims 1-17, wherein one or both of the ITRs comprises a sequence selected from one or more of the sequences in Table 3.

19. The ceDNA vector of any one of claims 1-18, wherein at least one of the ITRs is altered from a wild-type AAV ITR sequence by a deletion, addition, or substitution that affects the overall three- dimensional conformation of the ITR.

20. The ceDNA vector of any one of claims 1-19, wherein one or both of the ITRs are derived from an AAV serotype selected from AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV 10, AAV11, and AAV12.

21. The ceDNA vector of any one of claims 1-20, wherein one or both of the ITRs are synthetic.

22. The ceDNA vector of any one of claims 1-21, wherein one or both of the ITRs are not a wild type ITR, or wherein both of the ITRs are not wild-type ITRs.

23. The ceDNA vector of any one of claims 1-22, wherein one or both of the ITRs are modified by a deletion, insertion, and / or substitution in at least one of the ITR regions selected from A, A’, B,B’, C, C’, D, and D’.

24. The ceDNA vector of claim 23, wherein the deletion, insertion, and / or substitution results in the deletion of all or part of a stem-loop structure normally formed by the A, A’, B, B’, C, or C’ regions.

25. The ceDNA vector of any one of claims 1-24, wherein one or both of the ITRs are modified by a deletion, insertion, and / or substitution that results in the deletion of all or part of a stem-loop structure normally formed by the B and B’ regions.

26. The ceDNA vector of any one of claims 1-24, wherein one or both of the ITRs are modified by a deletion, insertion, and / or substitution that results in the deletion of all or part of a stem-loop structure normally formed by the C and C’ regions.

27. The ceDNA vector of any one of claims 1-24, wherein one or both of the ITRs are modified by a deletion, insertion, and / or substitution that results in the deletion of part of a stem-loop structure normally formed by the B and B ’ regions and / or part of a stem-loop structure normally formed by the C and C’ regions.

28. The ceDNA vector of any one of claims 1-27, wherein one or both of the ITRs comprise a single stem-loop structure in the region that normally comprises a first stem-loop structure formed by the B and B’ regions and a second stem-loop structure formed by the C and C’ regions.

29. The ceDNA vector of any one of claims 1-28, wherein one or both of the ITRs comprise a single stem and two loops in the region that normally comprises a first stem-loop structure formed by the B and B’ regions and a second stem-loop structure formed by the C and C’ regions.

30. The ceDNA vector of any one of claims 1-29, wherein one or both of the ITRs comprise a single stem and a single loop in the region that normally comprises a first stem-loop structure formedby the B and B’ regions and a second stem-loop structure formed by the C and C’ regions.

31. The ceDNA vector of any one of claims 1-30, wherein both ITRs are altered in a manner that results in an overall three-dimensional symmetry when the ITRs are inverted relative to each other.

32. The ceDNA vector of any one of claims 1-31, wherein one or both of the ITRs comprises a nucleic acid sequence selected from the sequences set forth in Tables 3, 5A, 5B, and 6.

33. The ceDNA vector of any one of claims 1-32, wherein at least one nucleic acid sequence is under the control of at least one regulatory switch.

34. The ceDNA vector of claim 33, wherein the at least one regulatory switch is selected from the group consisting of: a binary regulatory switch, a small molecule regulatory switch, a passcode regulatory switch, a nucleic acid-based regulatory switch, a post-transcriptional regulatory switch, a radiation-controlled or ultrasound controlled regulatory switch, a hypoxia-mediated regulatory switch, an inflammatory response regulatory switch, a shear-activated regulatory switch, and a kill switch.

35. A capsid-free close-ended DNA (ceDNA) vector comprising a nucleic acid sequence selected from Table 12.

36. A capsid-free close-ended DNA (ceDNA) vector comprising a nucleic acid sequence at least 85% identical to SEQ ID NO: 404, SEQ ID NO: 405 or SEQ ID NO: 406.

37. A capsid-free close-ended DNA (ceDNA) vector consisting of a nucleic acid sequence selected from the group consisting of SEQ ID NO: 404, SEQ ID NO: 405 and SEQ ID NO: 406.

38. A method of expressing an FIX protein in a cell comprising contacting the cell with the ceDNA vector of any one of claims 1-37.

39. The method of claim 38, wherein the cell is a hepatocyte.

40. The method of claim 38 or 39, wherein the cell in in vitro or in vivo.

41. The method of any one of claims 38-40, wherein the at least one nucleic acid sequence is codon optimized for expression in the eukaryotic cell.

42. The method of any one of claims 38-41, wherein the at least one nucleic acid sequence that is codon optimized is selected from any one of the sequences set forth in in Table 1 or any open reading frame (ORF) sequence included in any ceDNA sequence listed in Table 12.

43. A method of treating a subject with hemophilia B, comprising administering to the subject a ceDNA vector of any one of claims 1-37, wherein at least one nucleic acid sequence encodes at least one FIX protein.

44. The method of claim 43, wherein the least one nucleic acid sequence that encodes the at least one FIX protein is selected from any one of the sequences set forth in Table 1.

45. The method of claim 43 or 44, wherein the ceDNA vector is administered to a hepatocyte.

46. The method of any of claims 44 to 45, wherein the ceDNA vector expresses the FIX protein in a hepatocyte.

47. The method of any of claims 44-46, wherein the ceDNA vector is administered by intravenous or intramuscular injection.

48. The method of any one of claims 44-47, further comprising administering to the subject an immune modulating agent.

49. The method of claim 48, wherein the immune modulating agent is an immunosuppressant.

50. The method of claim 49, wherein the immunosuppressant is a tyrosine kinase inhibitor (TKI).

51. The method of claim 50, wherein the TKI is administered to the subject at a dosage of about0.5 mg / kg to about 700 mg / kg.

52. A pharmaceutical composition comprising the ceDNA vector of any one of claims 1-37.

53. The pharmaceutical composition of claim 52, further comprising an additional compound.

54. The pharmaceutical composition of claim 52, wherein the additional compound is an immune modulating agent.

55. The pharmaceutical composition of claim 54, wherein the immune modulating agent is an immunosuppressant.

56. The pharmaceutical composition of claim 55, wherein the immunosuppressant is a tyrosine kinase inhibitor (TKI).

57. The pharmaceutical composition of claim 56, wherein the composition further comprises an excipient or carrier.

58. A cell containing a ceDNA vector of any of claims 1-37.

59. The cell of claim 58, wherein the cell is a hepatocyte.

60. A composition comprising a ceDNA vector of any of claims 1-37 and a lipid.

61. The composition of claim 60, wherein the lipid is a lipid nanoparticle (LNP).

62. A kit comprising the ceDNA vector of any one of claims 1 -37 or the composition of any one of claims 52-57, or the cell of claim 58.