# Patent

## Title
Tissue preferential codon modified expression cassettes, vectors containing same, and uses thereof

## Abstract

Described herein are synonymously altered gene sequences which express protein in differing levels within secretory as compared to non-secretory target tissue. An expression cassette comprising an open reading frame (ORF) for a protein under the control of regulatory sequences which direct expression of the product in cell, which ORF has been modified to preferentially increase expression levels in a selected tissue, wherein the modified ORF is characterized by a triplet frequency of any one of Tables 3-12, 16 or 17.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a 371 of PCT/US2014/035880, filed Apr. 29, 2014, which claims the benefit of the priority of U.S. Provisional Patent Application No. 61/817,110, filed Apr. 29, 2013, now expired. These priority applications are hereby incorporated by reference herein.


STATEMENT OF GOVERNMENT INTEREST
This invention was made with government support under grant No. W911NF-13-2-0036 awarded by Defense Advanced Research Projects Agency. The government has certain rights in the invention.


BACKGROUND OF THE INVENTION
Various therapies in gene therapy rely upon the expression of recombinant genes in heterologous systems. A variety of viral vectors have been described for delivery of immunogenic and therapeutic products to a host. One vector system which has been described in the literature as very attractive for long-term expression of a transgene product is a recombinant adeno-associated virus, due to its relatively low immunogenicity and the fact that it is not associated with any clinical sequelae in humans. Adeno-associated virus (AAV) is a small, non-enveloped human parvovirus that packages a linear strand of single stranded DNA genome that is 4.7 kb. The capsid of an AAV contains 60 copies (in total) of three viral proteins (VPs), VP1, VP2, and VP3, in a predicted ratio of 1:1:10-20, arranged with T=1 icosahedral symmetry [H-J Nam, et al., J Virol., 81(22): 12260-12271 (November 2007)]. The three VPs are translated from the same mRNA, with VP1 containing a unique N-terminal domain in addition to the entire VP2 sequence at its C-terminal region [Nam et al., cited above]. VP2 contains an extra N-terminal sequence in addition to VP3 at its C terminus.
Codon usage bias has been reported for numerous organisms, from viruses to eukaryotes. Since the genetic code is degenerate (i.e., each amino acid can be coded by on average three different codons), the DNA sequence can be modified by synonymous nucleotide substitutions without altering the amino acid sequence of the encoded protein. Such synonymous codon optimization has been performed for the purpose of optimizing expression in a desired host, as described in the scientific literature and in patent documents. See, U.S. Pat. Nos. 5,786,464 and 6,114,148. Much of the early work in this called optimization, focused on altering the rare codons in the target gene so that they more closely reflect the codon usage of the host without modifying the amino acid sequence of the encoded protein. Since the early published work in this area, a variety of different algorithms have been described for modifying coding sequences for expression in different bacterial and eukaryotic host cell species.
In 2004, Plotkin, et al, Proc Natl Acad Sci. USA, 1010:12588-12591 (2004) reported significant differences in synonymous codon usage between genes specifically expressed in different tissues. However, more recent work by Sémon et al, Mol Biol Evol, 23(3):523-529 (2006) re-evaluated that work and concluded that variability of synonymous codon usage between tissues is much smaller than variability within tissues. Sémon et al further report that the synonymous codon usage variability reported by Plotkin et al was due only to GC-content differences, which affects introns and intergenic regions as well as synonymous codon positions.
For a variety of reasons, including cost, efficiency, and safety, there remains a need in the art for vectors which expression higher levels of gene products in a target cell.
SUMMARY OF THE INVENTION
Expression cassettes and vectors containing a gene which is designed to enhance expression in a selected type of tissue are provided herein. In one aspect, the present invention provides a gene sequence which is designed to preferentially express in a non-secretory tissue (e.g., muscle). In another aspect, the present invention provides a gene which has codons designed to preferentially express in a secretory tissue (e.g., muscle, respiratory epithelium or liver). And in another aspect, codon frequency tables are described which can be used to design a gene sequence for other, unrelated gene products, for example FIX, LDLR, unrelated antibodies, or any other therapeutic transgenes. to optimize tissue specific expression.
In a further aspect, the invention provides an AAV comprising a modified gene which has been designed to express in higher levels in muscle. In one example, the AAV has an AAV8 capsid. In another example, the modified gene is a modified antibody gene.
In still another aspect, the invention provides an AAV comprising a modified gene which has been codon optimized to express in higher levels in respiratory epithelium. In one example, the AAV has an AAV8 capsid.
In another aspect, the invention provides an expression cassette comprising an open reading frame (ORF) under the control of regulatory sequences which direct expression of the product in a muscle cell, which ORF has been modified to preferentially increase expression levels in muscle, wherein the modified ORF have\\s a sequence selected from the group consisting of ORF1 (SEQ ID NO: 9), ORF26 (SEQ ID NO: 6), ORF 28 (SEQ ID NO: 5), ORF 30 (SEQ ID NO: 4), ORF35 (SEQ ID NO: 3), ORF39 (SEQ ID NO: 2), ORF40 (SEQ ID NO: 1), ORF42 (SEQ ID NO: 30), IA (SEQ ID NO: 10), 201 (SEQ ID NO: 31) and IAM (SEQ ID NO: 11). In one example, the modified ORF is selected from ORF35 and ORF39. In another example, the modified ORF is ORF40. In a further example, the modified ORF is selected from ORF26 and ORF30. In another example, the modified ORF is selected from ORF26, ORF35 and ORFIAU. In one embodiment, the expression cassette comprises a tissue preferential promoter. When designed for packaging into a recombinant AAV, the expression cassette may comprise AAV inverted terminal repeats (ITRs) flanking (i.e., both 3′ and 5/upstream and downstream) of the coding sequence. Optionally, the ITRs are from a different source AAV than the AAV which provides the capsid. In another aspect, the invention provides an expression cassette comprising an open reading frame under the control of regulatory sequences which direct expression of the product in liver cells, where the ORF has been modified to preferentially increase expression levels in liver. Expression cassettes for directing expression in respiratory epithelium or other tissue are described.
In a further aspect, the invention provides a vector comprising the expression cassette described herein and other genetic elements. In one embodiment, the vector is a recombinant adeno-associated virus (AAV) having an AAV capsid in which the expression cassette is packaged.
In still a further aspect, the invention provides a recombinant AAV comprising an AAV8 capsid and an expression cassette for an anti-HIV antibody, wherein the expression cassette is adapted for expression in a selected target tissue, said expression cassette comprising a modified ORF having a sequence selected from the group consisting of ORF1 (SEQ ID NO: 9), ORF26 (SEQ ID NO: 6), ORF 28 (SEQ ID NO: 5), ORF 30 (SEQ ID NO: 4), ORF35 (SEQ ID NO: 3), ORF39 (SEQ ID NO: 2), ORF40 (SEQ ID NO: 1), ORF42 (SEQ ID NO: 30), IA (SEQ ID NO: 10), 201 (SEQ ID NO: 31) and IAM (SEQ ID NO: 11).
In another aspect, the invention provides a pharmaceutical composition comprising one or more vectors, each containing one or more expression cassettes. Each expression cassette comprises a modified ORF. In one embodiment, the ORF is selected from ORF26 (SEQ ID NO: 6), ORF 28 (SEQ ID NO: 5), ORF 30 (SEQ ID NO: 4), ORF35 (SEQ ID NO: 3), ORF39 (SEQ ID NO: 2), ORF40 (SEQ ID NO: 1), ORF42 (SEQ ID NO: 30), IA (SEQ ID NO: 10), IAM (SEQ ID NO: 11), and 201 (SEQ ID NO: 31).
Still other aspects and advantages will be apparent from the detailed description of the invention.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1A-1J is an alignment of the sequences of genes all encoding the same anti-HIV antibody protein construct. The gene constructs use different synonymous codons for the same amino acids and are aligned with the parental (base) gene sequences as a frame of reference.
FIG. 2 is a bar chart illustrating AAV-mediated expression of gene constructs modified according to 12 different schemas as compared to a base vector containing the original parental sequence. The codon frequencies used for those modifications are shown in the Tables 1-12, and the parent codon frequency is shown in Table 13. Table 14 shows the codon frequencies which are used in most mammalian codon optimization protocols. Expression of the gene under the control of human cytomegalovirus promoter (CMV (first bar)) or a CMV promoter with a commercially available enhancer (Promega intron, PI) (third bar) were assessed in HEK 293 cells at 72 hours post-infection. These were compared to expression observed with the CMV-PI construct in RAG knock-out mice injected intramuscularly as described in the Example (middle bar).
FIG. 3 is a line graph illustrating AAV-mediated expression of 12 codon biased constructs.
FIG. 4 is a bar chart of the data illustrated in FIG. 2 presented in a different format. For muscle expression, n=3 mice; for bronchial lavage n=2 mice; for transfections, n=2 wells, in addition two independent transfections were performed on different days with similar outcome. Each “n” was assayed by ELISA in duplicate (serum for muscle expression and transfections at 4 different dilutions and bronchial lavage at 2 different dilutions) using protein A capture, and detected using biotinylated anti-human IgG1 antibodies as primary, and streptavidin conjugated HRP as secondary. Affinity purified MAB was used as a standard to make 8 point calibration curve. Constructs were packaged into AAV8 vector using triple transfection production method in HEK293 cells and purified by tangential flow filtration followed by gradient centrifugation. Viral titer was determined by qPCR. 2×1010GC (genome copies)/mouse were administered intramuscularly in 30 μl injection into RAG KO mice. For bronchial lavage 8×1010 GC/mouse were administered by intranasal instillation in 50 μl into C57B16 mice. For IM injections, blood samples were collected weekly for 2 months via orbital bleeding, and serum was assayed by ELISA. For bronchial lavage, mice were sacrificed on day 7 after vector administration, and 1 ml of PBS was used to lavage the airways. Concentrations that are in the table are not recalculated for the mucosal surfaces, but rather are straight concentrations in the lavage sample. Transfections were done on 6 well plates using lipofectamine, using standard conditions with the recommended amount of the DNA as manufacturer suggests.
FIG. 5A-5AAA provides the sequences and features of the plasmid constructs used in Example 1 below.
FIG. 6 is a graph showing the expression of the 201 construct in muscle (bottom line) and liver (top line) of mice versus time post transduction. 5 mice per group were injected at the indicated dosages (1×1010 GC/per mouse or 1×1011 GC/mouse). Concentrations were determined by ELISA. Capture accomplished by binding to SIV mac251 gp120; detection by Fc chain antibody (IgG1) conjugated with biotin, followed by HRP-streptavidin.
FIG. 7 is a graph showing the expression of the 10A construct in muscle (bottom line) and liver (top line) of mice versus time post transduction. 5 mice per group were injected at the dosage of 1×1011GC/per mouse. CMV promoter was used for IM injections; TBG promoter was used for IV injections.
FIG. 8 is a graph demonstrating the effect of variable codon usage on expression of 3bnc117 in liver. The 3bnc117 antibody coding sequence was optimized using the codon frequency of human (Table 2)(top line) or 201 (Table 16)(bottom line). Expression is shown as μg/mL serum. The TBG promoter construct was used at a dosage of 1×1011 GC/per mouse.
FIG. 9A provides the nucleic acid sequences of the 3bcn117 antibody following modification according to the 201 frequency table (Table 16) [SEQ ID NO: 33].
FIG. 9B provides the nucleic acid sequences of the 3bcn117 antibody following modification according to the human frequency table (Table 2) [SEQ ID NO: 34].
FIG. 10A provides the nucleic acid sequences of the 201 construct [SEQ ID NO: 31].
FIG. 10B provides the nucleic acid sequences of the 10A construct [SEQ ID NO: 32].



DETAILED DESCRIPTION OF THE INVENTION
The present invention provides expression cassettes and vectors containing genes which are designed to enhance expression in a desired type of tissue. The present invention provides nucleic acid molecules and vectors carrying genes with codons which are designed for expression in various tissues (e.g., muscle, liver, respiratory epithelium, etc).
“Coding sequence” refers to a DNA sequence that encodes a specific amino acid sequence. An open reading frame (ORF) is a continuous sequence of DNA that contains a start codon, a subsequent region which usually has a length which is a multiple of 3 nucleotides, and a stop codon in the same reading frame.
Since the genetic code is degenerate (i.e., each amino acid can be coded by different codons), the DNA sequence can be modified by nucleotide substitutions without altering the amino acid sequence of the encoded protein. Such changes are referred to herein as synonymous codon modifications. Base combinations which encode some of the standard amino acids are provided below.










Codon Table 1











DNA
mRNA
tRNA Anti-codon





alanine (Ala, A)
CGA
GCU
CGA



CGG
GCC
CGG



CGT
GCA
CGU



CGC
GCG
CGC


 


arginine (Arg, R)
GCA
CGU
GCA



GCG
CGC
GCG



GCT
CGA
GCU



GCC
CGG
GCC



TCT
AGA
UCU



TCC
AGG
UCC


 


asparagine (Asn, N)
TTA
AAU
UUA



TTG
AAC
UUG


 


aspartate (Asp, D)
CTA
GAU
CUA



CTG
GAC
CUG


 


cysteine (Cys, C)
ACA
UGU
ACA



ACG
UGC
ACG


 


glutamate (Glu, E)
CTT
GAA
CUU



CTC
GAG
CUC


 


glutamine (Gln, Q)
GTT
CAA
GUU



GTC
CAG
GUC


 


glycine
CCA
GGU
CCA


(Gly, G)
CCG
GGC
CCG



CCT
GGA
CCU



CCC
GGG
CCC


 


histidine
GTA
CAU
GUA


(His, H)
GTG
CAC
GUG


 


isoleucine
TAA
AUU
UAA


(Ile, I)
TAG
AUC
UAG



TAT
AUA
UAU


 


leucine
AAT
UUA
AAU


(Leu, L)
AAC
UUG
AAC



GAA
CUU
GAA



GAG
CUC
GAG



GAT
CUA
GAU



GAC
CUG
GAC


 


lysine
TTT
AAA
UUU


(Lys, K)
TTC
AAG
UUC


 


methionine
TAC
AUG
UAC


(Met, M)





 


phenylalanine
AAA
UUU
AAA


(Phe, F)
AAG
UUC
AAG


 


proline
GGA
CCU
GGA


(Pro, P)
GGG
CCC
GGG



GGT
CCA
GGU



GGC
CCG
GGC


 


serine
AGA
UCU
AGA


(Ser, S)
AGG
UCC
AGG



AGT
UCA
AGU



AGC
UCG
 AGC,



TCA
AGU
UCA



TCG
AGC
UCG


 


stop
ATG
UAA
AUG



ATT
UAG
AUU



ACT
UGA
ACU


 


threonine
TGA
ACU
UGA


(Thr, T)
TGG
ACC
UGG



TGT
ACA
UGU



TGC
ACG
UGC


 


tryptophan
ACC
UGG
ACC


(Trp, W)





 


tyrosine
ATA
UAU
AUA


(Tyr, Y)
ATG
UAC
AUG


 


valine
CAA
GUU
CAA


(Val, V)
CAG
GUC
CAG



CAT
GUA
CAU



CAC
GUG
CAC









The term “codon usage bias” refers to differences in the frequency of occurrence of synonymous codons in coding DNA. A variety of statistical methods have been described to analyze codon frequency in the literature. Additionally, there are many computer programs available to implement these statistical analyses enumerated above, including CodonW, GCUA, INCA, etc. Methods of codon optimization for expression in a specific species have been described. For example, Table 2 provides a conventional codon frequency for Homo sapiens (human) as reported by the Codon Usage Database: http://www.kazusa.or.jp/codon/. These codon frequency are reported as frequency of an mRNA triplet (codon) per thousand codons. Given a table of codon frequencies presented based on the mRNA sequence, the corresponding cDNA or tRNA triplets may be readily determined by one of skill in the art, e.g., using Table 1 above.








TABLE 2





Sequence
Codon (frequency: per thousand)























HUMAN
UUU
17.6
UCU
15.2
UAU
12.2
UGU
10.6



UUC
20.3
UCC
17.7
UAC
15.3
UGC
12.6



UUA
7.7
UCA
12.2
UAA
1
UGA
1.6



UUG
12.9
UCG
4.4
UAG
0.8
UGG
13.2


 



CUU
13.2
CCU
17.5
CAU
10.9
CGU
4.5



CUC
19.6
CCC
19.8
CAC
15.1
CGC
10.4



CUA
7.2
CCA
16.9
CAA
12.3
CGA
6.2



CUG
39.6
CCG
6.
CAG
34.2
CGG
11.4


 



AUU
16
ACU
13.1
AAU
17
AGU
12.1



AUC
20.8
ACC
18.9
AAC
19.1
AGC
19.5



AUA
7.5
ACA
15.1
AAA
24.4
AGA
12.2



AUG
22
ACG
6.1
AAG
31.9
AGG
12


 



GUU
11
GCU
18.4
GAU
21.8
GGU
10.8



GUC
14.5
GCC
27.7
GAC
25.1
GGC
22.2



GUA
7.1
GCA
15.8
GAA
29
GGA
16



GUG
28.1
GCG
7.4
GAG
39.6
GGG
16.5









As described in the examples below, a study was designed to test whether codons play a role in expression levels which can be achieved in different tissues. The results of this study shows that modified codons do not express at the same levels in all cell or tissue types within a species (e.g., humans).
Using the information provided herein (e.g, in one or more of Table 3, Table 4, Table 5, Table 6, Table 7, Table 8, Table 9, Table 10, Table 11, Table 12, Table 16, and/or Table 17), one may design modified genes having codons which preferentially enhance expression levels in a selected target tissue. In one example, the target tissue is an organ, tissue, or cell type with natural secretory pathways, e.g., liver, lung, epithelial cells (e.g., lung, gastrointestinal, exocrine, etc), sebaceous glands, hormone secretory cells, tears (meibomiah glands), among others. The target tissue may be a secreting or non-secreting organ, tissue or cell type, e.g., skeletal muscle, brain, ocular photoreceptor cells, etc. In another example, the codons are selected for a more specific target, e.g., for skeletal muscle, or for respiratory epithelium, or liver. In one embodiment, the codons are optimized for a selected tissue or organ (e.g., muscle), using the triplet frequency shown in the analytic table for orf35 (Table 6), or a frequency within about 10% thereof. In another embodiment, the codons are optimized for a target (e.g., muscle), using the triplet frequency shown in the analytic table for orf39 (Table 5) or a frequency within 10% thereof. According to the invention, the nucleic acid sequence encoding the product is modified with synonymous codon sequences in a tissue-preferential manner. Suitably, the entire length of the open reading frame (ORF) for the product is modified. However, in some embodiments, only a fragment of the ORF may be altered.
In one embodiment, the codons are generated based on the codon frequency of a selected table, or a frequency within about 10%, within about 5%, within about 3%, or within about 1% of the codon frequency of any one of the Tables provided herein. As used herein, “within about 10% frequency” may encompass the frequency of codons for a selected amino acid (e.g., Ala) within a selected Table, or the codon frequencies within a selected Table may be within 10% for each represented amino acid within a selected Table. For example, computer programs currently exist (e.g., Vector NTIO (Life Technologies)) and/or may be readily designed, which allow importation or use of a codon frequency such as that of any of the tables provided herein and the backtranslation of a nucleic acid sequence (e.g., mRNA or cDNA). The resulting sequence may be synthesized or modified using genetic engineering techniques.
By utilizing a codon frequency selected from one or more of the Tables 3-12, 16, 17, or a frequency within about 10% thereof (or optionally Table 13, 14 or 15), one can apply the codon frequencies to a selected polypeptide sequence, and produce a nucleic acid fragment of a codon-optimized coding region which encodes the polypeptide, but which uses codons more optimal for a given tissue. Suitably, the entire length of the open reading frame (ORF) for the product is modified. However, in some embodiments, only a fragment of the ORF may be altered. By using one of these methods, one can apply the frequencies to any given protein, enzyme, polypeptide, peptide or other amino acid sequence, and produce a nucleic acid fragment of a codon-optimized coding region which encodes the amino acid product.








TABLE 3





Sequence
Codon (frequency: per thousand)























ORF 42
UUU
12.4
UCU
17.9
UAU
8.3
UGU
13.8



UUC
22
UCC
13.8
UAC
31.7
UGC
11



UUA
9.6
UCA
45.5
UAA
0
UGA
0



UUG
11
UCG
6.9
UAG
0
UGG
20.7


 



CUU
11
CCU
17.9
CAU
2.8
CGU
9.6



CUC
12.4
CCC
30.3
CAC
15.2
CGC
8.3



CUA
9.6
CCA
12.4
CAA
11
CGA
4.1



CUG
33.1
CCG
6.9
CAG
42.7
CGG
5.5


 



AUU
6.9
ACU
12.4
AAU
16.5
AGU
15.2



AUC
12.4
ACC
24.8
AAC
28.9
AGC
13.8



AUA
2.8
ACA
20.7
AAA
42.7
AGA
8.3



AUG
11
ACG
12.4
AAG
19.3
AGG
5.5


 



GUU
41.3
GCU
11
GAU
33.1
GGU
5.5



GUC
17.9
GCC
9.6
GAC
13.8
GGC
37.2



GUA
9.6
GCA
28.9
GAA
22
GGA
5.5



GUG
20.7
GCG
4.1
GAG
19.3
GGG
9.6

















TABLE 4





Sequence
Codon (frequency: per thousand)























ORF 40
UUU
24.8
UCU
11
UAU
8.3
UGU
13.8



UUC
9.6
UCC
39.9
UAC
31.7
UGC
11



UUA
8.3
UCA
5.5
UAA
0
UGA
0



UUG
11
UCG
4.1
UAG
0
UGG
20.7


 



CUU
11
CCU
17.9
CAU
12.4
CGU
9.6



CUC
12.4
CCC
30.3
CAC
5.5
CGC
8.3



CUA
11
CCA
12.4
CAA
5.5
CGA
4.1



CUG
33.1
CCG
6.9
CAG
48.2
CGG
5.5


 



AUU
6.9
ACU
12.4
AAU
24.8
AGU
9.6



AUC
5.5
ACC
11
AAC
20.7
AGC
42.7



AUA
9.6
ACA
41.3
AAA
33.1
AGA
8.3



AUG
11
ACG
5.5
AAG
28.9
AGG
5.5


 



GUU
16.5
GCU
12.4
GAU
16.5
GGU
4.1



GUC
16.5
GCC
27.5
GAC
30.3
GGC
13.8



GUA
15.2
GCA
8.3
GAA
8.3
GGA
9.6



GUG
41.3
GCG
5.5
GAG
33.1
GGG
30.3

















TABLE 5 





Sequence
Codon (frequency: per thousand)























ORF 39
UUU
12.4
UCU
17.9
UAU
22
UGU
5.5



UUC
22
UCC
13.8
UAC
17.9
UGC
19.3



UUA
4.1
UCA
45.5
UAA
0
UGA
0



UUG
11
UCG
5.5
UAG
0
UGG
20.7



CUU
9.6
CCU
12.4
CAU
12.4
CGU
2.8



CUC
24.8
CCC
44.1
CAC
5.5
CGC
5.5



CUA
5.5
CCA
6.9
CAA
5.5
CGA
6.9



CUG
31.7
CCG
4.1
CAG
48.2
CGG
8.3



AUU
8.3
ACU
9.6
AAU
16.5
AGU
15.2



AUC
8.3
ACC
22
AAC
28.9
AGC
15.2



AUA
5.5
ACA
17.9
AAA
42.7
AGA
11



AUG
11
ACG
20.7
AAG
19.3
AGG
6.9



GUU
24.8
GCU
28.9
GAU
26.2
GGU
9.6



GUC
22
GCC
13.8
GAC
20.7
GGC
13.8



GUA
11
GCA
8.3
GAA
8.3
GGA
20.7



GUG
31.7
GCG
2.8
GAG
33.1
GGG
13.8

















TABLE 6 





Sequence
Codon (frequency: per thousand)























ORF 35
UUU
19.3
UCU
12.4
UAU
22
UGU
13.8



UUC
15.2
UCC
23.4
UAC
17.9
UGC
11



UUA
5.5
UCA
17.9
UAA
0
UGA
0



UUG
13.8
UCG
20.7
UAG
0
UGG
20.7



CUU
6.9
CCU
12.4
CAU
9.6
CGU
1.4



CUC
13.8
CCC
44.1
CAC
8.3
CGC
4.1



CUA
5.5
CCA
6.9
CAA
27.5
CGA
2.8



CUG
41.3
CCG
4.1
CAG
26.2
CGG
13.8



AUU
13.8
ACU
11
AAU
9.6
AGU
11



AUC
5.5
ACC
46.8
AAC
35.8
AGC
27.5



AUA
2.8
ACA
6.9
AAA
20.7
AGA
5.5



AUG
11
ACG
5.5
AAG
41.3
AGG
13.8



GUU
41.3
GCU
19.3
GAU
11
GGU
8.3



GUC
17.9
GCC
19.3
GAC
35.8
GGC
26.2



GUA
9.6
GCA
11
GAA
28.9
GGA
9.6



GUG
20.7
GCG
4.1
GAG
12.4
GGG
13.8

















TABLE 7 





Sequence
Codon (frequency: per thousand)























ORF 30
UUU
24.8
UCU
16.5
UAU
22
UGU
13.8



UUC
9.6
UCC
26.2
UAC
17.9
UGC
11



UUA
5.5
UCA
17.9
UAA
0
UGA
0



UUG
6.9
UCG
11
UAG
0
UGG
20.7



CUU
31.7
CCU
37.2
CAU
5.5
CGU
2.8



CUC
16.5
CCC
15.2
CAC
12.4
CGC
2.8



CUA
6.9
CCA
12.4
CAA
9.6
CGA
8.3



CUG
19.3
CCG
2.8
CAG
44.1
CGG
5.5



AUU
5.5
ACU
12.4
AAU
16.5
AGU
13.8



AUC
12.4
ACC
11
AAC
28.9
AGC
27.5



AUA
4.1
ACA
41.3
AAA
20.7
AGA
16.5



AUG
11
ACG
5.5
AAG
41.3
AGG
5.5



GUU
15.2
GCU
27.5
GAU
33.1
GGU
4.1



GUC
28.9
GCC
15.2
GAC
13.8
GGC
13.8



GUA
6.9
GCA
8.3
GAA
22
GGA
9.6



GUG
38.6
GCG
2.8
GAG
19.3
GGG
30.3

















TABLE 8 





Sequence
Codon (frequency: per thousand)























ORF 28
UUU
12.4
UCU
27.5
UAU
22
UGU
13.8



UUC
22
UCC
20.7
UAC
17.9
UGC
11



UUA
5.5
UCA
13.8
UAA
0
UGA
0



UUG
6.9
UCG
4.1
UAG
0
UGG
20.7



CUU
31.7
CCU
37.2
CAU
9.6
CGU
2.8



CUC
16.5
CCC
15.2
CAC
8.3
CGC
2.8



CUA
6.9
CCA
12.4
CAA
8.3
CGA
8.3



CUG
19.3
CCG
2.8
CAG
45.5
CGG
5.5



AUU
9.6
ACU
13.8
AAU
24.8
AGU
22



AUC
9.6
ACC
24.8
AAC
20.7
AGC
24.8



AUA
2.8
ACA
20.7
AAA
12.4
AGA
16.5



AUG
11
ACG
11
AAG
49.6
AGG
5.5



GUU
5.5
GCU
11
GAU
16.5
GGU
6.9



GUC
12.4
GCC
22
GAC
30.3
GGC
37.2



GUA
5.5
GCA
12.4
GAA
8.3
GGA
5.5



GUG
66.1
GCG
8.3
GAG
33.1
GGG
8.3

















TABLE 9 





Sequence
Codon (frequency: per thousand)























ORF 26
UUU
19.3
UCU
22
UAU
8.3
UGU
5.5



UUC
15.2
UCC
19.3
UAC
31.7
UGC
19.3



UUA
6.9
UCA
26.2
UAA
0
UGA
0



UUG
8.3
UCG
6.9
UAG
0
UGG
20.7



CUU
17.9
CCU
17.9
CAU
9.6
CGU
2.8



CUC
17.9
CCC
30.3
CAC
8.3
CGC
12.4



CUA
8.3
CCA
12.4
CAA
5.5
CGA
4.1



CUG
27.5
CCG
6.9
CAG
48.2
CGG
8.3



AUU
5.5
ACU
11
AAU
24.8
AGU
17.9



AUC
12.4
ACC
46.8
AAC
20.7
AGC
20.7



AUA
4.1
ACA
6.9
AAA
12.4
AGA
5.5



AUG
11
ACG
5.5
AAG
49.6
AGG
8.3



GUU
5.5
GCU
19.3
GAU
11
GGU
22



GUC
11
GCC
19.3
GAC
35.8
GGC
16.5



GUA
5.5
GCA
11
GAA
22
GGA
12.4



GUG
67.5
GCG
4.1
GAG
19.3
GGG
6.9

















TABLE 10 





Sequence
Codon (frequency: per thousand)























ORF 11
UUU
23.4
UCU
16.5
UAU
27.5
UGU
17.9



UUC
11
UCC
30.3
UAC
12.4
UGC
6.9



UUA
2.8
UCA
11
UAA
0
UGA
0



UUG
16.5
UCG
5.5
UAG
0
UGG
20.7



CUU
4.1
CCU
15.2
CAU
12.4
CGU
1.4



CUC
8.3
CCC
22
CAC
5.5
CGC
6.9



CUA
4.1
CCA
19.3
CAA
17.9
CGA
4.1



CUG
51
CCG
11
CAG
35.8
CGG
11



AUU
9.6
ACU
12.4
AAU
16.5
AGU
15.2



AUC
9.6
ACC
24.8
AAC
28.9
AGC
34.4



AUA
2.8
ACA
20.7
AAA
12.4
AGA
6.9



AUG
11
ACG
12.4
AAG
49.6
AGG
11



GUU
15.2
GCU
28.9
GAU
16.5
GGU
5.5



GUC
16.5
GCC
13.8
GAC
30.3
GGC
37.2



GUA
16.5
GCA
8.3
GAA
22
GGA
5.5



GUG
41.3
GCG
2.8
GAG
19.3
GGG
9.6

















TABLE 11 





Sequence
Codon (frequency: per thousand)























ORF 2
UUU
22
UCU
37.2
UAU
13.8
UGU
8.3



UUC
12.4
UCC
15.2
UAC
26.2
UGC
16.5



UUA
5.5
UCA
11
UAA
0
UGA
0



UUG
5.5
UCG
2.8
UAG
0
UGG
20.7



CUU
31.7
CCU
11
CAU
12.4
CGU
2.8



CUC
16.5
CCC
19.3
CAC
5.5
CGC
17.9



CUA
6.9
CCA
16.5
CAA
9.6
CGA
2.8



CUG
20.7
CCG
20.7
CAG
44.1
CGG
6.9



AUU
6.9
ACU
12.4
AAU
33.1
AGU
30.3



AUC
11
ACC
26.2
AAC
12.4
AGC
16.5



AUA
4.1
ACA
20.7
AAA
20.7
AGA
4.1



AUG
11
ACG
11
AAG
41.3
AGG
6.9



GUU
15.2
GCU
28.9
GAU
16.5
GGU
13.8



GUC
28.9
GCC
13.8
GAC
30.3
GGC
19.3



GUA
6.9
GCA
8.3
GAA
28.9
GGA
13.8



GUG
38.6
GCG
2.8
GAG
12.4
GGG
11

















TABLE 12 





Sequence
Codon (frequency: per thousand)























ORF 1
UUU
6.9
UCU
12.4
UAU
8.3
UGU
5.5



UUC
27.5
UCC
24.8
UAC
31.7
UGC
19.3



UUA
2.8
UCA
16.5
UAA
0
UGA
0



UUG
16.5
UCG
22
UAG
0
UGG
20.7



CUU
2.8
CCU
11
CAU
2.8
CGU
1.4



CUC
8.3
CCC
20.7
CAC
15.2
CGC
4.1



CUA
4.1
CCA
16.5
CAA
5.5
CGA
2.8



CUG
52.3
CCG
19.3
CAG
48.2
CGG
15.2



AUU
5.5
ACU
9.6
AAU
9.6
AGU
11



AUC
12.4
ACC
22
AAC
35.8
AGC
26.2



AUA
4.1
ACA
17.9
AAA
12.4
AGA
4.1



AUG
11
ACG
20.7
AAG
49.6
AGG
13.8



GUU
5.5
GCU
8.3
GAU
11
GGU
4.1



GUC
12.4
GCC
19.3
GAC
35.8
GGC
13.8



GUA
5.5
GCA
11
GAA
8.3
GGA
9.6



GUG
66.1
GCG
15.2
GAG
33.1
GGG
30.3

















TABLE 13 





Sequence
Codon (frequency: per thousand)























IAU
UUU
13.8
UCU
0
UAU
13.8
UGU
0



UUC
20.7
UCC
51
UAC
26.2
UGC
24.8



UUA
0
UCA
0
UAA
0
UGA
0



UUG
0
UCG
0
UAG
0
UGG
20.7



CUU
0
CCU
16.5
CAU
4.1
CGU
0



CUC
0
CCC
26.2
CAC
13.8
CGC
0



CUA
0
CCA
24.8
CAA
11
CGA
12.4



CUG
86.8
CCG
0
CAG
42.7
CGG
12.4



AUU
6.9
ACU
0
AAU
15.2
AGU
0



AUC
15.2
ACC
45.5
AAC
30.3
AGC
62



AUA
0
ACA
24.8
AAA
23.4
AGA
16.5



AUG
11
ACG
0
AAG
38.6
AGG
0



GUU
0
GCU
0
GAU
12.4
GGU
0



GUC
46.8
GCC
27.5
GAC
34.4
GGC
19.3



GUA
0
GCA
26.2
GAA
15.2
GGA
20.7



GUG
42.7
GCG
0
GAG
26.2
GGG
17.9

















TABLE 14 





Sequence
Codon (frequency: per thousand)























IAM
UUU
0
UCU
0
UAU
0
UGU
11



UUC
34.4
UCC
41.3
UAC
39.9
UGC
13.8



UUA
0
UCA
0
UAA
0
UGA
0



UUG
0
UCG
0
UAG
0
UGG
20.7



CUU
0
CCU
17.9
CAU
4.1
CGU
0



CUC
0
CCC
20.7
CAC
13.8
CGC
0



CUA
0
CCA
28.9
CAA
4.1
CGA
1.4



CUG
86.8
CCG
0
CAG
49.6
CGG
39.9



AUU
5.5
ACU
0
AAU
9.6
AGU
0



AUC
16.5
ACC
44.1
AAC
35.8
AGC
71.6



AUA
0
ACA
26.2
AAA
19.3
AGA
0



AUG
11
ACG
0
AAG
42.7
AGG
0



GUU
0
GCU
0
GAU
33.1
GGU
0



GUC
19.3
GCC
52.3
GAC
13.8
GGC
23.4



GUA
0
GCA
1.4
GAA
12.4
GGA
34.4



GUG
70.2
GCG
0
GAG
28.9
GGG
0

















TABLE 15 





Sequence
Codon (frequency: per thousand)























BASE
UUU
11
UCU
19.3
UAU
9.7
UGU
5.5



UUC
24.8
UCC
31.7
UAC
29
UGC
19.3



UUA
2.8
UCA
11
UAA
0
UGA
0



UUG
6.9
UCG
8.3
UAG
0
UGG
22.1



CUU
5.5
CCU
13.8
CAU
5.5
CGU
5.5



CUC
16.6
CCC
26.2
CAC
13.8
CGC
1.4



CUA
5.5
CCA
17.9
CAA
8.3
CGA
8.3



CUG
45.5
CCG
9.7
CAG
44.1
CGG
5.5



AUU
5.5
ACU
9.7
AAU
13.8
AGU
6.9



AUC
17.9
ACC
33.1
AAC
30.3
AGC
34.5



AUA
0
ACA
19.3
AAA
20.7
AGA
13.8



AUG
9.7
ACG
9.7
AAG
41.4
AGG
5.5



GUU
4.1
GCU
5.5
GAU
11
GGU
4.1



GUC
34.5
GCC
24.8
GAC
35.9
GGC
20.7



GUA
4.1
GCA
16.6
GAA
16.6
GGA
17.9



GUG
48.3
GCG
6.9
GAG
24.8
GGG
17.9

















TABLE 16 





Sequence
Codon (frequency: per thousand)























201
UUU
11.8
UCU
23.5
UAU
17.6
UGU
11.8



UUC
17.6
UCC
27.5
UAC
33.3
UGC
15.7



UUA
0
UCA
17.6
UAA
0
UGA
0



UUG
0
UCG
0
UAG
0
UGG
17.6



CUU
0
CCU
21.6
CAU
5.9
CGU
0



CUC
0
CCC
17.6
CAC
7.8
CGC
5.9



CUA
0
CCA
27.5
CAA
2
CGA
7.8



CUG
78.4
CCG
0
CAG
47.1
CGG
9.8



AUU
9.8
ACU
21.6
AAU
13.7
AGU
17.6



AUC
21.6
ACC
31.4
AAC
17.6
AGC
29.4



AUA
0
ACA
25.5
AAA
19.6
AGA
7.8



AUG
9.8
ACG
0
AAG
31.4
AGG
7.8



GUU
0
GCU
9.8
GAU
23.5
GGU
0



GUC
27.5
GCC
15.7
GAC
23.5
GGC
33.3



GUA
0
GCA
9.8
GAA
19.6
GGA
45.1



GUG
54.9
GCG
0
GAG
25.5
GGG
21.6

















TABLE 17 





Sequence
Codon (frequency: per thousand)























10A
UUU
9.8
UCU
29.3
UAU
21.5
UGU
13.7



UUC
11.7
UCC
21.5
UAC
23.4
UGC
11.7



UUA
0
UCA
15.6
UAA
0
UGA
0



UUG
0
UCG
0
UAG
0
UGG
23.4



CUU
0
CCU
21.5
CAU
7.8
CGU
0



CUC
0
CCC
19.5
CAC
7.8
CGC
2



CUA
0
CCA
27.3
CAA
0
CGA
7.8



CUG
78.1
CCG
0
CAG
50.8
CGG
5.9



AUU
11.7
ACU
19.5
AAU
11.7
AGU
23.4



AUC
17.6
ACC
31.2
AAC
17.6
AGC
39.1



AUA
0
ACA
25.4
AAA
27.3
AGA
7.8



AUG
13.7
ACG
0
AAG
33.2
AGG
3.9



GUU
0
GCU
11.7
GAU
19.5
GGU
0



GUC
31.2
GCC
15.6
GAC
21.5
GGC
33.2



GUA
0
GCA
19.5
GAA
19.5
GGA
43



GUG
48.8
GCG
0
GAG
23.4
GGG
19.5









For example, the codon frequency of Table 5 or Table 6, or a codon frequency within 10% thereof, is particularly well suited to enhance expression of a selected gene product in muscle, and more particularly, skeletal muscle. In another example, the codon frequency of Table 9, Table 10, or Table 11, or a codon frequency within 10% thereof, is particularly well suited to enhance expression of a selected gene product in liver. In still another example, the codon frequency of Table 16 is particularly well suited to enhance expression of a selected gene product in respiratory epithelium (e.g., lung). In one embodiment, expression is mediated by an AAV. However, the codon frequency of these tables are useful in other methods and for other delivery vectors.
The methods provided herein are designed as the primary consideration to select the frequently used codon for a given amino acid as the primary consideration. However, as a secondary or tertiary consideration, the methods described herein may further select a codon or modify a selected sequence to exclude undesirable structural elements, e.g., (a) restriction sites, CpG islands, (b) exclusion of a hairpin turn in the initial polynucleotide sequence; (c) exclusion of a repeat element in the initial polynucleotide sequence; (d) exclusion of a ribosome binding site in the initial polynucleotide sequence; (e) exclusion of a polyadenylation signal in the initial polynucleotide sequence; (f) exclusion of a splice site in the initial polynucleotide sequence; (g) exclusion of an open reading frame in each possible 5′ reading frame in the initial polynucleotide sequence; (h) exclusion of a polynucleotide sequence that facilitates RNA degradation in the initial polynucleotide sequence; (i) exclusion of an RNA polymerase termination signal in the initial polynucleotide sequence; (j) exclusion of a transcriptional promoter in the initial polynucleotide sequence; (k) exclusion of an immunostimulatory sequence in the initial polynucleotide sequence; (l) incorporation of an immunostimulatory sequence in the initial polynucleotide sequence; (mi) exclusion of an RNA methylation signal in the initial polynucleotide sequence; (n) exclusion of a selenocysteine incorporation signal in the initial polynucleotide sequence; (o) exclusion of an RNA editing sequence in the initial polynucleotide sequence; (p) exclusion of an RNAi-targeted sequence in the initial polynucleotide sequence; and/or (q) exclusion of an inverted repeat within the first 45 nucleotides encoding said synthetic polypeptide in the initial polynucleotide sequence. See, e.g., US Patent Publication No. 20130196864, which is incorporated by reference herein.
Methods of modifying an existing nucleic acid sequence to provide a synonymous codon for a selected amino acid and/or back-translating a selected amino acid sequence into a desired nucleic acid have been described. For example, web-based or commercially available computer programs, as well as service based companies may be used to back translate the amino acids sequences to nucleic acid coding sequences, including both RNA and/or cDNA. See, e.g., backtranseq by EMBOSS, http://www.ebi.ac.uk/Tools/st/; Gene Infinity (http://www.geneinfinity.org/sms-/sms_backtranslation.html); ExPasy (http://www.expasy.org/tools/). A number of options are available for performing the changes to the codons or for synthesizing the codon-optimized coding regions designed as described herein. Such modifications or synthesis can be performed using standard and routine molecular biological manipulations well known to those of ordinary skill in the art. In one approach, a series of complementary oligonucleotide pairs of 80-90 nucleotides each in length and spanning the length of the desired sequence are synthesized by standard methods. These oligonucleotide pairs are synthesized such that upon annealing, they form double stranded fragments of 80-90 base pairs, containing cohesive ends, e.g., each oligonucleotide in the pair is synthesized to extend 3, 4, 5, 6, 7, 8, 9, 10, or more bases beyond the region that is complementary to the other oligonucleotide in the pair. The single-stranded ends of each pair of oligonucleotides is designed to anneal with the single-stranded end of another pair of oligonucleotides. The oligonucleotide pairs are allowed to anneal, and approximately five to six of these double-stranded fragments are then allowed to anneal together via the cohesive single stranded ends, and then they ligated together and cloned into a standard bacterial cloning vector, for example, a TOPO® vector available from Invitrogen Corporation, Carlsbad, Calif. The construct is then sequenced by standard methods. Several of these constructs consisting of 5 to 6 fragments of 80 to 90 base pair fragments ligated together, i.e., fragments of about 500 base pairs, are prepared, such that the entire desired sequence is represented in a series of plasmid constructs. The inserts of these plasmids are then cut with appropriate restriction enzymes and ligated together to form the final construct. The final construct is then cloned into a standard bacterial cloning vector, and sequenced. Additional methods would be immediately apparent to the skilled artisan. In addition, gene synthesis is readily available commercially.
As described above, the term “about” when used to modify a numerical value means a variation of ±10%, unless otherwise specified.
The terms “identical” or percent “identity,” in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same (i.e., about 70% identity, preferably 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or higher identity) over a specified region (e.g., any one of the modified ORFs provided herein when compared and aligned for maximum correspondence over a comparison window or designated region) as measured using a BLAST or BLAST 2.0 sequence comparison algorithms with default parameters described below, or by manual alignment and visual inspection (see, e.g., NCBI web site or the like). As another example, polynucleotide sequences can be compared using Fasta, a program in GCG Version 6.1. Fasta provides alignments and percent sequence identity of the regions of the best overlap between the query and search sequences. For instance, percent sequence identity between nucleic acid sequences can be determined using Fasta with its default parameters (a word size of 6 and the NOPAM factor for the scoring matrix) as provided in GCG Version 6.1, herein incorporated by reference. Generally, these programs are used at default settings, although one skilled in the art can alter these settings as needed. Alternatively, one of skill in the art can utilize another algorithm or computer program that provides at least the level of identity or alignment as that provided by the referenced algorithms and programs. This definition also refers to, or can be applied to, the compliment of a sequence. The definition also includes sequences that have deletions and/or additions, as well as those that have substitutions. As described below, the preferred algorithms can account for gaps and the like. Preferably, identity exists over a region that is at least about 25, 50, 75, 100, 150, 200 amino acids or nucleotides in length, and oftentimes over a region that is 225, 250, 300, 350, 400, 450, 500 amino acids or nucleotides in length or over the full-length of an amino acid or nucleic acid sequences.
Typically, when an alignment is prepared based upon an amino acid sequence, the alignment contains insertions and deletions which are so identified with respect to a reference AAV sequence and the numbering of the amino acid residues is based upon a reference scale provided for the alignment. However, any given AAV sequence may have fewer amino acid residues than the reference scale. In the present invention, when discussing the parental sequence, the term “the same position” or the “corresponding position” refers to the amino acid located at the same residue number in each of the sequences, with respect to the reference scale for the aligned sequences. However, when taken out of the alignment, each of the proteins may have these amino acids located at different residue numbers. Alignments are performed using any of a variety of publicly or commercially available Multiple Sequence Alignment Programs. Sequence alignment programs are available for amino acid sequences, e.g., the “Clustal X”, “MAP”, “PIMA”, “MSA”, “BLOCKMAKER”, “MEME”, and “Match-Box” programs. Generally, any of these programs are used at default settings, although one of skill in the art can alter these settings as needed. Alternatively, one of skill in the art can utilize another algorithm or computer program which provides at least the level of identity or alignment as that provided by the referenced algorithms and programs. See, e.g., J. D. Thomson et al, Nucl. Acids. Res., “A comprehensive comparison of multiple sequence alignments”, 27(13):2682-2690 (1999).
As used throughout this specification and the claims, the terms “comprise” and “contain” and its variants including, “comprises”, “comprising”, “contains” and “containing”, among other variants, is inclusive of other components, elements, integers, steps and the like. The term “consists of” or “consisting of” are exclusive of other components, elements, integers, steps and the like.
Gene Products
As described herein, a synonymously modified gene designed as described herein is typically engineered into an expression cassette. An expression cassette as described herein contains the modified gene which has codons preferentially modified and selected to express a product in a target tissue, which is operably linked to expression control sequences which direct expression thereof. Such an expression cassette may also include expression control sequences useful for transcription initiation, termination, promoter and enhancer sequences; efficient RNA processing signals such as splicing and polyadenylation (polyA) signals; sequences that stabilize cytoplasmic mRNA; sequences that enhance translation efficiency (i.e., Kozak consensus sequence); sequences that enhance protein stability; and when desired, sequences that enhance secretion of the encoded product. Alternatively, or additionally, such regulatory expression elements may be located outside of the expression cassette, e.g., within another region of a vector into which the expression cassette is engineered.
Provided in FIG. 5 and the sequence listing (SEQ ID Nos: 13-29), herein are the plasmid constructs utilized the Example below. The plasmids contain sequences encoding an anti-HIV antibody (3bcn117 antibody. See, Scheid et al, Sequence and structural convergence of broad and potent HIV antibodies that mimic CD4 binding. Science. 2011 Sep. 16; 333(6049):1633-7. Epub 2011 Jul. 14, which is incorporated herein by reference). Specific fragments of the sequences are identified and are, in one embodiment, of particular interest. These fragments may be used in conjunction with other fragments described herein, or other complementary fragments as known in the art. For example, certain fragments of interest include the constant regions of the heavy and light chains of an antibody such as the anti-SIV or anti-HIV antibody of the examples. These sequences, having been optimized for expression in a particular tissue type (e.g., liver, respiratory epithelial cells (e.g., lung)) may be utilized in conjunction with the variable regions of other antibodies, as described further below. The variable regions may be optimized for expression in the desired tissue using the codon frequency tables described herein. See Tables 3-12, 16, 17. Optionally, Tables 2, 23, 24, 15 may be used in conjunction with the methods and constructs described herein.
Desirable fragments of the plasmids include 5′ and 3′ ITR sequences, promoters, enhancers, TATA box, introns, IRES, F2A linkers, furin sites, forward primers, reverse primers, polyA signals. Other desirable fragments include the following:













Position (nt)











SEQ ID
SED ID
SEQ ID


Region
NO: 14
NO: 15
NO: 18





VH (variable region heavy chain)
1365-1750
1371-1756
1320-1705


CH1 (constant region 1 heavy chain)
1752-2027
1758-2033
1707-1982


HCH23 (constant region 2-3 heavy
2028-2716
2034-2722
1983-2671


chain)


CL (constant region light chain)
3111-3415
3181-3485
3130-3434


3nbc117 light
2798-3095
2854-3165
2803-3114









Corresponding regions of the ORFs described herein or other desirable sequences can be readily determined using standard alignment techniques known in the art and described herein.
Therapeutic Transgenes
A nucleotide sequence encoding any of a number of different therapeutic transgenes may be selected for codon modification to enhance tissue-preferential expression as described herein. Useful therapeutic products encoded by the transgene include hormones and growth and differentiation factors including, without limitation, insulin, glucagon, growth hormone (GH), parathyroid hormone (PTH), growth hormone releasing factor (GRF), follicle stimulating hormone (FSH), luteinizing hormone (LH), human chorionic gonadotropin (hCG), vascular endothelial growth factor (VEGF), angiopoietins, angiostatin, granulocyte colony stimulating factor (GCSF), erythropoietin (EPO), connective tissue growth factor (CTGF), basic fibroblast growth factor (bFGF), acidic fibroblast growth factor (aFGF), epidermal growth factor (EGF), platelet-derived growth factor (PDGF), insulin growth factors I and II (IGF-I and IGF-II), any one of the transforming growth factor α superfamily, including TGFα, activins, inhibins, or any of the bone morphogenic proteins (BMP) BMPs 1-15 as well as TGFb proteins, any one of the heregluin/neuregulin/ARIA/neu differentiation factor (NDF) family of growth factors, nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), neurotrophins NT-3 and NT-4/5, ciliary neurotrophic factor (CNTF), glial cell line derived neurotrophic factor (GDNF), neurturin, agrin, any one of the family of semaphorins/collapsins, netrin-1 and netrin-2, hepatocyte growth factor (HGF), ephrins, noggin, sonic hedgehog and tyrosine hydroxylase.
Other useful transgene products include proteins that regulate the immune system including, without limitation, cytokines and lymphokines such as thrombopoietin (TPO), interleukins (IL) IL-1 through IL-25 (including IL-2, IL-4, IL-12 and IL-18), monocyte chemoattractant protein, leukemia inhibitory factor, granulocyte-macrophage colony stimulating factor, Fas ligand, tumor necrosis factors α and β, interferons α, β, TGFb and γ, stem cell factor, flk-2/flt3 ligand. Gene products produced by the immune system are also useful in the invention. These include, without limitations, immunoglobulins IgG, IgM, IgA, IgD and IgE, chimeric immunoglobulins, humanized antibodies, single chain antibodies, T cell receptors, chimeric T cell receptors, single chain T cell receptors, class I and class II MHC molecules, as well as engineered immunoglobulins and MHC molecules. Useful gene products also include complement regulatory proteins such as complement regulatory proteins, membrane cofactor protein (MCP), decay accelerating factor (DAF), CR1, CF2 and CD59.
Still other useful gene products include any one of the receptors for the hormones, growth factors, cytokines, lymphokines, regulatory proteins and immune system proteins. The invention encompasses receptors for cholesterol regulation and/or lipid modulation, including the low density lipoprotein (LDL) receptor, high density lipoprotein (HDL) receptor, the very low density lipoprotein (VLDL) receptor, and scavenger receptors. The invention also encompasses gene products such as members of the steroid hormone receptor superfamily including glucocorticoid receptors and estrogen receptors, Vitamin D receptors and other nuclear receptors. In addition, useful gene products include transcription factors such as jun, fos, max, mad, serum response factor (SRF), AP-1, AP2, myb, MyoD and myogenin, ETS-box containing proteins, TFE3, E2F, ATF1, ATF2, ATF3, ATF4, ZFS, NFAT, CREB, HNF-4, C/EBP, SP1, CCAAT-box binding proteins, interferon regulation factor (IRF-1), Wilms tumor protein, ETS-binding protein, STAT, GATA-box binding proteins, e.g., GATA-3, and the forkhead family of winged helix proteins.
Other useful gene products include, carbamoyl synthetase I, ornithine transcarbamylase, arginosuccinate synthetase, arginosuccinate lyase, arginase, fumarylacetacetate hydrolase, phenylalanine hydroxylase, alpha-1 antitrypsin, glucose-6-phosphatase, porphobilinogen deaminase, cystathione beta-synthase, branched chain ketoacid decarboxylase, albumin, isovaleryl-coA dehydrogenase, propionyl CoA carboxylase, methyl malonyl CoA mutase, glutaryl CoA dehydrogenase, insulin, beta-glucosidase, pyruvate carboxylate, hepatic phosphorylase, phosphorylase kinase, glycine decarboxylase, H-protein, T-protein, a cystic fibrosis transmembrane regulator (CFTR) sequence, and a dystrophin cDNA sequence. Still other useful gene products include enzymes such as may be useful in enzyme replacement therapy, which is useful in a variety of conditions resulting from deficient activity of enzyme. For example, enzymes that contain mannose-6-phosphate may be utilized in therapies for lysosomal storage diseases (e.g., a suitable gene includes that encoding β-glucuronidase (GUSB)).
Still other useful gene products include those used for treatment of hemophilia, including hemophilia B (including Factor IX) and hemophilia A (including Factor VIII and its variants, such as the light chain and heavy chain of the heterodimer and the B-deleted domain; U.S. Pat. Nos. 6,200,560 and 6,221,349). The present invention is not limited to any specific Factor VIII sequence. Many natural and recombinant forms of Factor VIII have been isolated and generated. Examples of naturally occurring and recombinant forms of Factor VII can be found in the patent and scientific literature including, U.S. Pat. Nos. 5,563,045, 5,451,521, 5,422,260, 5,004,803, 4,757,006, 5,661,008, 5,789,203, 5,681,746, 5,595,886, 5,045,455, 5,668,108, 5,633,150, 5,693,499, 5,587,310, 5,171,844, 5,149,637, 5,112,950, 4,886,876, WO 94/11503, WO 87/07144, WO 92/16557, WO 91/09122, WO 97/03195, WO 96/21035, WO 91/07490, EP 0 672 138, EP 0 270 618, EP 0 182 448, EP 0 162 067, EP 0 786 474, EP 0 533 862, EP 0 506 757, EP 0 874 057, EP 0 795 021, EP 0 670 332, EP 0 500 734, EP 0 232 112, EP 0 160 457, Sanberg et al., XXth Int. Congress of the World Fed. Of Hemophilia (1992), and Lind et al., Eur. J. Biochem., 232:19 (1995).
Also included herein are non-naturally occurring gene sequences include antisense molecules and catalytic nucleic acids, such as ribozymes, which could be used to reduce overexpression of a target. “Knockdown gene therapy” is directed towards a gene product which is associated with a disease or conditions in which the targeted gene is overexpressed, but which is not entirely extinguished by the therapy. Molecules such as microRNA and small interfering RNA (siRNA) may be delivered to accomplish knock out or knock down.
Reduction and/or modulation of expression of a gene is particularly desirable for treatment of hyperproliferative conditions characterized by hyperproliferating cells, as are cancers and psoriasis. Target polypeptides include those polypeptides which are produced exclusively or at higher levels in hyperproliferative cells as compared to normal cells. Target antigens include polypeptides encoded by oncogenes such as myb, myc, fyn, and the translocation gene bcr/abl, ras, src, P53, neu, trk and EGRF. In addition to oncogene products as target antigens, target polypeptides for anti-cancer treatments and protective regimens include variable regions of antibodies made by B cell lymphomas and variable regions of T cell receptors of T cell lymphomas which, in some embodiments, are also used as target antigens for autoimmune disease. Other tumor associated polypeptides can be used as target polypeptides such as polypeptides which are found at higher levels in tumor cells including the polypeptide recognized by monoclonal antibody 17 1A and folate binding polypeptides.
Other suitable therapeutic polypeptides and proteins include those which may be useful for treating individuals suffering from autoimmune diseases and disorders by conferring a broad based protective immune response against targets that are associated with autoimmunity including cell receptors and cells which produce “self”-directed antibodies. T cell mediated autoimmune diseases include Rheumatoid arthritis (RA), multiple sclerosis (MS), Sjögren's syndrome, sarcoidosis, insulin dependent diabetes mellitus (IDDM), autoimmune thyroiditis, reactive arthritis, ankylosing spondylitis, scleroderma, polymyositis, dermatomyositis, psoriasis, vasculitis, Wegener's granulomatosis, Crohn's disease and ulcerative colitis. Each of these diseases is characterized by T cell receptors (TCRs) and antibodies (Ab) that bind to endogenous antigens and initiate the inflammatory cascade associated with autoimmune diseases.
Other suitable therapeutic polypeptides and protein include those useful for treating individuals suffering from a rare disease. Such rare disease include, e.g., acrocephalosyndactylia, Acrodermatitis, Addison Disease, Adie Syndrome, Alagille Syndrome, Amylose, Amyotrophic Lateral Sclerosis, Angelman Syndrome, Angiolymphoid Hyperplasia with Eosinophilia, Arnold-Chiari Malformation, juvenile rheumatoid arthritis, Asperger Syndrome, Bardet-Biedl Syndrome, Barrett Esophagus, Beckwith-Wiedemann Syndrome, Behcet Syndrome, Bloom Syndrome, Bowen's Disease, Brachial Plexus Neuropathies, Brown-Sequard Syndrome, Budd-Chiari Syndrome, Burkitt Lymphoma, Carcinoma 256, Walker Caroli Disease, Charcot-Marie-Tooth Disease, Chediak-Higashi Syndrome, Chiari-Frommel Syndrome, Chondrodysplasia Punctata, Colonic Pseudo-Obstruction, Colorectal Neoplasms, Hereditary Nonpolyposis, Craniofacial Dysostosis, Creutzfeldt-Jakob Syndrome, Crohn Disease, Cushing Syndrome, Cystic Fibrosis, Dandy-Walker Syndrome, De Lange Syndrome, Dementia, Vascular Dermatitis, Herpetiformis, DiGeorge Syndrome, Diffuse Cerebral Sclerosis of Schilder, Duane Retraction Syndrome, Dupuytren Contracture, Ebstein Anomaly, Eisenmenger Complex, Ellis-Van Creveld Syndrome, Encephalitis, Enchondromatosis, Epidermal Necrolysis, Toxic Facial Hemiatrophy, Factor XII Deficiency, Fanconi Anemia, Felty's Syndrome, Fibrous Dysplasia, Polyostotic, Fox-Fordyce Disease, Friedreich Ataxia, Fusobacterium, Gardner Syndrome, Gaucher Disease, Gerstmann Syndrome, Giant Lymph Node Hyperplasia, Glycogen Storage Disease Type I, Glycogen Storage Disease Type II, Glycogen Storage Disease Type IV, Glycogen Storage Disease Type V, Glycogen Storage Disease Type VII, Goldenhar Syndrome, Guillain-Barre Syndrome, Hallermann's Syndrome, Hamartoma Syndrome, Multiple Hartnup Disease, Hepatolenticular Degeneration, Hepatolenticular Degeneration, Hereditary Sensory and Motor Neuropathy Hirschsprung Disease, Histiocytic Necrotizing Lymphadenitis, Histiocytosis, Langerhans-Cell Hodgkin Disease, Horner Syndrome, Huntington Disease, Hyperaldosteronism, Hyperostosis, Diffuse Idiopathic Skeletal, Hypopituitarism, Inappropriate ADH Syndrome, Intestinal Polyps Isaacs Syndrome, Kartagener Syndrome, Kearns-Sayre Syndrome, Klippel-Feil Syndrome, Klippel-Trenaunay-Weber Syndrome, Kluver-Bucy Syndrome, Korsakoff Syndrome, Lafora Disease, Lambert-Eaton Myasthenic Syndrome, Landau-Kleffner Syndrome, Langer-Giedion Syndrome, Leigh Disease, Lesch-Nyhan Syndrome, Leukodystrophy, Globoid Cell, Li-Fraumeni Syndrome, Long QT Syndrome, Machado-Joseph Disease, Mallory-Weiss Syndrome, Marek Disease, Marfan Syndrome, Meckel Diverticulum, Meige Syndrome, Melkersson-Rosenthal Syndrome, Meniere Disease, Mikulicz' Disease, Miller Fisher Syndrome, Mobius Syndrome, Moyamoya Disease, Mucocutaneous Lymph Node Syndrome, Mucopolysaccharidosis I, Mucopolysaccharidosis II, Mucopolysaccharidosis III, Mucopolysaccharidosis IV, Mucopolysaccharidosis VI, Multiple Endocrine Neoplasia Type 1, Munchausen Syndrome by Proxy, Muscular Atrophy, Spinal Neuroaxonal Dystrophies, Neuromyelitis Optica, Neuronal Ceroid-Lipofuscinoses, Niemann-Pick Diseases, Noonan Syndrome, Optic Atrophies, Hereditary Osteitis Deformans, Osteochondritis, Osteochondrodysplasias, Osteolysis, Essential, Paget Disease Extramammary, Paget's Disease, Mammary, Panniculitis, Nodular Nonsuppurative, Papillon-Lefevre Disease, Paralysis, Pelizaeus-Merzbacher Disease, Pemphigus, Benign Familial Penile Induration, Pericarditis, Constrictive, Peroxisomal Disorders, Peutz-Jeghers Syndrome, Pick Disease of the Brain, Pierre Robin Syndrome, Pigmentation Disorders, Pityriasis Lichenoides, Polycystic Ovary Syndrome, Polyendocrinopathies, Autoimmune Prader-Willi Syndrome, Pupil Disorders, Rett Syndrome, Reye Syndrome, Rubinstein-Taybi Syndrome, Sandhoff Disease, Sarcoma, Ewing's, Sjogren's Syndrome, Sjogren-Larsson Syndrome, Smith-Lemli-Opitz Syndrome, Spinal Muscular Atrophies of Childhood, Sturge-Weber Syndrome, Sweating, Gustatory, Takayasu Arteritis, Tangier Disease, Tay-Sachs Disease, Thromboangiitis Obliterans, Thyroiditis, Autoimmune, Tietze's Syndrome, Togaviridae Infections, Tolosa-Hunt Syndrome, Tourette Syndrome, Uveomeningoencephalitic Syndrome Waardenburg's Syndrome, Wegener Granulomatosis, Weil Disease, Werner Syndrome, Williams Syndrome, Wilms Tumor, Wolff-Parkinson-White Syndrome, Wolfram Syndrome, Wolman Disease, Zellweger Syndrome, Zollinger-Ellison Syndrome, and von Willebrand Diseases.
Immunogenic Transgenes
The nucleotide sequence encoding of any of a number of immunogenic transgenes may be selected for codon modification to enhance tissue-preferential expression as described herein. Examples of suitable immunogenic transgenes include those selected from a variety of viral families. Example of desirable viral families against which an immune response would be desirable include, the picornavirus family, which includes the genera rhinoviruses, which are responsible for about 50% of cases of the common cold; the genera enteroviruses, which include polioviruses, coxsackieviruses, echoviruses, and human enteroviruses such as hepatitis A virus; and the genera apthoviruses, which are responsible for foot and mouth diseases, primarily in non-human animals. Within the picornavirus family of viruses, target antigens include the VP1, VP2, VP3, VP4, and VPG. Other viral families include the astroviruses and the calcivirus family. The calcivirus family encompasses the Norwalk group of viruses, which are an important causative agent of epidemic gastroenteritis. Still another viral family desirable for use in targeting antigens for inducing immune responses in humans and non-human animals is the togavirus family, which includes the genera alphavirus, which include Sindbis viruses, RossRiver virus, and Venezuelan, Eastern & Western Equine encephalitis, and rubivirus, including Rubella virus. The flaviviridae family includes dengue, yellow fever, Japanese encephalitis, St. Louis encephalitis and tick borne encephalitis viruses. Other target antigens may be generated from the Hepatitis C or the coronavirus family, which includes a number of non-human viruses such as infectious bronchitis virus (poultry), porcine transmissible gastroenteric virus (pig), porcine hemagglutinatin encephalomyelitis virus (pig), feline infectious peritonitis virus (cats), feline enteric coronavirus (cat), canine coronavirus (dog), and human respiratory coronaviruses, which may cause the common cold and/or non A, B or C hepatitis, and which include the putative cause of sudden acute respiratory syndrome (SARS). Within the coronavirus family, target antigens include the E1 (also called M or matrix protein), E2 (also called S or Spike protein), E3 (also called HE or hemagglutin elterose) glycoprotein (not present in all coronaviruses), or N (nucleocapsid). Still other antigens may be targeted against the arterivirus family and the rhabdovirus family. The rhabdovirus family includes the genera vesiculovirus (e.g., Vesicular Stomatitis Virus), and the general lyssavirus (e.g., rabies). Within the rhabdovirus family, suitable antigens may be derived from the G protein or the N protein. The family filoviridae, which includes hemorrhagic fever viruses such as Marburg and Ebola virus may be a suitable source of antigens. The paramyxovirus family includes parainfluenza Virus Type 1, parainfluenza Virus Type 3, bovine parainfluenza Virus Type 3, rubulavirus (mumps virus, parainfluenza Virus Type 2, parainfluenza virus Type 4, Newcastle disease virus (chickens), rinderpest, morbillivirus, which includes measles and canine distemper, and pneumovirus, which includes respiratory syncytial virus. The influenza virus is classified within the family orthomyxovirus and is a suitable source of antigen (e.g., the HA protein, the N1 protein). The bunyavirus family includes the genera bunyavirus (California encephalitis, La Crosse), phlebovirus (Rift Valley Fever), hantavirus (puremala is a hemahagin fever virus), nairovirus (Nairobi sheep disease) and various unassigned bungaviruses. The arenavirus family provides a source of antigens against LCM and Lassa fever virus. Another source of antigens is the bornavirus family. The reovirus family includes the genera reovirus, rotavirus (which causes acute gastroenteritis in children), orbiviruses, and cultivirus (Colorado Tick fever, Lebombo (humans), equine encephalosis, blue tongue). The retrovirus family includes the sub family oncorivirinal which encompasses such human and veterinary diseases as feline leukemia virus, HTLVI and HTLVII, lentivirinal (which includes HIV, simian immunodeficiency virus, feline immunodeficiency virus, equine infectious anemia virus, and spumavirinal). The papovavirus family includes the sub-family polyomaviruses (BKU and JCU viruses) and the sub family papillomavirus (associated with cancers or malignant progression of papilloma). The adenovirus family includes viruses (EX, AD7, ARD, O.B.) which cause respiratory disease and/or enteritis. The parvovirus family feline parvovirus (feline enteritis), feline panleucopeniavirus, canine parvovirus, and porcine parvovirus. The herpesvirus family includes the sub family alphaherpesvirinae, which encompasses the genera simplexvirus (HSVI, HSVII), varicellovirus (pseudorabies, varicella zoster) and the sub-family betaherpesvirinae, which includes the genera cytomegalovirus (HCMV, muromegalovirus) and the sub family gammaherpesvirinae, which includes the genera lymphocryptovirus, EBV (Burkitts lymphoma), human herpesviruses 6A, 6B and 7, Kaposi's sarcoma-associated herpesvirus and cercopithecine herpesvirus (B virus), infectious rhinotracheitis, Marek's disease virus, and rhadinovirus. The poxvirus family includes the sub family chordopoxvirinae, which encompasses the genera orthopoxvirus (Variola major (Smallpox) and Vaccinia (Cowpox)), parapoxvirus, avipoxvirus, capripoxvirus, leporipoxvirus, suipoxvirus, and the sub family entomopoxvirinae. The hepadnavirus family includes the Hepatitis B virus. One unclassified virus which may be suitable source of antigens is the Hepatitis delta virus, Hepatitis E virus, and prions. Another virus which is a source of antigens is Nipan Virus. Still other viral sources may include avian infectious bursal disease virus and porcine respiratory and reproductive syndrome virus. The alphavirus family includes equine arteritis virus and various Encephalitis viruses.
The present invention may also encompass immunogens which are useful to immunize a human or non-human animal against other pathogens including bacteria, fungi, parasitic microorganisms or multicellular parasites which infect human and non-human vertebrates, or from a cancer cell or tumor cell. Examples of bacterial pathogens include pathogenic gram positive cocci include pneumococci; staphylococci (and the toxins produced thereby, e.g., enterotoxin B); and streptococci. Pathogenic gram negative cocci include meningococcus; gonococcus. Pathogenic enteric gram negative bacilli include enterobacteriaceae; pseudomonas, acinetobacteria and eikenella; melioidosis; salmonella; shigella; haemophilus; moraxella; H. ducreyi (which causes chancroid); brucella species (brucellosis); Francisella tularensis (which causes tularemia); Yersinia pestis (plague) and other yersinia (pasteurella); streptobacillus moniliformis and spirillum; Gram-positive bacilli include listeria monocytogenes; erysipelothrix rhusiopathiae; Corynebacterium diphtheria (diphtheria); cholera; B. anthracis (anthrax); donovanosis (granuloma inguinale); and bartonellosis. Diseases caused by pathogenic anaerobic bacteria include tetanus; botulism (Clostridum botulinum and its toxin); Clostridium perfringens and its epsilon toxin; other clostridia; tuberculosis; leprosy; and other mycobacteria. Pathogenic spirochetal diseases include syphilis; treponematoses: yaws, pinta and endemic syphilis; and leptospirosis. Other infections caused by higher pathogen bacteria and pathogenic fungi include glanders (Burkholderia mallei); actinomycosis; nocardiosis; cryptococcosis, blastomycosis, histoplasmosis and coccidioidomycosis; candidiasis, aspergillosis, and mucormycosis; sporotrichosis; paracoccidiodomycosis, petriellidiosis, torulopsosis, mycetoma and chromomycosis; and dermatophytosis. Rickettsial infections include Typhus fever, Rocky Mountain spotted fever, Q fever (Coxiella burnetti), and Rickettsialpox. Examples of mycoplasma and chlamydial infections include: mycoplasma pneumoniae; lymphogranuloma venereum; psittacosis; and perinatal chlamydial infections. Pathogenic eukaryotes encompass pathogenic protozoans and helminths and infections produced thereby include: amebiasis; malaria; leishmaniasis; trypanosomiasis; toxoplasmosis; Pneumocystis carinii; Trichans; Toxoplasma gondii; babesiosis; giardiasis; trichinosis; filariasis; schistosomiasis; nematodes; trematodes or flukes; and cestode (tapeworm) infections.
Many of these organisms and/or the toxins produced thereby have been identified by the Centers for Disease Control [(CDC), Department of Health and Human Services, USA], as agents which have potential for use in biological attacks. For example, some of these biological agents, include, Bacillus anthracis (anthrax), Clostridium botulinum and its toxin (botulism), Yersinia pestis (plague), variola major (smallpox), Francisella tularensis (tularemia), and viral hemorrhagic fevers [filoviruses (e.g., Ebola, Marburg], and arenaviruses [e.g., Lassa, Machupo]), all of which are currently classified as Category A agents; Coxiella burnetti (Q fever); Brucella species (brucellosis), Burkholderia mallei (glanders), Burkholderia pseudomallei (meloidosis), Ricinus communis and its toxin (ricin toxin), Clostridium perfringens and its toxin (epsilon toxin), Staphylococcus species and their toxins (enterotoxin B), Chlamydia psittaci (psittacosis), water safety threats (e.g., Vibrio cholerae, Crytosporidium parvum), Typhus fever (Richettsia powazekii), and viral encephalitis (alphaviruses, e.g., Venezuelan equine encephalitis; eastern equine encephalitis; western equine encephalitis); all of which are currently classified as Category B agents; and Nipan virus and hantaviruses, which are currently classified as Category C agents. In addition, other organisms, which are so classified or differently classified, may be identified and/or used for such a purpose in the future. It will be readily understood that the viral vectors and other constructs described herein are useful to deliver antigens from these organisms, viruses, their toxins or other by-products, which will prevent and/or treat infection or other adverse reactions with these biological agents.
The vectors of the invention can be used to deliver immunogens. In rheumatoid arthritis (RA), several specific variable regions of T-cell receptors (TCRs) which are involved in the disease have been characterized. These TCRs include V 3, V 14, and V 17. Thus, delivery of a nucleic acid sequence that encodes at least one of these polypeptides will elicit an immune response that will target T cells involved in RA. In multiple sclerosis (MS), several specific variable regions of TCRs which are involved in the disease have been characterized. These TCRs include V 7 and V 10. Thus, delivery of a nucleic acid sequence that encodes at least one of these polypeptides will elicit an immune response that will target T cells involved in MS. In scleroderma, several specific variable regions of TCRs which are involved in the disease have been characterized. These TCRs include V 6, V 8, V 14, V 3C, V 7, V 14, V 15, V 16, V 28 and V 12. Thus, delivery of a nucleic acid molecule that encodes at least one of these polypeptides will elicit an immune response that will target T cells involved in scleroderma.
Other useful products include an “anti-pathogen construct” which is a protein, peptide, or other molecule encoded by a nucleic acid sequence carried on a viral vector as described herein, which is capable of providing passive immunity against the selected pathogenic agent or a cross-reactive strain of the pathogenic agent. In one embodiment, the anti-pathogen construct is a neutralizing antibody construct against the pathogenic agent, e.g., a virus, bacterium, fungus, or a pathogenic toxin of said agent (e.g., anthrax toxin). Examples of such pathogens are provided herein. As used herein, a “neutralizing antibody” is an antibody which defends a cell from an antigen or infectious body by inhibiting or neutralizing its biological effect. In one embodiment, “neutralizes” and grammatical variations thereof, refer to an activity of an antibody that prevents entry or translocation of the pathogen into the cytoplasm of a cell susceptible to infection. As used herein a “neutralizing antibody construct” includes a full-length antibody (an immunoglobulin molecule), as well as antibody fragments or artificial constructs which have the ability to inhibit or neutralize an antigen or infectious agent. These antibody fragments or artificial constructs may include a single chain antibody, a Fab fragment, a univalent antibody, or an immunoadhesin. The neutralizing antibody construct may be a monoclonal antibody, a “humanized” antibody, a polyclonal antibody, or another suitable construct. An “immunoglobulin molecule” is a protein containing the immunologically-active portions of an immunoglobulin heavy chain and immunoglobulin light chain covalently coupled together and capable of specifically combining with an antigen Immunoglobulin molecules are of any type (e.g., IgG, IgE, IgM, IgD, IgA and IgY), class (e.g., IgG1, IgG2, IgG3, IgG4, IgA1 and IgA2) or subclass. The terms “antibody” and “immunoglobulin” may be used interchangeably herein. An “immunoglobulin heavy chain” is a polypeptide that contains at least a portion of the antigen binding domain of an immunoglobulin and at least a portion of a variable region of an immunoglobulin heavy chain or at least a portion of a constant region of an immunoglobulin heavy chain. Thus, the immunoglobulin derived heavy chain has significant regions of amino acid sequence homology with a member of the immunoglobulin gene superfamily. For example, the heavy chain in a Fab fragment is an immunoglobulin-derived heavy chain. An “immunoglobulin light chain” is a polypeptide that contains at least a portion of the antigen binding domain of an immunoglobulin and at least a portion of the variable region or at least a portion of a constant region of an immunoglobulin light chain. Thus, the immunoglobulin-derived light chain has significant regions of amino acid homology with a member of the immunoglobulin gene superfamily. An “immunoadhesin” is a chimeric, antibody-like molecule that combines the functional domain of a binding protein, usually a receptor, ligand, or cell-adhesion molecule, with immunoglobulin constant domains, usually including the hinge and Fc regions. A ““fragment antigen-binding” (Fab) fragment” is a region on an antibody that binds to antigens. It is composed of one constant and one variable domain of each of the heavy and the light chain. With respect to immunoglobulins or antibodies as described herein, a fragment of an immunoglobulin coding sequence may be modified according to the methods described herein. Suitable fragments may include the coding region for one or more of, e.g., a heavy chain, a light chain, and/or fragments thereof such as the constant region of a heavy chain (CH1, CH2 and/or CH3) and/or or the constant region of a light chain. Alternatively, variable regions of a heavy chain or light chain may be modified. Examples of such fragments include, without limitation:













Position (nt)











SEQ
SED
SEQ


Region
ID NO: 14
ID NO: 15
ID NO: 18





VH (variable region heavy chain)
1365-1750
1371-1756
1320-1705


CH1 (constant region 1 heavy chain)
1752-2027
1758-2033
1707-1982


HCH23 (constant region 2-3 heavy
2028-2716
2034-2722
1983-2671


chain)


CL (constant region light chain)
3111-3415
3181-3485
3130-3434


3nbc117 light
2798-3095
2854-3165
2803-3114









Still other immunoglobulin coding regions may be modified.

Expression Cassette

For use in producing a viral vector (e.g., a recombinant (r) AAV), the expression cassette can be carried on any suitable vector, e.g., a plasmid, which is delivered to a packaging host cell. “Suitable regulatory sequences” refer to nucleotide sequences located upstream (5′ non-coding sequences), within, or downstream (3′ non-coding sequences) of a coding sequence, and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences may include promoters, translation leader sequences, introns, polyadenylation recognition sequences, RNA processing sites, effector binding sites and stem-loop structures. Suitable transfection techniques and packaging host cells are known and/or can be readily designed by one of skill in the art.
Examples of constitutive promoters suitable for controlling expression of the transgenes include, but are not limited to chicken β-actin (CB) promoter, human cytomegalovirus (CMV) promoter, the early and late promoters of simian virus 40 (SV40), U6 promoter, metallothionein promoters, EF1α promoter, ubiquitin promoter, hypoxanthine phosphoribosyl transferase (HPRT) promoter, dihydrofolate reductase (DHFR) promoter (Scharfmann et al., Proc. Natl. Acad. Sci. USA 88:4626-4630 (1991), adenosine deaminase promoter, phosphoglycerol kinase (PGK) promoter, pyruvate kinase promoter phosphoglycerol mutase promoter, the β-actin promoter (Lai et al., Proc. Natl. Acad. Sci. USA 86: 10006-10010 (1989)), the long terminal repeats (LTR) of Moloney Leukemia Virus and other retroviruses, the thymidine kinase promoter of Herpes Simplex Virus and other constitutive promoters known to those of skill in the art. Examples of tissue- or cell-preferential promoters suitable for use in the present invention include, but are not limited to, endothelin-I (ET-I) and Flt-I, which are for endothelial cells, FoxJ1 (that targets ciliated cells), human thyroxine binding globulin (TBG) and alpha-1 anti-trypsin (A1AT) for liver, troponin and T (TnT) for heart, clara cell 10 (CC10), surfactant protein C (SPC) and FoxJ1 for heart; synapsin, tyrosine hydroxylase, CaMKII (Ca2+/calmodulin-dependent protein kinase) for central nervous system/brain, insulin and elastase-I for pancrease, Ap2 and adiponector for adipocyte, desmin and MHC for muscle, and VMD for retina. Still others are known in the art.
Inducible promoters suitable for controlling expression of the transgene include promoters responsive to exogenous agents (e.g., pharmacological agents) or to physiological cues. These response elements include, but are not limited to a hypoxia response element (HRE) that binds HIF-Iα and β, a metal-ion response element such as described by Mayo et al. (1982, Cell 29:99-108); Brinster et al. (1982, Nature 296:39-42) and Searle et al. (1985, Mol. Cell. Biol. 5:1480-1489); or a heat shock response element such as described by Nouer et al. (in: Heat Shock Response, ed. Nouer, L., CRC, Boca Raton, Fla., ppI 67-220, 1991).
Examples of regulatable promoters which are ligand-dependent transcription factor complexes that may be used in the invention include, without limitation, members of the nuclear receptor superfamily activated by their respective ligands (e.g., glucocorticoid, estrogen, progestin, retinoid, ecdysone, and analogs and mimetics thereof) and rTTA activated by tetracycline. In one aspect of the invention, the gene switch is an EcR-based gene switch. Examples of such systems include, without limitation, the systems described in U.S. Pat. Nos. 6,258,603, 7,045,315, U.S. Published Patent Application Nos. 2006/0014711, 2007/0161086, and International Published Application No. WO 01/70816. Examples of chimeric ecdysone receptor systems are described in U.S. Pat. No. 7,091,038, U.S. Published Patent Application Nos. 2002/0110861, 2004/0033600, 2004/0096942, 2005/0266457, and 2006/0100416, and International Published Application Nos. WO 01/70816, WO 02/066612, WO 02/066613, WO 02/066614, WO 02/066615, WO 02/29075, and WO 2005/108617, each of which is incorporated by reference in its entirety. An example of a non-steroidal ecdysone agonist-regulated system is the RheoSwitch® Mammalian Inducible Expression System (New England Biolabs, Ipswich, Mass.).
Still other promoter systems may include response elements including but not limited to a tetracycline (tet) response element (such as described by Gossen & Bujard (1992, Proc. Natl. Acad. Sci. USA 89:5547-551); or a hormone response element such as described by Lee et al. (1981, Nature 294:228-232); Hynes et al. (1981, Proc. Natl. Acad. Sci. USA 78:2038-2042); Klock et al. (1987, Nature 329:734-736); and Israel & Kaufman (1989, Nucl. Acids Res. 17:2589-2604) and other inducible promoters known in the art. Using such promoters, expression of the neutralizing antibody construct can be controlled, for example, by the Tet-on/off system (Gossen et al., 1995, Science 268:1766-9; Gossen et al., 1992, Proc. Natl. Acad. Sci. USA., 89(12):5547-51); the TetR-KRAB system (Urrutia R., 2003, Genome Biol., 4(10):231; Deuschle U et al., 1995, Mol Cell Biol. (4):1907-14); the mifepristone (RU486) regulatable system (Geneswitch; Wang Y et al., 1994, Proc. Natl. Acad. Sci. USA., 91(17):8180-4; Schillinger et al., 2005, Proc. Natl. Acad. Sci. USA. 102(39):13789-94); the humanized tamoxifen-dep regulatable system (Roscilli et al., 2002, Mol. Ther. 6(5):653-63). In one system, a gene switch is based on heterodimerization of FK506 binding protein (FKBP) with FKBP rapamycin associated protein (FRAP) and is regulated through rapamycin or its non-immunosuppressive analogs. Examples of such systems, include, without limitation, the ARGENTTM Transcriptional Technology (ARIAD Pharmaceuticals, Cambridge, Mass.) and the systems described in U.S. Pat. Nos. 6,015,709, 6,117,680, 6,479,653, 6,187,757, and 6,649,595, U.S. Publication No. 2002/0173474, U.S. Publication No. 200910100535, U.S. Pat. Nos. 5,834,266, 7,109,317, 7,485,441, 5,830,462, 5,869,337, 5,871,753, 6,011,018, 6,043,082, 6,046,047, 6,063,625, 6,140,120, 6,165,787, 6,972,193, 6,326,166, 7,008,780, 6,133,456, 6,150,527, 6,506,379, 6,258,823, 6,693,189, 6,127,521, 6,150,137, 6,464,974, 6,509,152, 6,015,709, 6,117,680, 6,479,653, 6,187,757, 6,649,595, 6,984,635, 7,067,526, 7,196,192, 6,476,200, 6,492,106, WO 94/18347, WO 96/20951, WO 96/06097, WO 97/31898, WO 96/41865, WO 98/02441, WO 95/33052, WO 99110508, WO 99110510, WO 99/36553, WO 99/41258, WO 01114387, ARGENTTM Regulated Transcription Retrovirus Kit, Version 2.0 (9109102), and ARGENTTM Regulated Transcription Plasmid Kit, Version 2.0 (9109/02), each of which is incorporated herein by reference in its entirety. The Ariad system is designed to be induced by rapamycin and analogs thereof referred to as “rapalogs”. Examples of suitable rapamycins are provided in the documents listed above in connection with the description of the ARGENTTM system. In one embodiment, the molecule is rapamycin [e.g., marketed as RapamuneTM by Pfizer]. In another embodiment, a rapalog known as AP21967 [ARIAD] is used. Examples of these dimerizer molecules that can be used in the present invention include, but are not limited to rapamycin, FK506, FK1012 (a homodimer of FK506), rapamycin analogs (“rapalogs”) which are readily prepared by chemical modifications of the natural product to add a “bump” that reduces or eliminates affinity for endogenous FKBP and/or FRAP. Examples of rapalogs include, but are not limited to such as AP26113 (Ariad), AP1510 (Amara, J. F., et al., 1997, Proc Natl Acad Sci USA, 94(20): 10618-23) AP22660, AP22594, AP21370, AP22594, AP23054, AP1855, AP1856, AP1701, AP1861, AP1692 and AP1889, with designed ‘bumps’ that minimize interactions with endogenous FKBP. Still other rapalogs may be selected, e.g., AP23573 [Merck].
In addition to the elements identified above for the expression cassette, the vector may also include conventional control elements which are operably linked to the coding sequence in a manner which permits transcription, translation and/or expression of the encoded product (e.g., a neutralizing antibody or a portion thereof) in a cell transfected with the plasmid vector or infected with the virus produced by the invention. As used herein, “operably linked” sequences include both expression control sequences that are contiguous with the gene of interest and expression control sequences that act in trans or at a distance to control the gene of interest.
The term “heterologous” when used with reference to a protein or a nucleic acid indicates that the protein or the nucleic acid comprises two or more sequences or subsequences which are not found in the same relationship to each other in nature. For instance, the nucleic acid is typically recombinantly produced, having two or more sequences from unrelated genes arranged to make a new functional nucleic acid. For example, in one embodiment, the nucleic acid has a promoter from one gene arranged to direct the expression of a coding sequence from a different gene. Thus, with reference to the coding sequence, the promoter is heterologous.
As exemplified herein, the vector may be a plasmid and/or a recombinant AAV viral vector. However, it will be readily understood that the expression cassettes containing nucleic acid sequences generated as described herein may be engineered onto any number of vectors including, other viral vectors such as baculovirus, adenovirus, retroviruses, and the like. Methods for generating and isolating AAVs suitable for use as vectors are known in the art. See generally, e.g., Grieger & Samulski, 2005, “Adeno-associated virus as a gene therapy vector: Vector development, production and clinical applications,” Adv. Biochem. Engin/Biotechnol. 99: 119-145; Buning et al., 2008, “Recent developments in adeno-associated virus vector technology,” J. Gene Med. 10:717-733; and the references cited below, each of which is incorporated herein by reference in its entirety.
An adeno-associated virus (AAV) viral vector is an AAV DNase-resistant particle having an AAV protein capsid into which is packaged nucleic acid sequences for delivery to target cells. In one embodiment, the AAV sequences on the expression cassette comprise only minimal AAV sequences to avoid the risk of replication. In one embodiment, the minimal AAV sequences include the AAV inverted terminal repeat sequences (ITR). In one embodiment, the 5′ ITR and the 3′ ITR are the minimal AAV sequences required in cis in order to express a transgene encoded by a nucleic acid sequence packaged in the AAV capsid. Typically, the ITRs flank the modified coding sequence for a selected gene product. In one embodiment, the AAV vector contains AAV 5′ and 3′ ITRs, which may be of the same AAV origin as the capsid, or which may be of a different AAV origin (to produce an AAV pseudotype). In one embodiment, the coding sequences for the replication (rep) and/or capsid (cap) are removed from the AAV genome and supplied in trans or by a packaging cell line in order to generate the AAV vector.
An AAV capsid is composed of 60 capsid protein subunits, VP1, VP2, and VP3, that are arranged in an icosahedral symmetry in a ratio of approximately 1:1:10 to 1:1:20, depending upon the selected AAV. The capsid type does play a role in tissue specificity. The sequences of a variety of AAV have been described, as have methods of generating vectors having the AAV capsids. Examples of AAV which may be selected as sources for capsids of AAV viral vectors (DNase resistant viral particles) include, e.g., AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV6.2, AAV7, AAV8, AAV9, rh10, AAVrh64R1, AAVrh64R2, rh8 [See, e.g., US Published Patent Application No. 2007-0036760-A1; US Published Patent Application No. 2009-0197338-A1; EP 1310571]. See also, WO 2003/042397 (AAV7 and other simian AAV), U.S. Pat. No. 7,790,449 and U.S. Pat. No. 7,282,199 (AAV8), WO 2005/033321 and U.S. Pat. No. 7,906,111 (AAV9), and WO 2006/110689]. As yet to be discovered AAV, or a recombinant AAV based thereon, may be used as a source for the AAV capsid. These documents also describe other AAV which may be selected for generating AAV and are incorporated by reference. In some embodiments, an AAV cap for use in the viral vector can be generated by mutagenesis (i.e., by insertions, deletions, or substitutions) of one of the aforementioned AAV Caps or its encoding nucleic acid. In some embodiments, the AAV capsid is chimeric, comprising domains from two or three or four or more of the aforementioned AAV capsid proteins. In some embodiments, the AAV capsid is a mosaic of Vp1, Vp2, and Vp3 monomers from two or three different AAVs or recombinant AAVs. In some embodiments, an rAAV composition comprises more than one of the aforementioned Caps.
For packaging a transgene into virions, the ITRs are the only AAV components required in cis in the same construct as the transgene. The cap and rep genes can be supplied in trans. Accordingly, DNA constructs can be designed so that the AAV ITRs flank the coding sequence, thus defining the region to be amplified and packaged—the only design constraint being the upper limit of the size of the DNA to be packaged (approximately 4.5 kb). Adeno-associated virus engineering and design choices that can be used to save space are known in the art.
The components required to be cultured in the host cell to package an AAV minigene in an AAV capsid may be provided to the host cell in trans. Alternatively, any one or more of the required components (e.g., minigene, rep sequences, cap sequences, and/or helper functions) may be provided by a stable host cell which has been engineered to contain one or more of the required components using methods known to those of skill in the art. Most suitably, such a stable host cell will contain the required component(s) under the control of an inducible promoter. However, the required component(s) may be under the control of a constitutive promoter. Examples of suitable inducible and constitutive promoters are provided herein, in the discussion of regulatory elements suitable for use with the transgene. In still another alternative, a selected stable host cell may contain selected component(s) under the control of a constitutive promoter and other selected component(s) under the control of one or more inducible promoters. For example, a stable host cell may be generated which is derived from 293 cells (which contain E1 helper functions under the control of a constitutive promoter), but which contains the rep and/or cap proteins under the control of inducible promoters. Still other stable host cells may be generated by one of skill in the art.
The minigene, rep sequences, cap sequences, and helper functions required for producing the rAAV of the invention may be delivered to the packaging host cell in the form of any genetic element which transfer the sequences carried thereon. The selected genetic element may be delivered by any suitable method, including those described herein. The methods used to construct any embodiment of this invention are known to those with skill in nucleic acid manipulation and include genetic engineering, recombinant engineering, and synthetic techniques. See, e.g., Sambrook et al, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press, Cold Spring Harbor, N.Y. Similarly, methods of generating rAAV virions are well known and the selection of a suitable method is not a limitation on the present invention. See, e.g., K. Fisher et al, (1993) J. Virol., 70:520-532 and U.S. Pat. No. 5,478,745.
Unless otherwise specified, the AAV ITRs, and other selected AAV components described herein, may be readily selected from among any AAV. Further, more than one AAV source may provide elements to an AAV vector. For example, as described above, a pseudotyped AAV may contain ITRs from a source which differs from the source of the AAV capsid. Additionally or alternatively, a chimeric AAV capsid may be utilized. Still other AAV components may be selected. Sources of such AAV sequences are described herein and may also be isolated or obtained from academic, commercial, or public sources (e.g., the American Type Culture Collection, Manassas, Va.). Alternatively, the AAV sequences may be obtained through synthetic or other suitable means by reference to published sequences such as are available in the literature or in databases such as, e.g., GenBank®, PubMed®, or the like.
In one embodiment, the pharmaceutical compositions include a single vector containing an expression cassette comprising a modified ORF as described above. In another embodiment, the composition includes more than one vector, each containing one or more expression cassettes. Each expression cassette comprises a modified ORF. In another embodiment, the composition includes multiple viral vectors, each containing one or more expression cassettes as described herein.
The AAV vectors may be suspended in a physiologically compatible carrier for administration to a human or non-human mammalian patient. Suitable carriers may be readily selected by one of skill in the art in view of the route of delivery. For example, one suitable carrier includes saline, which may be formulated with a variety of buffering solutions (e.g., phosphate buffered saline). Other exemplary carriers include sterile saline, lactose, sucrose, calcium phosphate, gelatin, dextran, agar, pectin, peanut oil, sesame oil, and water. The selection of the carrier is not a limitation of the present invention. Optionally, the compositions of the invention may contain, in addition to the rAAV and carrier(s), other conventional pharmaceutical ingredients, such as preservatives, or chemical stabilizers. Suitable exemplary preservatives include chlorobutanol, potassium sorbate, sorbic acid, sulfur dioxide, propyl gallate, the parabens, ethyl vanillin, glycerin, phenol, and parachlorophenol. Suitable chemical stabilizers include gelatin and albumin.
The following examples are illustrative only and are not a limitation on the invention described herein.
EXAMPLE 1
Modification of Open Reading Frame (ORF) of Anti-HIV Antibody
The ORF of an anti-SIV antibody which had previously been shown to express at unusually high levels in liver as compared to other tissue types and other ORFs. From this observation, the study described herein was designed. Using an anti-HIV antibody coding sequence as a base sequence for proof-of-principal, 12 alternative synonymous codon modified ORFs were generated using different methods by DNA2.0 [Menlo Park, Calif.]. These sequences are provided in FIG. 1, which is incorporated by reference herein. The ORF for the anti-HIV antibody which served as the base ORF in the study described herein had previously been altered in our laboratory and was observed to preferentially express at very high levels in liver. The base sequence, which served as the control, was modified using the coding frequencies for human, as provided by http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=9606 (Table 2). Additional modifications were made by hand to remove restriction sites and other non-desirable features (e.g., CpG islands).
The following Table 18 provides a comparison of the identity of the modified ORFs generated and studied herein. The sequences of the ORFs are contained in SEQ ID NOs: 1-12 and 30. An alignment of the sequences is provided in FIGS. 1A-1J.







TABLE 18







Comparison of Identity of Modified ORFs





















ORF1
ORFBASE
ORFIAM
ORFIAU
ORF11
ORF2
ORF26
ORF28
ORF30
ORF35
ORF42
ORF39
ORF40























ORF1
77
79
79
77
76
77
77
75
76
76
76
77


ORFBASE

80
80
75
75
76
76
76
75
75
75
76


ORFIAM


85
78
75
78
78
76
76
76
76
78


ORFIAU



79
76
77
77
76
76
76
76
78


ORF11




76
75
76
76
77
75
76
77


ORF2





77
76
76
74
74
76
75


ORF26






77
74
77
76
76
76


ORF28







77
76
75
75
76


ORF30








75
74
76
75


ORF35









77
76
75


ORF42










76
76


ORF39











76


ORF40









These ORFs were engineered into a plasmid construct (F2A) and expression levels were assessed in HEK 293 cells. The sequences of these plasmids are provided in the attached FIG. 5 (SEQ ID NOs: 13-29), which is incorporated by reference herein.
The data in Table 19 provides the results on an in vitro assessment of the plasmid constructs in HEK 293 cells. As shown in FIG. 2, expression of the gene under the control of human cytomegalovirus promoter (CMV (first bar)) or a CMV promoter with a commercially available enhancer (Promega intron, PI)(third bar) were assessed in HEK 293 cells at 72 hours post-transfection. Cells were transfected with 2×1010 GC/per mouse and expression levels were assessed at day 50. The pZac is an empty vector carrying only the promoter and enhancer. F2A is a plasmid containing the “base” or parental anti-HIV antibody ORF under the control of the CMV-IE promoter. Mini-C is similar to the F2a, in that it contains the “base” or parental anti-HIV antibody ORF under the control of the CMV-IE promoter, but it further contains a 5′UTR.
Protein levels determined by ELISA for 2-3 transfections (HEK) approximately 72 hours (three days) after the last transfection.









TABLE 19









ng/ml -- 72 hours post transfection --



serum free supernatant










HEK293- CMV
HEK293-CMV-PI












NAME
DESCRIPTION
AVE
STDEV
AVE
STDEV















pZac
empty vector
1.33
1.89
0
0



CMV-PI


F2A
base vector


593.11
59.61



(BV) CMV-PI


mini C
BV (CMV-PI) +


568.19
24.16



5′UTR


ORF 1
ORF 1
233.11
46.55
377.71
125.58


ORF 2
ORF 2
151.37
18.73
394.76
31.7


ORF 11
ORF 11
54.44
0.95
451.54
42.98


ORF26
ORF26
508.44
316.51
391.6
5.69


ORF 28
ORF 28
19.15
0.48
245.54
66.1


ORF 30
ORF 30
12.55
1.05
188.01
30.46


ORF 35
ORF 35
183.19
17.72
557.51
7.94


ORF 39
ORF 39
40.4
8.45
262.2
20.99


ORF 40
ORF 40
114.43
15.01
368.84
92.69


ORF 42
ORF 42
66.22
8.53
335.76
62.74


IA U
IA USAGE
537.17
66.15
397.79
159.8


IAM U
IAM USAGE
463.23
60.76
135.78
66.53





Open squares indicate that the study was not done to date.






As shown in Table 19, in the 293 cells, there were significant differences in expression levels for all modified genes expressed from the CMV promoter, with the ORF26, IA U and IAM U constructs showing the strongest expression levels. There were also significant differences in in vitro expression levels for all modified genes expressed under the CMV promoter with the enhancer (CMV-IE). These data show that none of the modified constructs provide expression levels significantly higher than the base vector. With the promoter-enhancer, ORF 35 show the strongest expression levels followed by ORF11.
The plasmids carrying the genes described above expressed under the CMV-PI promoter/enhancer were packaged into AAV8 capsids using published methods and the resulting AAV.CMV-IE.modified genes were expressed in a non-secretory tissue (muscle) and a secretory tissue (lung). Except where otherwise specified, animals (RAG KO) were delivered 2×1010 genomic particles/mL. For those animals injected im, serum levels of protein were determined on day 50 post-injection by ELISA (FIG. 2 (middle bars)). For those animals for which the constructs were delivered by nasal installation, protein levels in bronchial lavage were determined by ELISA seven days following installation. Table 20 provides the results.










TABLE 20










ng/ml --




BRONCHIAL




LAVAGE




ROA:



μg/ml - SERUM
INTRANASAL



ROA: INTRAMUSCULAR
INSTILLATION














NAME
DESCRIPTION
AVE
STDEV
AVE
STDEV
AVE
STDEV

















F2A
base vector (BV)
23.76
5.10
**21.94
10.45





CMV-PI


mini C
BV (CMV-PI) + 5′UTR
76.31
19.71
**63.59
21.35
24.79
0.12


ORF 1
ORF 1
*21.34
*0.94


8.77
0.01


ORF 2
ORF 2
20.95
2.71


13.58
5.82


ORF
ORF 11
23.00
4.58


11


ORF26
ORF26
48.98
16.75


ORF
ORF 28
34.14
7.97


6.69
0.97


28


ORF
ORF 30
46.26
22.32


3.15
1.45


30


ORF
ORF 35
115.68
64.61


6.31
1.03


35


ORF
ORF 39
139.30
60.16


10.07
2.09


39


ORF
ORF 40
*46.54
*20.12


14.73
1.76


40


ORF
ORF 42


**15.24
3.69


42


IA U
IA USAGE


**48.82
2.29
18.04
1.55


IAM U
IAM USAGE


**42.60
14.18
7.04
1.1





Open squares indicate that the study was not done to date.


*Vector 1 × 1010


**Day 35, rather than day 50






With the exception of AAV8 vectors carrying ORF2 and ORF11 which were approximately the same as the parental gene, the tested constructs outperformed the vector expressing the parental gene in muscle. The muscle expression levels observed for the ORF 1 vector was about the same as for the vector carrying the parental gene, but at half the dose. The highest expression levels for muscle were observed for ORF35 and ORF39, which were both approximately four times the expression level of the parental gene.
In respiratory epithelium, the expression levels observed for vector carrying the parental gene were higher than those for the vectors carrying the other modified genes. Significant variations in expression levels were observed, with the vectors carrying IA U, ORF40 and ORF2 expressing at higher levels that the other vectors with the exception of the vector carrying the parental gene.
These observations demonstrate that in vitro assessment of codon optimization is not predictive of expression levels in all tissues. As seen above, in the HEK 293 cells, none of the codon modified genes tested expressed at a higher level than the parental gene. It is possible that the derivation of the 293 cell line from human embryonic kidney cells would be predictive of expression levels in kidney. While in this example, the results observed in 293 cells are consistent with the expression levels observed in lung, significantly different expression results were observed in muscle. This suggests that there are tissue-specific codon patterns and that one can select an algorithmic schema for modification of a selected gene which will preferentially enhance its expression in a selected target tissue.
EXAMPLE 2
A further study was conducted using, 2×1010 GC/mouse of AAV8 containing modified transgenes were injected IV for liver expression into RAG KO mice (n=5 mice per construct) as described above. Expression of circulating antibody in serum was monitored by ELISA for 56 days. The results are shown the following Table 21 and demonstrate significant differences in expression in liver between the modified open reading frames. For example, the ORF2, ORF11, ORF26, ORF35 and IAU constructs consistently expressed at a higher level in liver than the 5′ UTR construct, which served as a control. ORF39 expressed slightly higher in liver than the control at longer time periods, while ORF 42, ORF28 and ORF1 expressed at a similar level to the control. The IAM construct showed consistently low levels of expression in liver.














TABLE 21









ORF1

ORF2

ORF11

















Average
stdev.
average
stdev.
average
stdev.







Day 0
0.00

0.00

0.00



Day 7
46.82
18.21
215.47
106.95
222.35
54.94



Day
118.62
67.49
587.67
310.10
554.69
143.95



14



Day
186.39
96.52
692.40
370.28
653.54
138.25



21



Day
160.17
86.25
930.70
463.55
903.50
269.02



28



Day
170.25
93.65
636.50
270.23
745.29
223.72



35



Day
227.29
105.22
918.11
406.00
855.00
325.39



42



Day
158.40
98.97
544.80
277.30
776.80
244.22



49



Day
169.89
101.71
670.25
267.16
723.00
239.23



56
















ORF26
ORF28
ORF35
ORF39
















Average
stdev.
average
stdev.
average
stdev.
average
stdev.





Day 0
0.00

0.00

0.00

0.00


Day 7
175.90
40.07
35.63
26.45
77.92
14.59
67.62
4.14


Day
469.47
69.45
96.84
76.09
153.03
38.47
165.09
42.15


14


Day
537.23
25.46
132.45
94.81
164.75
41.16
164.05
49.03


21


Day
748.77
168.21
181.26
130.79
321.21
135.05
352.53
79.62


28


Day
561.00
112.60
165.43
100.77
207.27
67.00
181.73
59.40


35


Day
722.25
83.83
135.64
93.70
173.80
64.06
146.20
50.80


42


Day
505.40
145.27
135.82
90.23
147.54
46.28
128.63
47.71


49


Day
434.22
105.62
153.39
115.28
160.80
52.88
149.05
47.03


56




















5′UTR (mini C)



ORF40
ORF42
IAU
IAM
(Control)


















Average
stdev.
average
stdev.
average
stdev.
average
stdev.
average
stdev.





Day 0
0.00

0.00

0.00

0.00

0.00


Day 7
24.27
9.77
39.76
21.52
97.67
48.61
12.20
4.71
69.92
50.36


Day
51.19
20.44
95.10
49.91
265.20
108.20
16.36
8.31
104.01
77.79


14


Day
62.95
25.19
88.78
49.39
330.53
162.77
15.54
6.32
104.33
64.62


21


Day
62.13
23.99
121.84
63.78
485.02
212.38
16.88
7.47
178.63
98.22


28


Day
53.33
23.81
141.57
78.12
303.62
112.68
11.24
5.86
108.76
61.08


35


Day
60.89
27.56
92.60
56.49
369.47
144.21
10.88
5.07
107.73
44.34


42


Day
53.40
23.19
96.15
61.31
320.29
164.55
16.89
8.70
118.86
53.48


49


Day
53.47
21.99
105.53
64.25
377.35
158.09
12.24
6.49
93.13
37.43


56









EXAMPLE 3
AAV8 containing one of two modified constructs, 10A (SEQ ID NO: 32) or 201 (SEQ ID NO: 31), were injected into mice as described above (1×1011 GC/mouse). Expression in muscle and liver was determined by ELISA. FIG. 6 is a graph showing the expression of the 201 construct in muscle (bottom line) and liver (top line) of mice versus time post transduction. 5 mice per group were injected at the indicated dosages (1×1010 or 1×1011 GC/per mouse). Concentrations were determined by ELISA. Capture accomplished by binding to SIV mac251 gp120; detection by Fc chain antibody (IgG1) conjugated with biotin, followed by HRP-streptavidin.
FIG. 7 is a graph showing the expression of the 10A construct in muscle (bottom line) and liver (top line) of mice versus time post transduction. 5 mice per group were injected at the dosage of 1×1011 GC/per mouse. CMV promoter was used for IM injections; TBG promoter was used for IV injections.
A comparison of these two figures shows that, in both muscle and liver, the 201 construct expresses levels greater than 10 fold as compared to the 10A construct.
The 3bnc117 antibody coding sequence was optimized using the codon frequency of human (Table 2) or 201 (Table 16) manually. The codon frequencies for the final sequences are shown in tables 22 (human) and 23 (201) below. AAV8 constructs utilizing the TBM promoter and incorporating 3bnC117/hum (SEQ ID NO: 34) or 3bnC117/201 (SEQ ID NO: 33) sequence were injected intravenously into mice at a dosage of 1×1011 GC/per mouse. Expression in liver is shown in FIG. 8. Expression of the 3bnC117/201 in liver was  ̃2.5 to over 3 times greater than expression using the human codon frequency optimized sequence.








TABLE 22 





Sequence
Codon (frequency: per thousand)























3bnC117/HUM
UUU
14.3
UCU
14.3
UAU
14.3
UGU
4.1



UUC
20.4
UCC
22.4
UAC
28.5
UGC
18.3



UUA
4.1
UCA
12.2
UAA
0
UGA
0



UUG
6.1
UCG
8.1
UAG
0
UGG
26.5



CUU
6.1
CCU
14.3
CAU
4.1
CGU
8.1



CUC
14.3
CCC
24.4
CAC
12.2
CGC
2



CUA
4.1
CCA
22.4
CAA
12.2
CGA
10.2



CUG
42.8
CCG
6.1
CAG
46.8
CGG
10.2



AUU
8.1
ACU
8.1
AAU
14.3
AGU
10.2



AUC
18.3
ACC
34.6
AAC
28.5
AGC
32.6



AUA
0
ACA
14.3
AAA
20.4
AGA
14.3



AUG
12.2
ACG
8.1
AAG
34.6
AGG
4.1



GUU
2
GCU
2
GAU
12.2
GGU
4.1



GUC
40.7
GCC
20.4
GAC
36.7
GGC
26.5



GUA
2
GCA
18.3
GAA
14.3
GGA
28.5



GUG
36.7
GCG
8.1
GAG
26.5
GGG
24.4

















TABLE 23 





Sequence
Codon (frequency: per thousand)























3bnC117/201
UUU
6.1
UCU
6.1
UAU
6.1
UGU
10.2



UUC
32.7
UCC
20.4
UAC
34.7
UGC
12.2



UUA
0
UCA
12.2
UAA
0
UGA
0



UUG
0
UCG
2
UAG
0
UGG
28.6



CUU
0
CCU
18.4
CAU
4.1
CGU
2



CUC
0
CCC
20.4
CAC
12.2
CGC
4.1



CUA
0
CCA
28.6
CAA
0
CGA
4.1



CUG
75.5
CCG
0
CAG
59.2
CGG
24.5



AUU
6.1
ACU
12.2
AAU
8.2
AGU
8.2



AUC
18.4
ACC
32.7
AAC
32.7
AGC
46.9



AUA
0
ACA
16.3
AAA
18.4
AGA
4.1



AUG
10.2
ACG
2
AAG
38.8
AGG
8.2



GUU
0
GCU
4.1
GAU
34.7
GGU
0



GUC
18.4
GCC
34.7
GAC
14.3
GGC
28.6



GUA
0
GCA
4.1
GAA
12.2
GGA
44.9



GUG
67.3
GCG
2
GAG
30.6
GGG
16.3



















Table for Free Text in Feature <220>











<220><223>


SEQ ID NO:
221
Feature












1
Artificial sequence
synthetic sequence


2
Artificial sequence
synthetic sequence


3
Artificial sequence
synthetic sequence


4
Artificial sequence
synthetic sequence


5
Artificial sequence
synthetic sequence


6
Artificial sequence
synthetic sequence


7
Artificial sequence
synthetic sequence


8
Artificial sequence
synthetic sequence


9
Artificial sequence
synthetic sequence


10
Artificial sequence
synthetic sequence


11
Artificial sequence
synthetic sequence


12
Artificial sequence
synthetic sequence


13
Artificial sequence
synthetic sequence


14
Artificial sequence
synthetic sequence


15
Artificial sequence
synthetic sequence


16
Artificial sequence
synthetic sequence


17
Artificial sequence
synthetic sequence


18
Artificial sequence
synthetic sequence


19
Artificial sequence
synthetic sequence


20
Artificial sequence
synthetic sequence


21
Artificial sequence
synthetic sequence


22
Artificial sequence
synthetic sequence


23
Artificial sequence
synthetic sequence


24
Artificial sequence
synthetic sequence


25
Artificial sequence
synthetic sequence


26
Artificial sequence
synthetic sequence


27
Artificial sequence
synthetic sequence


28
Artificial sequence
synthetic sequence


29
Artificial sequence
synthetic sequence


30
Artificial sequence
synthetic sequence


31
Artificial sequence
synthetic sequence


32
Artificial sequence
synthetic sequence


33
Artificial sequence
synthetic sequence


34
Artificial sequence
synthetic sequence









This application contains sequences and a sequence listing, filed herewith as a text file named Z6688PCT_SEQ_LIST_042914_ST25. All publications, patents, and patent applications cited in this application are hereby incorporated by reference in their entireties as if each individual publication or patent application were specifically and individually indicated to be incorporated by reference. Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be readily apparent to those of ordinary skill in the art in light of the teachings of this invention that certain changes and modifications can be made thereto without departing from the spirit or scope of the appended claims.

## Claims

1. An expression cassette comprising an open reading frame (ORF) for an antibody construct under the control of regulatory sequences which direct expression of the antibody construct in a muscle cell, which ORF has been modified to preferentially increase expression levels in muscle, wherein the modified ORF has a sequence of ORF 201 (SEQ ID NO: 31).

2. The expression cassette according to claim 1, wherein the regulatory sequences comprise a tissue specific promoter.

3. A vector comprising the expression cassette according to claim 1 and other genetic elements.

4. The vector according to claim 3, wherein said vector is a recombinant adeno-associated virus (AAV) having an AAV capsid in which the expression cassette is packaged.

5. The vector according to claim 4, wherein the AAV capsid is selected from AAV1, AAV2,AAV3, AAV4, AAV5, AAV6, AAV6.2, AAV7, AAV8, AAV9, rh10, AAVrh64R1, AAVrh64R2, and rh8.

6. The vector according to claim 3, wherein the vector is a plasmid.

7. A recombinant AAV comprising an AAV8 capsid and an expression cassette for an anti-HIV antibody, wherein the expression cassette is adapted for expression in a selected target tissue, said expression cassette comprising a modified ORF having a sequence of ORF 201 (SEQ ID NO: 31).

8. A packaging host cell in culture comprising the expression cassette according to claim 1.

9. An rAAV production system comprising (a) a packaging host cell culture comprising the expression cassette according to claim 1, (b) AAV rep sequences, AAV cap sequence, and necessary helper functions.

10. The expression cassette according to claim 1, wherein the expression cassette comprises AAV inverted terminal repeat (ITR) sequences flanking the modified ORF.

11. The recombinant AAV according to claim 7, further comprising regulatory elements operably linked to the 201 (SEQ ID NO: 31) ORF, which direct expression of the 201 gene product in a host cell.

12. The recombinant AAV according to claim 7, further comprising AAV inverted terminal repeat (ITR) sequences flanking the ORF.

13. The recombinant AAV according to claim 12, wherein the ITRs are from a different AAV than the AAV source for the capsid.