US20080227736A1

US20080227736A1 - Targeting Pseudotyped Retroviral Vectors

Info

Publication number: US20080227736A1
Application number: US11/628,586
Authority: US
Inventors: Irvin S.Y. Chen; Kouki Morizono
Original assignee: University of California
Current assignee: University of California
Priority date: 2004-06-03
Filing date: 2005-06-03
Publication date: 2008-09-18
Also published as: US20100184206A1; WO2005118802A3; WO2005118802A2; US9163248B2; US20140017766A1; US8449875B2

Abstract

The present invention relates to retroviral vectors, particularly lentiviral vectors, pseudotyped with Sindbis envelope and targeted to specific cell types via a targeting moiety linked to the envelope.

Description

CROSS-REFERENCES TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Patent Application No. 60/577,248, filed Jun. 3, 2004, the disclosure of which is hereby incorporated herein by reference in its entirety for all purposes.

STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED RESEARCH AND DEVELOPMENT

This invention was made with Government support under Grant Nos. 5R01 DK54912-06 and 5R01AI39975-01, awarded by the National Institutes of Health. The Government has certain rights in this invention.

FIELD OF THE INVENTION

The present invention relates to lentiviral vectors pseudotyped with Sindbis envelope and targeted to specific cell types via a targeting moiety linked to the envelope.

BACKGROUND OF THE INVENTION

Clinically effective gene therapy protocols for various diseases would ideally utilize procedures for efficient and specific targeting of therapeutic genes to affected cells while maintaining stable transduction and long term expression. This would be accomplished by direct injection into the bloodstream followed by homing of the vector to the desired target cells or organs. Thus, there have been many attempts to develop targeted gene transduction systems based upon various viral vectors. Adenovirus and adeno-associated virus vectors have been used in targeted gene delivery strategies because of their simple binding and entry mechanisms. (Nicklin and Baker, Curr Gene Ther. 2, 273-293 (2002)) Although these vectors have been used successfully in vitro, for targeting to specific cells, their usefulness in vivo has been limited by their natural tropism (Muller et al., Nat. Blotechnol. 21, 1040-1046 (2003)), especially to liver cells (Martin et al., Mol. Ther. 8, 485-494 (2003)).
Oncoretroviral- and lentiviral-based vectors have several properties that make them ideal for use in gene therapy (Sandrin et al., Curr. Top. Microbiol. Immunol. 281:137-78, 137-178 (2003)). Efficient integration of retroviral DNA into the host genome enables stable long-term transgene expression. Unlike oncoretroviral vectors, lentiviral vectors are capable of transducing non-dividing cells. The application of specific targeting with retroviral vectors has been problematic and the few studies of retroviral vector targeting in living animals are not efficient (Martin et al., Mol. Ther. 5, 269-274 (2002); Jiang and Domburg, Gene Ther. 6, 1982-1987 (1999)). Inserting ligands, peptides or single chain antibodies into the retroviral receptor binding envelope subunit has been the most common approach used to alter and/or restrict the host range of retroviral vectors (Han et al., Proc Natl. Acad Sci U.S.A. 92, 9747-9751 (1995); Jiang et al., J. Virol. 72, 10148-10156 (1998); Marin et al., J. Virol. 70, 2957-2962 (1996); Martin et al., J. Virol. 73, 6923-6929 (1999); Nilson et al., Gene Ther. 3, 280-286 (1996); Somia et al., Proc Natl. Acad Sci U.S.A. 92, 7570-7574 (1995); Valsesia-Wittmann et al., J Virol 68, 4609-4619 (1994)). Another approach is bridging virus vector and cells by antibodies or ligands (Boerger et al., Proc Natl Acad Sci U.S.A. 96, 9867-9872 (1999); Roux et al., Proc Natl Acad Sci U.S.A. 86, 9079-9083 (1989)). In general, most strategies have suffered from inconsistent specificity and low viral titers as a result of modification of the retroviral envelope (Han et al., Proc Natl. Acad Sci U.S.A. 92, 9747-9751 (1995); Marin et al., J. Virol. 70, 2957-2962 (1996); Nilson et al., Gene Ther. 3, 280-286 (1996); Somia et al., Proc Natl. Acad Sci U.S.A. 92, 7570-7574 (1995); Valsesia-Wittmann et al., J. Virol 68, 4609-4619 (1994); Kasahara et al., Science 266, 1373-1376 (1994)). The modified envelope proteins appear to have specific binding activity but low fusion activity resulting in inefficient entry into cells (Martin et al., J. Virol. 73, 6923-6929 (1999); Zhao et al., Proc Natl. Acad Sci U.S.A. 96, 4005-4010 (1999)). In the absence of specific targeting, current strategies depend upon direct injection to a localized site (Akporiaye and Hersh, Curr. Opin. Mol. Ther. 1, 443-453 (1999)) or, as in the case of the only successful treatment of a heritable disease, X-linked SCID, ex vivo isolation, purification and transduction of target hematopoietic cells (Kohn et al., Nat. Med. 1, 1017-1023 (1995); Cavazzana-Calvo et al., Science 288, 669-672 (2000)).
Sindbis virus is a member of the Alphavirus genius (Schlesinger and Schlesinger, Fundamental Virology 523-539, Raven, Philadelphia (1996)). In mature Sindbis virions the plus-stranded RNA viral genome is complexed with the capsid protein to form an icosahedral nucleocapsid surrounded by a lipid bilayer embedded with two integral membrane glycoproteins, E1 and E2, that form a heterodimer and function as a unit. E1 and E2 are anchored in the membrane independently. E2 binds to the host cell receptor. E1 can mediate membrane fusion as long as it is exposed to the low pH of the endosome and in the absence of a specific interaction with a receptor. Monoclonal antibodies capable of neutralizing virus infection are usually E2 specific, and mutation of E2 is frequently associated with altered host range and virulence. E2 can be modified substantially yet retain viral infectivity. This property of E2 has been exploited to develop Sindbis virus vectors that target specific cells (Ohno et al., Nat. Biotechnol. 15, 763-767 (1997)). However, since Sindbis virus vectors are cytotoxic (Tseng et al. Systemic tumor targeting and killing by Sindbis viral vectors, Nat. Biotechnol. (2003)) and unable to stably transduce their target cells, they cannot be used where stable expression is desired.
We previously found that the Sindbis virus envelope (with E1 and E2) is able to pseudotype oncoretroviruses and lentiviruses (Morizono et al., J. Virol., September; 75.(17.):8015.-20. 75, 8016-8020 (2001)). We used the flexibility of the Sindbis virus E2 protein to our advantage in developing oncoretroviral and lentiviral vectors with the capacity to target specific cells. We previously reported an oncoretroviral and lentiviral gene targeting system based on antibody-mediated specific binding of a modified Sindbis virus envelope (ZZ SINDBIS) that encoded the ZZ domain of protein A. We demonstrated that monoclonal antibodies directed to cell surface antigens can be used to redirect the target specificity of these vectors when pseudotyped with the modified Sindbis envelope. Of particular note, the vectors maintained high viral titers, which could be further increased by simple ultracentrifugation.
Sindbis virus has a broad natural host range. The high-affinity laminin receptor (Wang et al., J. Virol. 66, 4992-5001 (1992)) and heparin sulfate are among the known receptors (Klimstra et al., J, Virol. 72, 7357-7366 (1998)). Their wide distribution and highly conserved nature may be in part responsible for the residual non-specific tropism observed with the ZZ SINDBIS pseudotyped vector. Accordingly, there exists a need for targeted retroviral vectors with decreased binding of endogenous receptors. The present invention fulfills this and other needs.

BRIEF SUMMARY OF THE INVENTION

In order to further reduce the natural tropism of the Sindbis virus envelope and thereby increase the specificity of targeted gene transduction in vivo, we screened a panel of E2 mutants. We identified several mutants within E2 that reduced the endogenous tropism of E2. We utilized our modified ZZ SINDBIS envelope, designated m168, and a lentiviral reporter vector to target P-glycoprotein (P-gp) expressing melanoma cells in the lungs of a murine model for metastatic melanoma. We demonstrate specific targeting of metastatic tumor cells through direct injection of the vector into the bloodstream.
The present invention therefore provides targeted lentiviral vectors that are pseudotyped with mutated Sindbis envelopes. In particular, mutations in the E2 protein and are used to alter viral titer, specificity, specificity index, tropism, and susceptibility to host immune response. The pseudotyped, targeted lentiviral vectors of the invention are used to transduce heterologous genes into a cell and can be used for in vivo and ex vivo therapeutic applications, as well as for diagnostic and research tool applications.
Accordingly, in a first aspect, the invention provides a pseudotyped, targeted retroviral vector comprising:

- a) a mutated Sindbis envelope comprising Sindbis envelope proteins E1, E2, and E3, wherein at least one of E1, E2, or E3 is mutated as compared to a wild-type sequence;
- b) a targeting moiety linked to the Sindbis envelope.

In certain embodiments, the vector further comprises a retroviral-based nucleic acid genome. In certain embodiments, the retroviral-based nucleic acid genome is a lentivirus or an oncoretrovirus genome. The genome can also optionally comprise a heterologous gene.
In certain embodiments, the vector is isolated. Typically, one or more of the E1, E2, or E3 proteins can be mutated at one or more amino acid positions. In one preferred embodiment, the vector comprises the following envelope protein mutations in comparison to wild-type Sindbis virus envelope proteins: (i) deletion of E3 amino acids 61-64; (ii) E2 KE159-160AA; and (iii) E2 SLKQ68-71AAAA (SEQ ID NOs: 3-4). In a further embodiment, the vector additionally comprises the envelope protein mutation E1 AK226-227SG. The vectors can also have a protein binding domain that specifically binds a protein of interest (i.e., a targeting moiety, including an antibody, an integrin, a transferrin receptor). In certain embodiments, the targeting moiety is an antibody.
The invention further encompasses a packaging system comprising a cell comprising one or more nucleic acids encoding the pseudotyped, targeted retroviral vectors described herein. In a related aspect, the invention provides expression vectors comprising one or more nucleic acids encoding Sindbis envelope proteins E1, E2, and E3, wherein at least one of E1, E2 or E3 is mutated as compared to a wild-type sequence.
In another aspect, the invention provides methods of making the pseudotyped, targeted retroviral vectors of the invention, the methods comprising the steps of expressing in a cell one or more nucleic acids comprising Sindbis envelope proteins E1, E2, and E3. The vector can optionally comprise a nucleic acid comprising the retroviral based nucleic acid genome. The Sindbis envelope proteins E1, E2 and E3 and the retroviral-based nucleic acid genome can be encoded on the same or separate nucleic acids.
In a related aspect, the invention also provides methods of transducing cells with a heterologous gene; methods of treating or preventing a disease state; and methods of diagnosing a disease state, the methods comprising the step of contacting the cell with the pseudotyped, targeted retroviral vectors described herein. In certain embodiments the cells are contacted in vitro, ex vivo, or in vivo. The pseudotyped, targeted retroviral vectors are typically administered intravenously.
In a another aspect, the invention provides a method for delivering a pseudotyped, targeted retroviral vector across the blood brain barrier in a subject, the method comprising the step of contacting a cell with a pseudotyped, targeted retroviral vector of the present invention, wherein the targeting moiety specifically binds to a transferrin receptor.

DEFINITIONS

“Sindbis envelope,” “ZZSINDBIS,” and “m168” refer to a viral envelope comprising the Sindbis E1, E2, and E3 proteins. The terms “Sindbis E1 protein,” “Sindbis E2 protein” and “Sindbis E3 protein” or a nucleic acid encoding “Sindbis E1 protein,” “Sindbis E2 protein” and “Sindbis E3 protein” refer to nucleic acids and polypeptide polymorphic variants, alleles, mutants, and interspecies homologs that: (1) have a nucleotide sequence that has greater than about 60% nucleotide sequence identity, 65%, 70%, 75%, 80%, 85%, 90%, preferably 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% or greater nucleotide sequence identity, preferably over a region of at least about 25, 50, 100, 200, 500, 1000, or more nucleic acids, up to the full length sequence, to the nucleotide sequence of E1, E2, and/or E3; (2) bind to antibodies, e.g., polyclonal or monoclonal antibodies, raised against an immunogen comprising an amino acid sequence of an E1, E2, and/or E3 protein, and conservatively modified variants thereof; (3) specifically hybridize under stringent hybridization conditions to an anti-sense strand corresponding to a nucleic acid sequence of E1, E2, and/or E3 and conservatively modified variants thereof; (4) encode a protein having an amino acid sequence that has greater than about 60% nucleotide sequence identity, 65%, 70%, 75%, 80%, 85%, 90%, preferably 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% or greater nucleotide sequence identity, preferably over a region of at least about 25, 50, 100, 200, 500, 1000, or more amino acids, to a E1, E2, and/or E3 protein. The nucleic acids and proteins of the invention include both naturally occurring or recombinant molecules, as well as point mutations, including randomly generated point mutations and those generated by site-directed mutagenesis. E1, E2, and E3 are encoded by a polyprotein, the amino acid sequence of which is provided, e.g., by Accession No. VHWVB, VHWVB2, and P03316; the nucleic acid sequence is provided, e.g., by Accession No. SVU90536 and V01403 (see also Rice & Strauss, Proc. Nat'l Acad. Sci. USA 78:2062-2066 (1981); and Strauss et al., Virology 133:92-110 (1984)). Other Togaviridae family envelopes, e.g., from the Alphavirus genus, e.g., Semliki Forest Virus, Ross River Virus, and equine encephalitis virus, can also be used to pseudotype the vectors of the invention. The envelope protein sequences for such Alphaviruses are known in the art.
“Pseudotype” refers to a virus particle, where the envelope or capsid includes heterologous viral proteins.
“Nucleic acid genome” refers to the genomic or nucleic acid component of a virus particle, which encodes the genome of the virus particle, including any proteins required for replication and/or integration of the genome, if required, and optionally a heterologous protein operably linked to a promoter, the promoter being either native to the protein or heterologous (viral or non-viral). The nucleic acid genome can be based on any virus, and have an RNA or DNA genome, either single stranded or double stranded. Preferably, the nucleic acid genome is from the family Retroviridae.
“Lentiviral vector” refers to viruses comprising nucleic acid genomes based on viruses of the Lentiviral genus of the family Retroviridae. Optionally, the vector encodes a heterologous gene.
“Retroviral vectors,” as used herein, refer to viruses based on viruses of the Retroviridae family. In their wild-type form, retroviral vectors typically contain a genomic nucleic acid. The pseudotyped, targeted retroviral vectors of the invention can optionally comprise a nucleic acid genome. The vectors of the invention can also comprise a heterologous gene.
“Targeting moiety” refers to a heterologous protein linked, either covalently or non-covalently, to a pseudotyped virus particle, typically linked to an envelope protein, e.g., E1, E2, or E3. The targeting moiety binds to a protein on the cell surface of a selected cell type. Representative targeting moieties include antibodies and receptor ligands.
A viral “envelope” protein, or “Env” protein, as used herein, refers to any polypeptide sequence that resides on the surface lipid bilayer of a retroviral virion whose function is to mediate the adsorption to and the penetration of host cells susceptible to infection. A retroviral envelope is formed by a cell-derived lipid bilayer into which proteins encoded by the env region of the viral genome are inserted. Envelope proteins are typically glycoproteins and usually comprise a transmembrane (TM) and a surface (SU) component linked together by disulfide bonds. Virus structure is described in detail in, for example, Coffin, et al., Retroviruses, 1997, Cold Spring Harbor Laboratory Press.
A viral “capsid,” as used herein, refers to the principal structural protein of the virion core derived from the central region of the Gag polyprotein. The capsid protein in a mature viral particle forms a shell surrounding the ribonucleoprotein complex that contains the genomic nucleic acid. This shell, which includes additional proteins, is also referred to as a capsid. A capsid shell can exist as a component of a virion without surrounding a genomic nucleic acid.
A “virion” refers to a retrovirus body, including the outer lipid bilayer which surrounds a capsid shell which in turn surrounds a genomic nucleic acid, when present. A virion of the invention, can, but need not, have a genomic nucleic acid.
“Mutated Sindbis envelope” refers to a point mutation, insertion, or deletion in the amino acid sequence of a wild-type Sindbis E1, E2, or E3 protein. The E1, E2, or E3 protein can have one or more mutations. In addition, combinations of mutations in E1, E2, and E3 are encompassed by the invention, e.g., mutations in E1 and E2, or in E2 and E3, or E3 and E1, or E1, E2, and E3. Exemplary wild type sequences of E1, E2, and E3 proteins from Sindbis strains include Accession No. VHWVB, VHWVB2, and P03316.
“Biological sample” includes sections of tissues such as biopsy and autopsy samples, and frozen sections taken for histologic purposes. Such samples include blood and blood fractions or products (e.g., serum, plasma, platelets, red blood cells, and the like), sputum, tissue, cultured cells, e.g., primary cultures, explants, and transformed cells, stool, urine, etc. A biological sample is typically obtained from a eukaryotic organism, most preferably a mammal such as a primate e.g., chimpanzee or human; cow; dog; cat; a rodent, e.g., guinea pig, rat, mouse; rabbit; bird; reptile; or fish.
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 60% identity, preferably 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or higher identity over a specified region, 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 http://www.ncbi.nlm.nih.gov/BLAST/or the like). Such sequences are then said to be “substantially identical.” This definition also refers to, or may be applied to, the compliment of a test 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 amino acids or nucleotides in length, or more preferably over a region that is 50-100 amino acids or nucleotides in length.
For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Preferably, default program parameters can be used, or alternative parameters can be designated. The sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters.
A “comparison window”, as used herein, includes reference to a segment of any one of the number of contiguous positions selected from the group consisting of from 20 to 600, usually about 50 to about 200, more usually about 100 to about 150 in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned. Methods of alignment of sequences for comparison are well-known in the art. Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat'l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by manual alignment and visual inspection (see, e.g., Current Protocols in Molecular Biology (Ausubel et al., eds. 1995 supplement)).
A preferred example of algorithm that is suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al., Nuc. Acids Res. 25:3389-3402 (1977) and Altschul et al., J. Mol. Biol. 215:403-410 (1990), respectively. BLAST and BLAST 2.0 are used, with the parameters described herein, to determine percent sequence identity for the nucleic acids and proteins of the invention. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/). This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, M=5, N=−4 and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength of 3, and expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89:10915 (1989)) alignments (B) of 50, expectation (E) of 10, M=5, N=−4, and a comparison of both strands.
“Nucleic acid” refers to deoxyribonucleotides or ribonucleotides and polymers thereof in either single- or double-stranded form, and complements thereof. The term encompasses nucleic acids containing known nucleotide analogs or modified backbone residues or linkages, which are synthetic, naturally occurring, and non-naturally occurring, which have similar binding properties as the reference nucleic acid, and which are metabolized in a manner similar to the reference nucleotides. Examples of such analogs include, without limitation, phosphorothioates, phosphoramidates, methyl phosphonates, chiral-methyl phosphonates, 2-O-methyl ribonucleotides, peptide-nucleic acids (PNAs).
Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions) and complementary sequences, as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al., Nucleic Acid Res. 19:5081 (1991); Ohtsuka et al., J. Biol. Chem. 260:2605-2608 (1985); Rossolini et al., Mol. Cell. Probes 8:91-98 (1994)). The term nucleic acid is used interchangeably with gene, cDNA, mRNA, oligonucleotide, and polynucleotide.
A particular nucleic acid sequence also implicitly encompasses “splice variants.” Similarly, a particular protein encoded by a nucleic acid implicitly encompasses any protein encoded by a splice variant of that nucleic acid. “Splice variants,” as the name suggests, are products of alternative splicing of a gene. After transcription, an initial nucleic acid transcript may be spliced such that different (alternate) nucleic acid splice products encode different polypeptides. Mechanisms for the production of splice variants vary, but include alternate splicing of exons. Alternate polypeptides derived from the same nucleic acid by read-through transcription are also encompassed by this definition. Any products of a splicing reaction, including recombinant forms of the splice products, are included in this definition. An example of potassium channel splice variants is discussed in Leicher, et al., J. Biol. Chem. 273(52):35095-35101 (1998).
The terms “polypeptide,” “peptide” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers and non-naturally occurring amino acid polymer.
The term “amino acid” refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids. Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, γ-carboxyglutamate, and O-phosphoserine. Amino acid analogs refers to compounds that have the same basic chemical structure as a naturally occurring amino acid, i.e., an α carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs have modified R groups (e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid. Amino acid mimetics refers to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that functions in a manner similar to a naturally occurring amino acid.
Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes.
“Conservatively modified variants” applies to both amino acid and nucleic acid sequences. With respect to particular nucleic acid sequences, conservatively modified variants refers to those nucleic acids which encode identical or essentially identical amino acid sequences, or where the nucleic acid does not encode an amino acid sequence, to essentially identical sequences. Because of the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode any given protein. For instance, the codons GCA, GCC, GCG and GCU all encode the amino acid alanine. Thus, at every position where an alanine is specified by a codon, the codon can be altered to any of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are “silent variations,” which are one species of conservatively modified variations. Every nucleic acid sequence herein which encodes a polypeptide also describes every possible silent variation of the nucleic acid. One of skill will recognize that each codon in a nucleic acid (except AUG, which is ordinarily the only codon for methionine, and TGG, which is ordinarily the only codon for tryptophan) can be modified to yield a functionally identical molecule. Accordingly, each silent variation of a nucleic acid which encodes a polypeptide is implicit in each described sequence with respect to the expression product, but not with respect to actual probe sequences.
As to amino acid sequences, one of skill will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a “conservatively modified variant” where the alteration results in the substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables providing functionally similar amino acids are well known in the art. Such conservatively modified variants are in addition to and do not exclude polymorphic variants, interspecies homologs, and alleles of the invention.
The following eight groups each contain amino acids that are conservative substitutions for one another: 1) Alanine (A), Glycine (G); 2) Aspartic acid (D), Glutamic acid (E); 3) Asparagine (N), Glutamine (Q); 4) Arginine (R), Lysine (K); 5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); 6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W); 7) Serine (S), Threonine (T); and 8) Cysteine (C), Methionine (M) (see, e.g., Creighton, Proteins (1984)).
A “label” or a “detectable moiety” is a composition detectable by spectroscopic, photochemical, biochemical, immunochemical, chemical, or other physical means. For example, useful labels include ³²P, fluorescent dyes, electron-dense reagents, enzymes (e.g., as commonly used in an ELISA), biotin, digoxigenin, or haptens and proteins which can be made detectable, e.g., by incorporating a radiolabel into the peptide or used to detect antibodies specifically reactive with the peptide.
The term “recombinant” when used with reference, e.g., to a cell, or nucleic acid, protein, or vector, indicates that the cell, nucleic acid, protein or vector, has been modified by the introduction of a heterologous nucleic acid or protein or the alteration of a native nucleic acid or protein, or that the cell is derived from a cell so modified. Thus, for example, recombinant cells express genes that are not found within the native (non-recombinant) form of the cell or express native genes that are otherwise abnormally expressed, under expressed or not expressed at all.
The term “heterologous” when used with reference to portions of a nucleic acid indicates that the nucleic acid comprises two or more subsequences that 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, e.g., a promoter from one source and a coding region from another source. Similarly, a heterologous protein indicates that the protein comprises two or more subsequences that are not found in the same relationship to each other in nature (e.g., a fusion protein).
The phrase “stringent hybridization conditions” refers to conditions under which a probe will hybridize to its target subsequence, typically in a complex mixture of nucleic acids, but to no other sequences. Stringent conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in Tijssen, Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Probes, “Overview of principles of hybridization and the strategy of nucleic acid assays” (1993). Generally, stringent conditions are selected to be about 5-10° C. lower than the thermal melting point (T_m) for the specific sequence at a defined ionic strength pH. The T_mis the temperature (under defined ionic strength, pH, and nucleic concentration) at which 50% of the probes complementary to the target hybridize to the target sequence at equilibrium (as the target sequences are present in excess, at T_m, 50% of the probes are occupied at equilibrium). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. For selective or specific hybridization, a positive signal is at least two times background, preferably 10 times background hybridization. Exemplary stringent hybridization conditions can be as following: 50% formamide, 5×SSC, and 1% SDS, incubating at 42° C., or, 5×SSC, 1% SDS, incubating at 65° C., with wash in 0.2×SSC, and 0.1% SDS at 65° C.
Nucleic acids that do not hybridize to each other under stringent conditions are still substantially identical if the polypeptides which they encode are substantially identical. This occurs, for example, when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code. In such cases, the nucleic acids typically hybridize under moderately stringent hybridization conditions. Exemplary “moderately stringent hybridization conditions” include a hybridization in a buffer of 40% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 1×SSC at 45° C. A positive hybridization is at least twice background. Those of ordinary skill will readily recognize that alternative hybridization and wash conditions can be utilized to provide conditions of similar stringency. Additional guidelines for determining hybridization parameters are provided in numerous reference, e.g., and Current Protocols in Molecular Biology, ed. Ausubel, et al.
For PCR, a temperature of about 36° C. is typical for low stringency amplification, although annealing temperatures may vary between about 32° C. and 48° C. depending on primer length. For high stringency PCR amplification, a temperature of about 62° C. is typical, although high stringency annealing temperatures can range from about 50° C. to about 65° C., depending on the primer length and specificity. Typical cycle conditions for both high and low stringency amplifications include a denaturation phase of 90° C.-95° C. for 30 sec-2 min., an annealing phase lasting 30 sec.-2 min., and an extension phase of about 72° C. for 1-2 min. Protocols and guidelines for low and high stringency amplification reactions are provided, e.g., in Innis et al. (1990) PCR Protocols, A Guide to Methods and Applications, Academic Press, Inc. N.Y.).
“Antibody” refers to a polypeptide comprising a framework region from an immunoglobulin gene or fragments thereof that specifically binds and recognizes an antigen. The recognized immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon, and mu constant region genes, as well as the myriad immunoglobulin variable region genes. Light chains are classified as either kappa or lambda. Heavy chains are classified as gamma, mu, alpha, delta, or epsilon, which in turn define the immunoglobulin classes, IgG, IgM, IgA, IgD and IgE, respectively. Typically, the antigen-binding region of an antibody will be most critical in specificity and affinity of binding.
An exemplary immunoglobulin (antibody) structural unit comprises a tetramer. Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one “light” (about 25 kD) and one “heavy” chain (about 50-70 kD). The N-terminus of each chain defines a variable region of about 100 to 110 or more amino acids primarily responsible for antigen recognition. The terms variable light chain (V_L) and variable heavy chain (V_H) refer to these light and heavy chains respectively.
Antibodies exist, e.g., as intact immunoglobulins or as a number of well-characterized fragments produced by digestion with various peptidases. Thus, for example, pepsin digests an antibody below the disulfide linkages in the hinge region to produce F(ab)′₂, a dimer of Fab which itself is a light chain joined to V_H-C _H1 by a disulfide bond. The F(ab)′₂may be reduced under mild conditions to break the disulfide linkage in the hinge region, thereby converting the F(ab)′₂dimer into an Fab′ monomer. The Fab′ monomer is essentially Fab with part of the hinge region (see Fundamental Immunology (Paul ed., 3d ed. 1993). While various antibody fragments are defined in terms of the digestion of an intact antibody, one of skill will appreciate that such fragments may be synthesized de novo either chemically or by using recombinant DNA methodology. Thus, the term antibody, as used herein, also includes antibody fragments either produced by the modification of whole antibodies, or those synthesized de novo using recombinant DNA methodologies (e.g., single chain Fv) or those identified using phage display libraries (see, e.g., McCafferty et al., Nature 348:552-554 (1990))
For preparation of antibodies, e.g., recombinant, monoclonal, or polyclonal antibodies, many technique known in the art can be used (see, e.g., Kohler & Milstein, Nature 256:495-497 (1975); Kozbor et al., Immunology Today 4: 72 (1983); Cole et al., pp. 77-96 in Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc. (1985); Coligan, Current Protocols in Immunology (1991); Harlow & Lane, Antibodies, A Laboratory Manual (1988); and Goding, Monoclonal Antibodies: Principles and Practice (2d ed. 1986)). The genes encoding the heavy and light chains of an antibody of interest can be cloned from a cell, e.g., the genes encoding a monoclonal antibody can be cloned from a hybridoma and used to produce a recombinant monoclonal antibody. Gene libraries encoding heavy and light chains of monoclonal antibodies can also be made from hybridoma or plasma cells. Random combinations of the heavy and light chain gene products generate a large pool of antibodies with different antigenic specificity (see, e.g., Kuby, Immunology (3^rded. 1997)). Techniques for the production of single chain antibodies or recombinant antibodies (U.S. Pat. No. 4,946,778, U.S. Pat. No. 4,816,567) can be adapted to produce antibodies to polypeptides of this invention. Also, transgenic mice, or other organisms such as other mammals, may be used to express humanized or human antibodies (see, e.g., U.S. Pat. Nos. 5,545,807; 5,545,806; 5,569,825; 5,625,126; 5,633,425; 5,661,016, Marks et al., Bio/Technology 10:779-783 (1992); Lonberg et al., Nature 368:856-859 (1994); Morrison, Nature 368:812-13 (1994); Fishwild et al., Nature Biotechnology 14:845-51 (1996); Neuberger, Nature Biotechnology 14:826 (1996); and Lonberg & Huszar, Intern. Rev. Immunol. 13:65-93 (1995)). Alternatively, phage display technology can be used to identify antibodies and heteromeric Fab fragments that specifically bind to selected antigens (see, e.g., McCafferty et al., Nature 348:552-554 (1990); Marks et al., Biotechnology 10:779-783 (1992)). Antibodies can also be made bispecific, i.e., able to recognize two different antigens (see, e.g., WO 93/08829, Traunecker et al., EMBO J. 10:3655-3659 (1991); and Suresh et al., Methods in Enzymology 121:210 (1986)). Antibodies can also be heteroconjugates, e.g., two covalently joined antibodies, or immunotoxins (see, e.g., U.S. Pat. No. 4,676,980, WO 91/00360; WO 92/200373; and EP 03089).
Methods for humanizing or primatizing non-human antibodies are well known in the art. Generally, a humanized antibody has one or more amino acid residues introduced into it from a source which is non-human. These non-human amino acid residues are often referred to as import residues, which are typically taken from an import variable domain. Humanization can be essentially performed following the method of Winter and co-workers (see, e.g., Jones et al., Nature 321:522-525 (1986); Riechmann et al., Nature 332:323-327 (1988); Verhoeyen et al., Science 239:1534-1536 (1988) and Presta, Curr. Op. Struct. Biol. 2:593-596 (1992)), by substituting rodent CDRs or CDR sequences for the corresponding sequences of a human antibody. Accordingly, such humanized antibodies are chimeric antibodies (U.S. Pat. No. 4,816,567), wherein substantially less than an intact human variable domain has been substituted by the corresponding sequence from a non-human species. In practice, humanized antibodies are typically human antibodies in which some CDR residues and possibly some FR residues are substituted by residues from analogous sites in rodent antibodies.
A “chimeric antibody” is an antibody molecule in which (a) the constant region, or a portion thereof, is altered, replaced or exchanged so that the antigen binding site (variable region) is linked to a constant region of a different or altered class, effector function and/or species, or an entirely different molecule which confers new properties to the chimeric antibody, e.g., an enzyme, toxin, hormone, growth factor, drug, etc.; or (b) the variable region, or a portion thereof, is altered, replaced or exchanged with a variable region having a different or altered antigen specificity.
In one embodiment, the antibody is conjugated to an “effector” moiety. The effector moiety can be any number of molecules, including labeling moieties such as radioactive labels or fluorescent labels, or can be a therapeutic moiety. In one aspect the antibody modulates the activity of the protein.
The phrase “specifically (or selectively) binds” to an antibody or “specifically (or selectively) immunoreactive with,” when referring to a protein or peptide, refers to a binding reaction that is determinative of the presence of the protein, often in a heterogeneous population of proteins and other biologics. Thus, under designated immunoassay conditions, the specified antibodies bind to a particular protein at least two times the background and more typically more than 10 to 100 times background. Specific binding to an antibody under such conditions requires an antibody that is selected for its specificity for a particular protein. For example, polyclonal antibodies can be selected to obtain only those polyclonal antibodies that are specifically immunoreactive with the selected antigen and not with other proteins. This selection may be achieved by subtracting out antibodies that cross-react with other molecules. A variety of immunoassay formats may be used to select antibodies specifically immunoreactive with a particular protein. For example, solid-phase ELISA immunoassays are routinely used to select antibodies specifically immunoreactive with a protein (see, e.g., Harlow & Lane, Antibodies, A Laboratory Manual (1988) for a description of immunoassay formats and conditions that can be used to determine specific immunoreactivity).
By “therapeutically effective dose” herein is meant a dose that produces effects for which it is administered. The exact dose will depend on the purpose of the treatment, and will be ascertainable by one skilled in the art using known techniques (see, e.g., Lieberman, Pharmaceutical Dosage Forms (vols. 1-3, 1992); Lloyd, The Art, Science and Technology of Pharmaceutical Compounding (1999); and Pickar, Dosage Calculations (1999)).

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Schematic representation of FUhLucW, FUIntronRW and CCRMDRsc1. FUhLucW and FUIntronRW have the CMV enhancer and CCRMDRsc1 has the RSV enhancer/promoter substituted for the U3 region of the 5′ LTR. AU3 denotes a deletion in the U3 region of the 3′ LTR that renders the 5′ LTR of the integrated provirus transcriptionally inactive. FUhLucW and FUIntronRW have the Ubiqutin-C promoter as an internal promoter to express humanized Firefly luciferase or humanized Renilla luciferase respectively. CCRMDRsc1 has the CMV promoter as internal promoter to express MDRsc1 (P-glycoprotein). All vectors have the central polypurine tract (cPPT). FUhLucW and FUIntronRW contain the Woodchuck hepatitis virus post transcriptional element (WRE). CCRMDRsc1 has the human hepatitis virus post-transcriptional element (PRE). FUIntronRW has a chimeric intron derived from phRL-CMV.

FIG. 2. HIV vector pseudotyped by ZZ SINDBIS has non-specific infectivity in the absence of target specific antibody in vitro and in vivo. a) 293T cells (2×10⁵) were infected with TRIP GFP (ZZ SINDBIS) (34 ng of HIV p24) with or without anti-HLA (1 μg/ml). For comparison of titers, cells were infected with TRIP GFP (VSV-G) (8 ng of HIV p24). Three days after infection, EGFP expression was analyzed by flow cytometry. The titers of TRIP GFP (ZZ SINDBIS) and TRIP GFP (VSV-G) with 1 μg/ml of anti-HLA were 3×10⁵and 1.3×10⁶EGFP transduction units/100 ng HIV p24. (b) FUhLucW (VSV-G) (15 pg HIV p24), FUhLucW (Sindbis) (30 μg HIV p24) and FUhLucW (ZZ SINDBIS) (30 μg HIV p24) were injected intravenously through the tail vein. Five days after injection, mice were anesthetized and injected intraperitonially with 30 μg of D-luciferin. The reporter gene (Firefly luciferase) expression was imaged using a CCCD camera for 1 min prior to imaging. The acquisition time was determined to avoid saturation of the signal.

FIG. 3. Anti-SINDBIS virus antibody blocked non-specific background infectivity of the ZZ SINDBIS pesudotyped lentiviral vector. TRIP GFP (VSV-G) (3 ng HIV p24), TRIP GFP (Sindbis) (35 ng HIV p24) and TRIP GFP (ZZ SINDBIS 103 ng HIV p24) were incubated with anti-Sindbis virus antibody (0.1% volume) or control antibody for 1 hour at 4° C. The viruses were used for infection of 293T cells (2×10⁵).

FIG. 4. Schematic representation of mutated domains and mutants.

FIG. 5. Analysis of the m168 mutant by flow cytometry and Western blotting. (a) 293T cells (1×10⁵) were infected with 200 μl of unconcentrated TRIP GFP (ZZ SINDBIS) (24 ng HIV p24) or TRIP GFP (m168) (40 ng HIV p24) with or without anti-HLA (1 μg/ml). Three days after infection, EGFP expression was analyzed by flow cytometry. (b) SDS-PAGE and Western blotting of ZZ SINDBIS and m168 pseudotyped virions. Ultracentrifuged samples of HIV vectors (FUhLucW) pseudotyped by ZZ SINDBIS or m168 were lysed and subjected to SDS-polyacrylamide gel electrophoresis and Western blotting as described in the Methods section. The amount of virus for each sample was normalized by the amount of HIV p24 antigen (5 ng/sample). Viral proteins were detected with anti-Sindbis virus mouse immune ascites fluid. The band at approximately 65 kD in the ZZ SINDBIS lane is the chimeric E2 protein. The band at approximately 75 kD in the m168 lane is chimeric E2 protein with uncleaved E3 protein.

FIG. 6. The m168 pseudotyped lentiviral vector has reduced non-specific infectivity in vivo. FUhLucW (ZZ SINDBIS) (30 μg HIV p24) and FUhLucW (m168) were each injected into 3 mice via the tail vein. Five days after injection, mice were anesthetized and injected intraperitonially with D-luciferin (30 μg). The reporter gene (Firefly luciferase) expression was imaged in the dorsal and abdominal aspects of the mice using a CCCD camera for 1 min. The acquisition time was determined to avoid saturation of the signal.

FIG. 7. The m168 pseudotyped lentiviral vector mediates antibody-directed targeted gene transduction after systemic injection into mouse. Renilla luciferase expressing B16F10MDR5 (2×10⁵cells in 150 μl of PBS) were injected into mice via the tail vein. Thirty minutes later, FUhLucW (ZZ SINDBIS) or FUhLucW (m168) to which we had added anti P-glycoprotein monoclonal antibody or isotype (IgG2a) control antibody (10 μg/ml) was injected into the tail vein. The amount of each virus used for injection was normalized to the amount of HIV p24 (36 μg of HIV p24 in 150 μl PBS). Ten days later, the level of metastasis in the lungs of mice that had received B16F10MDR5 was investigated by CCCD imaging to determine the level of Renilla luciferase expression as described in the Methods section. Twelve days after cell and virus injection, virus infection was determined by imaging the expression level of Firefly luciferase reporter gene as described in the Methods section.

FIG. 8. Nucleic acid sequence encoding ZZ SINDBIS.

FIG. 9. Nucleic acid sequence encoding m168.

FIG. 10. Immunohistochemical analysis of metastasized tumors targeted by FUGW (m168) with anti-P-Glycoprotein. Frozen sections were prepared from the lungs of mice injected with B16F10 MDR5 cells and FUGW (m168) plus anti-P-Glycoprotein. Serial 10 μm sections were prepared and processed. a) Slides were stained for hematoxylin-eosin (HE). b) An adjacent serial section (to that shown in (a)) was stained for transgene expression (EGFP) and nuclei (DAPI). c) Another adjacent serial section was stained for melanoma antigen (S-100) and nuclei (DAPI). d) A EGFP and S-100 positive colony stained with HE is pictured at a higher magnification to show the morphology of the colony.

FIG. 11. Confocal microscopy analysis of frozen liver sections prepared from mice which had been injected with B16F10 MDR5 cells, and FUGW (VSV-G) or FUGW (m168) and anti-P-Glycoprotein. The sections were stained for Kupffer cell marker F4/80 (red) and EGFP (green).

FIG. 12. a) Flow cytometric analysis of Mac-1 expression on splenocytes of NOD/SCID mice. b) Flow cytometric analysis of EGFP expression in splenocytes isolated from mice injected with B16F10MDR5 cells, and FUGW (VSV-G) or FUGW (m168) and anti-P-Glycoprotein. The cells were stained to determine Mac-1 expression. EGFP expression in Mac-1 positive and negative population was analyzed.

FIG. 13. (a) B16F10MDR5 cells were injected into mice via the tail vein. Twelve days later, FUhLucW (m168), to which we had added anti-P-glycoprotein monoclonal antibody or isotype control antibody, or FUhLucW (VSV-G) was injected into the tail vein. The amount of each virus used for injection was normalized to the amount of HIV p24 (2.5 μg of HIV p24 in 250 μl PBS). Fifteen days after virus injection, virus infection was determined by imaging the level of Firefly luciferase reporter gene expression. (b) The mice were sacrificed immediately after whole body imaging and each organ was isolated to image luciferase expression.

FIG. 14. Prostate cells can be targeted in vitro through the prostate stem cell antigen. LPSCA4 cells were derived from LNCaP cells after stable transfection of the prostate stem cell antigen (PSCA). 1×10⁵LNCaP and LPSCA4 cells were infected with FUGW pseudotyped with m168 envelope (12 ng HIV-1 p24) without Ab targeting, or with αHLA or 1G8 mAb (1G8 mAB recognizes PSCA (Saffran, et al., Proc Natl Acad Sci (2001) 98:2658-2663)). Three days after infection, eGFP expression was analyzed by flow cytometry (ten thousand events acquired per sample). The x-axis indicates eGFP fluorescence intensity. Percentage and mean flourescence intensity of the positive population (R2) is indicated in each plot. Infection of LPSCA4 cells targeted with 1G8 is comparable to infection targeted with αHLA, whereas in LNCaP cells targeting with 1G8 antibody gives background levels similar to those without any antibody targeting.

FIG. 15. Transcription from the PSE-BC promoter in vitro in prostate cell lines (A) and non-prostate cell lines (B). 1×10⁵cells were infected with lentivirus vectors expressing eGFP under the control of the ubiquitin-C promoter (FUGW) or the PSE-BC promoter (FPGW) pseudotyped with VSV G (40 ng of HIV-1 p24). Three days after infection eGFP expression was analyzed by flow cytometry (ten thousand events acquired per sample). The x-axis indicates eGFP fluorescence intensity. Percentage and mean fluorescence intensity of the positive population (R2) is indicated in each plot. Expression from the PSE-BC promoter is comparable to ubiquitin-C promoter in prostate cell lines and up to 30 times lower in non-prostate cell lines.

FIG. 16. New targeting envelope (2.2), comprised of m168+E1 AK226-227SG, mediated transferrin receptor (TfR) targeted gene transduction more efficiently than previous targeting envelope (m168). 4×10⁴HUVEC cells were infected with lentiviral vector (40 ng HIV-1 p24) pseudotyped with m168 envelope protein or 2.2 envelope protein with or without anti-transferrin receptor antibody (2 μg/ml). The lentiviral vector carried EGFP as reporter gene. Three days after infection, EGFP expression was analyzed by flow cytometry. The X-axis indicates EGFP fluorescence intensity. Percentage of the positive population is indicated in each plot.

FIG. 17. Targeting envelope mediates targeted gene transduction to CNS via transferrin receptor (TfR). Lentiviral vector (3 μg HIV-1 p24) pseudotyped with 2.2 envelope protein was injected into NOD/SCID mice via the tail vein with or without anti-transferrin receptor antibody (50 μg/ml). The lentiviral vector carried Firefly luciferase as reporter gene. Five days after injection, mice were anesthetized and injected intraperitoneally with D-luciferin (30 ng). The reporter gene expression was imaged using a CCCD camera. Luciferase expression from the brain and spinal column was confirmed by removing the skin from the back after sacrifice.

DETAILED DESCRIPTION

Targeted gene transduction to specific tissues and organs via intravenous injection would be the ultimate preferred method of gene delivery. Here, we report successful targeting in a living animal via intravenous injection of a lentiviral vector pseudotyped with a modified chimeric Sindbis virus envelope. After intravenous administration into mice, the previously reported parental vector has non-specific infectivity in liver and spleen due to the residual natural tropism of Sindbis virus. Mutagenesis of domains within the Sindbis envelope ablated regions necessary for this natural tropism. M168 pseudotypes had significantly less non-specific infectivity to liver and spleen and these pseudotypes have high titer and high targeting specificity. A murine cancer model for metastatic melanoma was utilized to test specific targeting with m168. Human P-glycoprotein was ectopically expressed on the surface of melanoma cells and targeted by the m168 pseudotyped lentiviral vector conjugated with anti P-glycoprotein antibody. M168 pseudotypes successfully targeted metastatic melanoma cells growing in the lung after systemic administration via tail vein injection. This targeting technology has applications not only for cancers but also for genetic, infectious and autoimmune diseases.
The present invention therefore provides a pseudotyped virus or viral vector comprising an envelope comprising Sindbis E1, E2, and E3 proteins linked to a targeting moiety. The vector optionally further comprises a viral nucleic acid genome from the Retroviridae family, preferably the lentiviral genus. The vector can also optionally comprise a heterologous gene.
Structurally, at least one of the E1, E2, or E3 proteins has one or more mutations (preferably point mutations) in comparison to a wild type sequence in order to provide altered titer, specificity, specificity index, tropism, or host immune reaction. Combinations of mutated E1, E2, and E3 are also contemplated by the invention. Functionally, the mutated Sinbis viral envelope proteins of the present invention have a decreased ability to bind to endogenous receptors, including glycosaminoglycans (e.g., heparin sulfate). In certain embodiments, the pseudotyped virus vectors are isolated.
In certain embodiments, the pseudotyped viruses comprise one or more of the following mutations in a wild-type Sindbis or the Sindbis ZZ envelope sequence (SEQ ID NO:2): m1 (deletion of E3 amino acids 61-64), m2 (E2 R1D), m3 (m1+m2), m4 (deletion of E2 amino acids 68-71), m5 (E2 S114 P), m6 (E2 KE159-160AA), m7 (E2 E216A T218A), m8 (E2 SLKQ68-71AAAA), m9 (E3 RSKRS60-64AAAAA), m16 (m1+m6), m17 (m1+m7), m18 (m1+m8) or E1 AK226-227SG. In one embodiment, the mutation is exemplified by the m168 sequence (SEQ ID NO:4), which comprises the mutations m1 (deletion of E3 amino acids 61-64), m6 (E2 KE159-160AA), and m8 (E2 SLKQ68-71AAAA). In another embodiment, the m168 sequence comprises a further mutation in the E1 domain that makes the m168 titer 2-10 fold higher. The sequence “aagccttccgccaag” on the sequence of m168 was modified to “aagccttcctccggg” (SEQ ID NOs: 5 and 6). In this embodiment, the m168 sequence is further modified to eliminate cholesterol dependence for cell entry, (e.g. E1 AK226-227SG).
Mutations into one or more of the Sindbis viral envelope protein sequences can be introduced using any known methods in the art. Mutations can be targeted or random. For example, targeted mutations can be introduced using site-directed mutagenesis, for instance employing overlapping PCR or overlap extension PCR (see, for example, Aiyar, et al., Methods Mol Biol (1996) 57:177-91; and Pogulis, et al., Methods Mol Biol (1996) 57:167-76). Alternatively, mutations can be introduced by taking advantage of the error prone replication process of Sindbis viruses, which lack proof-reading and mismatch repair activities, and recombination between quasispecies in a virus population, for instance, by using a replication competent virus (see, Domingo and Holland, Annu Rev Microbiol (1997) 51:151-178). Mutant Sindbis virus envelope proteins of particular interest have a diminished ability to bind to endogenous receptors and therefore demonstrate decreased background infectivity in comparison to wild-type sequences. Preferably, the mutated Sinbis virus envelope proteins of the present invention have a decreased ability to bind to glycosaminoglycans (GAGs), including heparin sulfate (HS), in comparison to wild-type sequences.
The targeting moiety is covalently or non-covalently linked to the E1, E2, or E3 protein, preferably the E2 or E3 protein, or is linked to another portion of the envelope. In one embodiment, the targeting moiety is linked to E1, E2, or E3 via non-covalent interactions with a protein binding domain, where the protein binding domain is fused with E1, E2, or E3. In one embodiment, the protein binding domain is fused with E2 or E3. Exemplary protein binding domains include, e.g., the ZZ domain of protein A, streptavidin, avidin, a leucine zipper, a STAT protein N terminal domain, an FK506 binding protein, integrin binding sequence “4C-RGD” (CDCRGDCFC encoded by tgcgactgtagaggcgactgtttctgc), and transferrin receptor targeting sequence “B6” (GHKAKGPRK encoded by ggacataaagctaagggtcctagaaag) (see, e.g., O'Shea, Science 254: 539 (1991), Barahmand-Pour et al., Curr. Top. Microbiol. Immunol. 211:121-128 (1996); Klemm et al., Annu. Rev. Immunol. 16:569-592 (1998); Klemm et al., Annu. Rev. Immunol. 16:569-592 (1998); Ho et al, Nature 382:822-826 (1996); Pomeranz et al., Biochem. 37:965 (1998); and Xia, et al., J Virol (2000) 74:11359-66). In another embodiment, the targeting moiety is a fusion protein with either the E1, E2, or E3 protein. In one embodiment, the targeting moiety is fused with the E2 or the E3 protein. The targeting moiety can be, e.g., an antibody, such as a monoclonal or single chain antibody that specifically binds to an antigen or a cell surface molecule, or a ligand or binding partner of a cell surface molecule.
The targeting moiety can target normal or diseased tissue. For example, the targeting antigen can be directed to a transferrin receptor for delivery of the present vectors across the blood-brain barrier. The targeting moiety also can be directed to marker proteins indicative of diseases including cancers (e.g., breast, lung, ovarian, prostate, colon, lymphoma, leukemia, and melanoma); autoimmune disease (e.g., myasthenia gravis, multiple sclerosis, systemic lupus erythymatosis, rheumatoid arthritis, and diabetes mellitus); infectious disease, including infection by HIV, HCV, HBV, CMV, and HPV; and genetic diseases including sickle cell anemia, cystic fibrosis, Tay-Sachs, β-thalassemia, neurofibromatosis, polycystic kidney disease, hemophilia, etc. In certain embodiments, the targeting moiety targets a cell surface antigen specific to a particular cell or tissue type, e.g., lymphocytes, myocytes, keratinocytes, neurons, hepatocytes, lung, kidney, muscle, vascular, thyroid, ocular, breast, ovarian, testis, prostate tissue.
Exemplary antigens and cell surface molecules for targeting include, e.g., P-glycoprotein, Her2/Neu, erythropoietin (EPO), epidermal growth factor receptor (EGFR), vascular endothelial growth factor receptor (VEGF-R), cadherin, carcinoembryonic antigen (CEA), CD4, CD8, CD19, CD20, CD33, CD34, CD45, CD117 (c-kit), CD133, HLA-A, HLA-B, HLA-C, chemokine receptor 5 (CCR5), stem cell marker ABCG2 transporter, ovarian cancer antigen CA125, immunoglobulins, integrins, prostate specific antigen (PSA), prostate stem cell antigen (PSCA), dendritic cell-specific intercellular adhesion molecule 3-grabbing nonintegrin (DC-SIGN), thyroglobulin, granulocyte-macrophage colony stimulating factor (GM-CSF), myogenic differentiation promoting factor-1 (MyoD-1), Leu-7 (CD57), LeuM-1, cell proliferation-associated human nuclear antigen defined by the monoclonal antibody Ki-67 (Ki-67), viral envelope proteins, HIV gp120, transferrin receptor, etc. Any cell surface protein, known in the art or yet to be identified, preferentially expressed on a particular cell or tissue type can find use as a potential target for the pseudotyped, targeted vector of the invention.
The pseudotyped, targeted vectors of the invention can optionally comprise a genomic nucleic acid. The nucleic acid genome can be from any suitable virus and in one embodiment, is derived from the Retroviridae family of viruses, e.g., from the lentiviral genus: HIV1, HIV2, SIV, FIV, BIV, Visna, CAEV, and EIAV; and from oncogenic retroviruses or oncoretroviruses, e.g., avian sarcoma/leucosis viruses (ASLV); mammalian C-type viruses (murine leukemia viruses (MuLV); feline leukemia viruses (FeLV)); B-type viruses (mouse mammary tumor viruses (MMTV); D-type viruses; and HTLV-BLV group of viruses (human T cell leukemia viruses (HTLV). Preferably, the oncogenic retroviruses lack an oncogene. Retroviruses are reviewed in Coffin, et al., Retroviruses, 1997, Cold Spring Harbor Laboratory Press. The nucleic acid genome is based on any suitable virus, and contains genetic components and encodes proteins so that the genome can be replicated and transcribed. However, vectors of the present invention can be replication competent or replication incompetent. In one embodiment, the nucleic acid genome is from the family Retroviridae and contains genetic components and encodes proteins so that it can be reverse transcribed and integrated into the host genome. Optionally, the genome is replication incompetent so that it cannot make productive, infectious viral particles. In certain embodiments, the genome is replication competent. Retroviral nucleic acid genomes known to those of skill in the art can be used in the invention, or made according to methods known to those of skill in the art (see, Coffin, et al, supra). Within the genome, the E1, E2, E3 and optional heterologous gene sequences can be encoded as individual polypeptides, or one or more fusion proteins. The E1, E2, E3 and optional heterologous gene sequences can be on the same or separate nucleic acid sequences. The nucleic acid genome can be RNA or DNA.
Vectors that do not comprise a genomic nucleic acid find use in the targeted delivery of a desired protein. For example, a protein to be delivered can be expressed as a fusion protein with a viral protein that is incorporated into a viral capsid. Viral proteins that are incorporated into a capsid shell, including, for example, the virion-associated regulatory proteins, viral protein r (VPR), viral protein x (VPX); and integrase, are well known in the art. See, for example, Wu, et al., J Virol (1995) 69:3389-98; and Katz, et al., Virology (1996) 217:178-90.
The genome also optionally comprises a heterologous gene operably linked to a promoter, either a viral promoter or a heterologous promoter. The heterologous gene can be a marker gene, a cytotoxic gene, a gene encoding an inhibitory sequence or protein for therapeutic applications, or a gene encoding a wild type protein for gene therapy applications. Exemplary marker genes include luciferase, a fluorescent protein (green fluorescent protein, red fluorescent protein, yellow fluorescent protein), and β-galactosidase. Exemplary cytotoxic genes include ricin, tumor necrosis factor (TNF) and apoptin. Exemplary inhibitory sequences include those that encode antisense RNA, small inhibitory RNA, oligonucleotide aptamers, and antibodies. Exemplary wild-type proteins for gene therapy applications include glial cell-derived neurotrophic factor (GDNF), Factor VIII, adenosine deaminase (ADA), hypoxanthine guanine phosphoribosyl transferase, LDL receptor, cystic fibrosis (CF) transmembrane conductance regulators (CFTR), hexosaminidase gene (HEXA), hemoglobin, β-globin, proliferative kidney disease 1 gene (PKD1) and tumor suppressor genes including neurofibromatosis gene (NF1 and NF2), breast cancer marker genes (BRCA1 and BRCA2), retinoblastoma gene (Rb), von-Hippel Lindau gene (VHL). Additional heterologous genes of use in the present invention are described in, for example, Strachan and Read, Human Genetics 2, 2^ndEd., 1999, BIOS Scientific Publishers Ltd.; Gene Therapy in Inflammatory Diseases, Evans and Robbing, eds., 2000, Springer Verlag; Vascular Disease: Molecular Biology and Gene Therapy Protocols, Baker, ed., 1999, Human Press; Cancer Gene Therapy, Curiel and Douglas, 2005, Human Press; Gene Therapy for Autoimmune Diseases, 2004, Kluwer Academic Pub.; and Progress In Gene Technology And Skin Gene Therapy: Special Issue Cells Tissues Organs 2004, Hengge, ed., 2004, S Karger Pub.
The promoter can be a constitutive promoter (e.g., ubiquitin, actin) or an inducible promoter (e.g. metallothionein). In certain embodiments, the promoter allows for preferential expression of a heterologous gene in tissues of interest, including for example, prostate tissue (e.g., a prostate specific antigen (PSA) promoter (PSE-BC; see, Adams, et al., Nat Med (2002) 8:891-897; and Wu, et al., Gene Ther (2001) 8:1416-1426); testis tissue (Grimes, Gene (2004) 343:11-22; cardiovascular tissue (Beck, et al., Curr Gene Ther (2004) 4:457-467; breast tissue (e.g., a mammoglobin promoter; see, Goedegebuure, et al., Curr Cancer Drug Targets (2004) 4:531-542); thyroid tissue (e.g., a thyroglobulin promoter; see, DeGroot, and Zhang, Curr Drug Targets Immune Endocr Metabol Disord (2004) 4:235-44); a gastrointestinal tissue (e.g., UDP glucuronosyltransferase promoter; see, Gregory, et al., Toxicol Appl Pharmacol (2004) 199:354-63); and cervical tissue (see, Rein, et al., J. Gene Med (2004) 6:1281-9). Tissue specific promoters of use in cancer gene therapy are reviewed in Saukkonen and Hemminki, Expert Opin Biol Ther (2004) 4:683-96. Tissue specific promoters of use in the gene therapy treatment of prostate cancer are reviewed in Shiradawa, et al., Mol Urol (2000) 4:73-82. Additional tissue specific promoters of use in the present vectors and methods include those reviewed in Hart, Semin Oncol (1996) 23:154-8.
Packaging cells and systems, packaging techniques and vectors for packaging the nucleic acid genome into the pseudotyped viral particle are also known to those of skill in the art and can be made according to methods known to those of skill in the art (see, for example, Polo, et al, Proc Natl Acad Sci USA, (1999) 96:4598-4603). Methods of packaging include using packaging cells that permanently express the envelope components, or by transiently transfecting cells with plasmids encoding the components of the vector, or by using an adenoviral system that encodes the components of the vector. Virus packaging cells and kits are commercially available, for example, from BD Sciences/Clontech in Mountain View, Calif.).
The pseudotyped virus of the invention can be used for diagnostic and therapeutic applications, as well as for research tool applications. Diagnostic applications include both in vitro, ex vivo, and in vivo uses, e.g., in vivo imaging. Therapeutic applications include both in vivo, in vitro, and ex vivo uses. For example, a virus particle of the invention can be administered to a subject via IV injection to treat or prevent cancers, e.g., breast, lung, ovarian, prostate, colon, lymphoma, leukemia, and melanoma; autoimmune disease such as myasthenia gravis, multiple sclerosis, systemic lupus erythymatosis, rheumatoid arthritis, and diabetes mellitus; infectious disease such as infection by HIV, HCV, HBV, CMV, and HPV; and genetic diseases such as sickle cell anemia, cystic fibrosis, Tay-Sachs, β-thalassemia, neurofibromatosis, polycystic kidney disease, hemophilia, etc. For in vivo applications, preferably the targeting moiety is covalently linked. The virus particles of the invention can also be administered ex vivo, e.g., to whole bone marrow by targeting CD34+ cells with the targeting moiety. In this embodiment, the targeting moiety can be covalently or non-covalently linked (e.g., via protein A or its ZZ domain). The virus particles can be used for diagnostic applications with heterologous marker genes, and can be used as research tools to transduce specific cell types. The targeted Sindbis envelope of the invention can also be used to target cell to cell interactions, by expressing the targeted envelope in a cell such as a lympohocyte, and then allowing the cell to contact the targeted cell in vivo, in vitro, or ex vivo.
The present invention also provides methods of purifying the virus from cells. In one embodiment, the virus is purified from cells by the following method: Virus is filtered through 0.22-microM-pore-size filter before concentration. Virus (30 mL) was loaded onto sucrose cushion (7 mL) and spinned using SW32 (Beckman) roter. 20% Sucrose (wt/wt) in 1×PBS with 1 mM EDTA was used for cushion. The spinning condition is 40000×g for 90 min at 4 degree. The supernatant is discarded and pellet is resuspended in 300 microL of Hanks Balanced Salt Solution. The concentrated virus is filtered again using same size filter before administration into animal.
The present invention also provides methods of transducing cells with the virus, as follows: some primarily hematopoietic cells are resistant to gene transduction (primary T cells and stem cell) in vitro. However changing the pH of the medium (7.4 to 5.5) during gene transduction makes gene transduction efficiency higher. (3-20 fold). This method is useful for ex vivo and in vitro transduction of some cell types.

Pharmaceutical Compositions And Administration

Pharmaceutically acceptable carriers are determined in part by the particular composition being administered (e.g., nucleic acid, protein, virus or transduced cell), as well as by the particular method used to administer the composition. Accordingly, there are a wide variety of suitable formulations of pharmaceutical compositions of the present invention (see, e.g., Remington's Pharmaceutical Sciences, 17^thed., 1989). Administration can be in any convenient manner, e.g., by injection, oral administration, inhalation, transdermal application, or rectal administration.
In the practice of this invention, compositions can be administered, for example, by intravenous infusion, orally, topically, intraperitoneally, intravesically or intrathecally. Parenteral administration and intravenous administration are the preferred methods of administration. The formulations of commends can be presented in unit-dose or multi-dose sealed containers, such as ampules and vials.
Injection solutions and suspensions can be prepared from sterile powders, granules, and tablets of the kind previously described. Cells transduced by nucleic acids for ex vivo therapy can also be administered intravenously or parenterally as described above.
The dose administered to a patient, in the context of the present invention should be sufficient to effect a beneficial therapeutic response in the patient over time. The dose will be determined by the efficacy of the particular vector employed and the condition of the patient, as well as the body weight or surface area of the patient to be treated. The size of the dose also will be determined by the existence, nature, and extent of any adverse side-effects that accompany the administration of a particular vector, or transduced cell type in a particular patient.
In determining the effective amount of the vector to be administered in the treatment or prophylaxis of conditions owing to diminished or aberrant expression of the protein, the physician evaluates circulating plasma levels of the vector, vector toxicities, progression of the disease, and the production of anti-vector antibodies. In general, the dose equivalent of a naked nucleic acid from a vector is from about 1 μg to 100 μg for a typical 70 kilogram patient, and doses of vectors are calculated to yield an equivalent amount of therapeutic nucleic acid.
For administration, compounds and transduced cells of the present invention can be administered at a rate determined by the LD-50 of the inhibitor, vector, or transduced cell type, and the side-effects of the inhibitor, vector or cell type at various concentrations, as applied to the mass and overall health of the patient. Administration can be accomplished via single or divided doses.

EXAMPLES

The following examples are offered to illustrate, but not to limit the claimed invention.

Example 1

Targeted Lentiviral Vectors with Mutated Sindbis Envelopes

Methods

Plasmid construction. All mutants of pIntron ZZ SINDBIS were generated using a site directed mutagenesis kit (Stratagene, La Jolla, Calif.). Initially, the envelope region of pIntronZZ SINDBIS was cloned into pBS-SKII. Mutagenesis was performed using various oligonucleotide corresponding to the mutations (Table 1) following the manufacturer's protocol. The mutations were confirmed by sequence analysis. The sequenced regions were then cloned back into pIntron ZZSINBIS. CCR MDRsc1 was constructed from pRRL-cPPTCMV-X-PRE (kindly provided by Dr. William Osborne) (Barry et al., Hum. Gene Ther. 12, 1103-1108 (2001)) and ha-MDRsc (kindly provided by Dr. Brian Sorrentino) (Bunting et al., Blood 92, 2269-2279 (1998)). FUhLucW was constructed from FUGW (kindly provided by Dr. David Baltimore) and pGL3-Basic (Promega, Madison, Wis.). FUIntronRW was constructed from FUGW and phRL-CMV (Promega).

TABLE 1

Sindbis Envelope Mutations

* Selectivity Index

** Titer (% of ZZ SINDBIS)

Mutant	Domain	Details of mutation	293T	HepG2	293T	HepG2

ZZ SINDBIS			9	4.9	100	100
m1	R1	deletion of E3 a.a. 61-64	21	11.4	38	69
m2	R1	E2 R1D	7.5	4.6	85	97
m3	R1	m1 + m2	21	9.8	30	64
m9	R1	E3 RSKRS60-64AAAAA	32	9.2	47	71
m4	R2	deletion of E2 a.a. 68-71	11	5.3	30	59
m8	R2	E2 SLKQ68-71AAAA	17	5.7	101	78
m5	R3	E2 S114P	***	***	***	***
m6	R4	E2 K159A E160A	10	4.9	113	95
m7	R5	E2 E216A T218A	11	4.6	111	86

1st combination of mutations

ZZ SINDBIS			34	6.9	100	100
m1	R1	deletion of E3 a.a. 61-64	132	13.2	40	109
m16	R1 + 4	m1 + m6	151	14.9	53	115
m17	R1 + 5	m1 + m7	80	12.0	21	87
m18	R1 + 2	m1 + m8	120	15.4	42	105

2nd combination of mutations

ZZ SINDBIS			42	6.3	100	100
m1	R1	deletion of E3 a.a. 61-64	127	14.8	68	133
m168	R1 + 2 + 4	m1 + m6 + m8	125	18.6	89	143

The results are average of three independent infection and flow cytrometry. a.a. is abbreviation of amino acid
* Selectivity index was calculated as follows: (% EGFP + cells infected in the presence of anti-HLA monoclonal antibody)/(% EGFP + infected in the absence of antibody)
** Titer was calculated as follows: (% EGFP positive cells infected by lentiviral pseudotyped by each mutant in the presence of anti-HLA monoclonal antibody)/(% EGFP positive cells infected by lentiviral vector pseudotyped by ZZ SINDBIS in the presence of anti-HLA monoclonal antibody) × 100
*** m5 did not have any infectivity.

Cells. Hep G2 cells and B16F10 cells were purchased from ATCC and cultured in DMEM (Invitrogen, Carlsbad, Calif.) containing FCS (10%) (Hycione, Logan, Utah), penicillin (100 units/ml) and streptomycin (100 μg/ml). 293T cells were grown in IMDM (HRH Biosciences, Lenexa, Kans.) containing FCS (10%), penicillin (100 units/ml) and streptomycin (100 μg/ml). B16F10MDR 5 cells were generated by stable gene transduction of CCRMDRsc1 (VSV-G). After lentiviral gene transduction, cells were cloned by limiting dilution. The clones were analyzed for the expression of MDR-1 (P-gp) by flow cytometry. The clone designated B16F10MDR5 showed the highest level of the expression of the MDR-1 gene and was used for all further experiments.
Virus production. All lentivirus vectors were produced by calcium phosphate-mediated transient transfection of 293T cells. 293 T cells (1.8×10⁷) were transfected with pCMVR8.2DVPR (12.5 μg), the appropriate lentiviral vector plasmid (12.5 μg), and pHCMVG (5 μg) or pIntron SINDBIS, pIntron ZZ SINDBIS or mutants derived thereof (10 μg). For in vitro screening of the mutant pIntron ZZ SINDBIS, TRIP GFP (kindly provided by Dr. Pierre Charneau) (Zennou et al., Cell, 101, 173-185 (2000)) was used as the lentiviral vector plasmid. CCRMDRsci was used as the lentiviral vector and pHCMVG as the envelope plasmid for generation of the MDR-1 expressing lentiviral vector. The Renilla luciferase expressing lentiviral vector was generated using FUIntronRW as the lentiviral vector plasmid and pHCMVG as the envelope plasmid. FUhLucW was used as the lentivirus vector for generation of the humanized Firefly luciferase expressing lentivirus vector.
Antibodies. Anti-HLA ABC was purchased from Sigma (St. Louis, Mo.). Anti-P-gp (multiple drug resistant gene-1 product) was purchased from Kamiya Biomedical Company (Seattle, Wash.). Anti-Sindbis virus ascites fluid and control ascites fluid were purchased from ATCC. Anti-mouse IL-2 receptor beta-chain (TM-Beta 1) was kindly provided by Dr. Masayukiso Miyasaka.
In vitro infection of cells. 293T cells (5×10⁴) and HepG2 cells (5×10⁴) were seeded on 24-well plates the day before infection. The cells were incubated with 200 μl of unconcentrated HIV vector (TRIP GFP) pseudotyped by ZZ SINDBIS or its mutants with or without anti-HLA (1 μg/ml) for 2 hours at 37° C. with 5% CO₂. The virus was removed and replaced with fresh medium (1 ml). Three days post infection; the cells were trypsinized and analyzed by flow cytometry. Background infectivity of TRIP GFP (ZZ SINDBIS) was blocked by anti-Sindbis virus ascites fluid. Anti-Sindbis virus ascites fluid or control acites fluid was added to unconcentrated TRIP GFP (VSV-G), TRIP GFP (Sindbis) or TRIP GFP (ZZ SINDBIS) (0.1% volume) and incubated for 1 hour at 4° C. The virus was used for infection of 293T cells and infectivity was analyzed as previously described.
Immunoblot assay. The HIV vectors (FUhLucW) pseudotyped with ZZ SINDBIS or m168 were concentrated 100-fold by ultracentrifugation and resuspended in PBS. The concentrated virus was mixed with equal volume of electrophoresis loading buffer [glycerol (20%), β-mercaptoethanol (10%), sodium dodecyl sulfate (4%), Tris-HCl pH 6.8 (125 mM), bromophenol blue (0.02%)] and boiled for 5 min. The amount of virus sample was normalized to the amount of HIV p24 (5 μg of p24/lane). The samples were subjected to electrophoresis through an SDS polyacrylamide gel (10%) as described previously (Morizono et al., J. Virol., September; 75.(17.):8015.-20. 75, 8016-8020 (2001)). Immunoblot analysis was performed with anti-Sindbis virus ascites fluid and horseradish peroxidase-conjugated anti-mouse antibody (Santa Cruz Biotechnology, Santa Cruz, Calif.). The protein bands were visualized by enhanced chemiluminescence (Pierce, Rockford, Ill.).
In vivo analysis of background infection. HIV vector (FUhLucW) pseudotyped by VSV-G, Sindbis virus, ZZ SINDBIS or m168 were injected into the tail vein of 6-week old female NOD/SCID mouse. The amount injected for each virus was normalized to the amount of HIV p24 (30 pg of HIV p24 in 300 μl PBS). Five days post injection, the mice were anesthetized and injected with D-luciferin (3 mg/mouse) (Xenogen, Alameda, Calif.) intraperitonially. CCCD images were obtained using a cooled IVIS CCD camera (Xenogen), and analyzed with IGOR-PRO Living Image Software. The data acquisition was performed 20 min after D-luciferin injection for 1 min. Mice were sacrificed by CO₂narcosis after CCCD imaging. The organs from each mouse were excised and genomic DNA was isolated using a Dneasy kit (QIAGEN, Valencia, Calif.) following the manufacturer's protocol. Quantitation of the vector copy number and cell number in the DNA isolate was performed by using SYBRgreen real time PCR kit (QIAGEN) and an ABI PRISM 7700 sequence detector (Perkin Elmer, Wellesley, Mass.). The primers for the analysis of vector copy number (Firefly Luciferase) were Fluc-a (gagatacgccctggttcctg) and Fluc-b (gcatacgacgattctgtgatttg). The standard for quantitation of vector copy number was FUhLucW. The primers for the analysis of cell number (mouse beta actin) were beta-actin-F (caactccatcatgaagtgtgac) and beta-actin-R (ccacacggagtacttgcgctc). The standard for the analysis of cell number was made using genomic DNA isolated from normal mouse peripheral blood mononuclear cell.
Targeted infection of melanoma cells in vitro. B16F10MDR5 cells (1×10⁴) were seeded on 48-well plate at the day before infection. The cells were incubated with FUhLucW (ZZ SINDBIS) or FUhLucW (m168) (10 ng HIV p24) with or without anti-P-gap antibody (1 μg/ml) for 2 hours at 37° C. with 5% CO₂. The virus was subsequently removed and replaced with fresh medium (500 μl). Three days post infection, cells were lysed in passive lysis buffer (Promega) and Firefly luciferase activity was measured following the manufacturer's protocol.
Targeted infection of melanoma cells in vivo. To express Renilla luciferase as a marker, the human P-gp expressing mouse cell line, B16F10MDR5, was transduced by the lentiviral vector FUIntronRW (VSV-G). One day prior to subsequent cell and virus injection, TMbeta-1 (1 mg) was injected into 6-week old female NOD/SCID mice. Renilla luciferase expressing B16F10MDR5 (2×10⁵cells in 150 μl of PBS) were injected into mouse via the tail vein. Thirty minutes later, FUhLucW (ZZ SINDBIS) or FUhLucW (m168), to which we had added anti P-glycoprotein monoclonal antibody or Isotype (IgG2a) control antibody (10 μg/ml) was injected into the tail vein. The amount of each virus used for injection was normalized to the amount of HIV p24 (36 pg of HIV p24 in 150 μl PBS). Ten days after cells and virus injection, lung metastasis of B16F10MDR5 was determined by imaging the Renilla luciferase. Mice were anesthetized and coelenterazine (20 μg) (Prolume, Pinetop, Ariz.) was injected via the tail vein. Data acquisition was performed directly following coelenterazine injection for 1 min. Twelve days after cell and virus injection, virus infection was determined by imaging the expression of Firefly luciferase reporter gene. Mice were anesthetized and injected intraperitonially with D-luciferin (6 mg/mouse). Imaging was performed as previously described. Mice were sacrificed after imaging using D-Luciferin. To isolate tumor cells, whole lung was isolated, ground and passed through a cell strainer (BD, San Jose, Calif.). The cells were cultured for 10 days in DMEM supplemented with FCS (20%), penicillin (100 units/ml) and streptomycin (100>ag/ml). Cultured cells were trypsinized, counted, stained by anti-P-Glycoprotein monoclonal antibody conjugated to PE (BD) and analyzed by flow cytometry. More than 99% of cells expressed P-gp demonstrating that nearly all of the cells we harvested were B16F10MDR5 cells. Cells were not recovered from control mice that did not receive tumor cells. One million cells were then harvested and lysed in passive lysis buffer (200 μl) (Promega) and analyzed for Firefly luciferase activity following the manufacturer's protocol. Genomic DNA was isolated using a DNeasy kit (QIAGEN). The primers and standard for quantitation of vector copy number were the same as those used to quantitate the background level of infection as previously described. Quantitation of the cell number was performed using primers for murine beta-actin as described above and the standard was generated by using known numbers of B16F10MDR5 cells.

Results

We previously demonstrated specific targeting of our ZZ SINDBIS lentiviral vector and murine retroviral vectors to CD4⁺ and HLA⁺, cells using monoclonal antibodies specific for CD4 and HLA (Morizono et al., J. Virol., September; 75.(17.):8015.-20. 75, 8016-8020 (2001)). These vectors demonstrated an approximately 30-fold selectivity for infection of target cells in the presence of the specific cell surface monoclonal antibody. Our goal is to utilize these vectors for direct targeting of gene therapy vectors to specific target cells via direct injection in the bloodstream. We utilized lentiviral vectors bearing two distinct types of reporter genes to assess transduction efficiency (FIG. 1). The EGFP-expressing virus vector allowed a quantitative assessment of infectivity in vitro as monitored by flow cytometry (Zennou et al., Cell, 101, 173-185 (2000)). We utilized both Firefly and Renilla luciferase-expressing virus vectors and non-invasive cooled charged-coupled device (CCCD) imaging to quantitate the level of specific targeting of vectors in live mice (Bhaumik and Gambhir, Proc Natl. Acad. Sci. U.S.A. 99, 377-382 (2002)).

HIV Vector Pseudotyped by ZZ Sindbis has Non-Specific Infectivity In Vivo.

FIG. 2 a shows the typical enhancement in infectivity of the ZZ SINDBIS pseudotyped virus vector in vitro using a monoclonal antibody directed to HLA. We observed approximately a 30-fold enhancement of EGFP⁺ cells in the presence of anti-HLA antibody relative to that seen in the absence of monoclonal antibody. As a comparison, VSV-G envelope pseudotyped virus infected cells at a high level in the absence of antibody. The titer of ZZ SINDBIS virus is usually about 5-fold lower than that of VSV-G pseudotyped virus but, like VSV-G pseudotypes can be further concentrated at least 100-fold by ultracentrifugation.
ZZ SINDBIS pseudotyped virus vectors expressing Firefly luciferase were utilized to quantitate the level and specificity of targeting in transduced cells in the organs of live mice. We used a lentiviral vector containing the Ubiquitin-C promoter for in vivo experiments since this vector has been shown to express well in all mouse tissues (Lois et al., Science, 295, 868-872 (2002)). ZZ SINDBIS virus vectors were injected into the tail vein in the absence of monoclonal antibody. The expression of virus was monitored by luciferase expression utilizing CCCD imaging (FIG. 2 b). Lentiviral vectors pseudotyped with each of the envelopes, VSV-G, wild type Sindbis, and ZZ SINDBIS infected both liver and spleen. VSV-G and wild type Sindbis pseudotypes resulted in a strong signal. Although ZZ SINDBIS gave a weaker signal, consistent with its infectivity in vitro, there was still clear expression in liver and spleen. Injection of recombinant luciferase did not show a signal in major organs, indicating that the signal observed with ZZ SINDBIS was due to infection of cells in the organs (data not shown). We verified infection of Sindbis and ZZ SINDBIS in the liver and spleen by quantitative DNA PCR analysis (Table 2).

TABLE 2

Copy Number of Lentiviral Vector/10⁴Cells

Vector	Liver	Heart	Spleen	Kidney	Lung	Ovary

No vector	*<	*<	*<	*<	*<	*<
SINDBIS	569	*<	1407	*<	*<	*<
ZZ SINDBIS	75	*<	538	*<	*<	*<
ZZ SINDBIS	397	*<	520	*<	*<	*<
ZZ SINDBIS	146	*<	295	*<	*<	*<
m168	26	*<	36	*<	*<	*<
m168	66	*<	15	*<	*<	*<
m168	38	*<	28	*<	*<	*<

Genomic DNA from each organ was isolated and analyzed as described in materials and methods.
*< represents undetectable
The threshold for the copy number for detection from each organ was as below.
Liver: 11 copies/10⁴cells. Heart: 26 copies/10⁴cells. Spleen: 3 copies/10⁴cells. Kidney: 3.3 copies/10⁴cells. Lung: 8.3 copies/10⁴cells. Ovary: 13 copies/10⁴cells.

The Non-Specific Infectivity of ZZ Sindbis Pseudotypes is Due to Sindbis Envelope Sequences.

We further investigated the nature of the non-specific background infectivity of ZZ SINDBIS pseudotypes. A mouse polyclonal antibody which neutralizes wild type Sindbis virus infectivity was utilized to demonstrate that the background infectivity was the result of Sindbis virus domains and not the ZZ protein A sequences (FIG. 3). Using flow cytometry we determined that the level of GFP⁺ cells in the wild type and ZZ SINDBIS virus pseudotypes was substantially reduced in the presence of the anti-Sindbis antibody. Infectivity of VSV-G pseudotypes was not blocked nor was infection with the control antibody. These results indicate that Sindbis virus domains within the Sindbis virus envelope are responsible for the non-specific infectivity of ZZ SINDBIS pseudotypes. Thus, we undertook a structure-function analysis of the Sinbis virus envelope through site-directed mutagenesis of ZZ SINDBIS with the aim of ablating residual background infectivity.
Identification of a ZZ SINDBIS E2 mutant with enhanced cell targeting specificity. We first determined the regions responsible for the residual infectivity of our ZZ SINDBIS envelope. The domains we targeted for mutagenesis have previously been reported to affect binding to target cells, block epitopes for neutralizing antibody and function in Sindbis virus tropism (Klimstra et al., J, Virol. 72, 7357-7366 (1998); London et al., Proc Natl. Acad Sci U.S.A. 89, 207-211 (1992); Klimstra et al., J. Virol. 73, 6299-6306 (1999); Byrnes and Griffin, J. Virol. 74, 644-651 (2000); Pence et al., Virology 175, 41-49 (1990); Gardner et al., J. Virol 74, 11849-11857 (2000); Dubuisson and Rice, Journal of Virology 67, 3363-3374 (1993); Polo and Johnston, J. Virol. 65, 6358-6361 (1991); Lee et al., J. Virol. 76, 6302-6310 (2002)). All these domains were located in the E2 protein of the Sindbis virus envelope (FIG. 4). We analyzed E2 mutant pseudotyped virus vectors for infectivity in 293T cells using flow cytometry. The infectivity of mutants was tested on two different cell types, 293T, a human kidney cell line used for standard titration of virus stocks and HepG2 cells, derived from a human hepatocellular carcinoma (Table 1). We tested infectivity in HepG2 cells, because of the background infectivity we observed in liver cells in vivo. We identified several E2 mutants with reduced levels of nonspecific infectivity and thus, an enhanced selectivity for targeting. Since some of these mutations also reduced the titer of viruses produced, we combined the mutations conferring enhanced selectivity with other mutations that enhanced infectivity. Five domains of Sindbis E2 previously reported to affect the infectivity of Sindbis virus were analyzed for their level of infectivity. Mutation ml in domain R1 enhanced the selectivity on 293T cells relative to wild type ZZ SINDBIS virus. However, this mutation also resulted in a decrease in virus titer. Mutations in domain R4 enhanced the titer without altering the specificity. Combining mutation m1 and m6 resulted in partial restoration of the titer and maintenance of the higher selectivity of ml. A double mutant of m1 and m8 resulted in enhanced selectivity on HepG2 liver cells. The combination of mutations of m1, m6, and m8 in domains R1, R2, and R4, respectively, resulted in a pseudotyped virus with enhanced selectivity on 293T and HepG2 liver cells while maintaining stability during concentration by ultracentrifugation high viral titers. This mutant ZZ SINDBIS envelope was termed m168. Our data is consistent with previous studies that demonstrate the role of the R1 and R2 domains for heparin sulfate binding and the R5 domain for rescue of the reduced titer of an R1 mutant in replication competent Sindbis virus (Heidner et al., J. Virol. 68, 2683-2692 (1994)). Identification of a neurotropic strain of Sindbis virus suggested use of an alternative receptor in neuronal cells (Lee et al., J. Virol. 76, 6302-6310 (2002)). m168 also displayed a higher level of specificity than ZZ SINDBIS (>20-fold) in the neuroblastoma cell line, NB41A3 (data not shown).
Enhanced Specificity of the Modified m168 ZZ Sindbis Pseudotyped Virus In Vitro.
A representative experiment illustrating enhanced specificity of m168 infection in 293T cells, in the presence of an HLA monoclonal antibody is shown in FIG. 5 a. In the absence of antibody the background level of infectivity is reduced when compared to the ZZ SINDBIS virus and the levels of infectivity and stability are maintained. A Western blot of m168 pseudotyped virions shows the E2 envelope protein expressed from wild type ZZ SINDBIS and m168 (FIG. 5 b). Note that the m168 envelope protein is larger as a result of mutation ml that prevents cleavage of E2 and E3. This mutant was used in subsequent experiments.
m168 ZZ SINDBIS Pseudotyped Virus Displays Reduced Non-Specific Infectivity in Mice.
The ultimate goal of these studies is to develop a gene transfer vector capable of delivery directly into the bloodstream to target specific tissues or cells. The ability of the genetically modified M168 lentiviral pseudotypes to infect target cells in live mice was tested. First, we determined the level of non-specific infectivity in the absence of targeting antibody. Viruses bearing luciferase reporter genes were injected via the tail vein into SCID mice and the location of the infectivity was assessed using a CCCD camera to determine the level of luciferase expression in the mice. Consistent with the in vitro results, the modified m168 ZZ SINDBIS pseudotyped virus displayed a substantially lower infectivity in the liver and spleen of inoculated animals, relative to the parental ZZ SINDBIS pseudotyped virus (FIG. 6). Because the intensity of the CCCD imaging for luciferase expression can be influenced by a number of variables such as depth of tissue and positioning of the animal during imaging, we confirmed these results by isolation of organs and PCR analysis for vector DNA sequences (Table 2). These results confirm that infectivity in liver and spleen is substantially reduced. Of note, we could not detect infection in ovaries indicating that transduction of our vector into germ line cells was unlikely to occur. Having successfully reduced the background infectivity, we tested the ability of these m168 pseudotypes to target cancer cells in the presence of monoclonal antibody directed to a tumor specific cell surface antigen, P-gp in mice.
m168 Virus Specifically Targets P-gp Expressing Melanoma Cells in NOD/SCID Mice.
Malignant melanoma is an aggressive human tumor that metastasizes to multiple tissues including remote skin, soft tissue, lympho node and lung (Allen and Coit, Curr. Opin. Oncol. 14, 221-226 (2002)). Several intrinsic properties of tumor cells contribute to the development of resistance to chemotherapeutic drugs. Increased expression of the multi-drug resistant (MDR) genes causes overproduction of the transmembrane transport protein P-gp (Ambudkar et al., Oncogene. 22, 7468-7485 (2003)). P-gp transports neutral and cationic hydrophobic compounds across the cell membrane. Selection for tumor cells that are resistant to natural product amphiphilic anticancer drugs can induce expression of P-gp. Elevated levels of P-gp have been found in many solid tumors of the colon, kidney, liver and lung that had not been exposed to chemotherapy accompanied by development of the multi-drug resistance. One study demonstrated that 33 to 76% of the melanoma cell lines derived from primary tumors or metastases of untreated patients scored positive for P-gP (Berger et al., Int. J. Cancer 59, 717-723 (1994)).
We selected a murine model for human malignant metastatic melanoma where the tumor cells migrate through the bloodstream to engraft and form tumors in the lungs. We engineered the murine melanoma cells to express the human MDRsc1 gene (the vector is shown in FIG. 1) in order to provide a cell surface molecule for targeting. This served as our live animal model system that allowed us to stringently test whether our mutant E2 virus vector can target P-gp on the surface of the melanoma cells within live animals.
First, we demonstrated the specificity of the targeting for the P-gp expressing melanoma cells in vitro. A Firefly luciferase reporter gene was used to quantitate transduction of the melanoma cells by flow cytometry. Our results demonstrate that P-gp can be specifically targeted on the surface of the melanoma cells. In the presence of monoclonal antibody, infection of the melanoma cells is significantly greater than the original ZZ SINDBIS pseudotyped vector (Table 3). The P-gp transducing vector does not significantly infect cells that do not bear P-gp (data not shown). Thus, this combination of tumor cells and transducing vector was utilized for vector targeting in live mice.

TABLE 3

Luciferase Assay of Melanomas

			Vector
			Copy#/
Virus	Antibody	RLU		10⁴cells

§In vitro transduction

—	—	<200*
FUhLucW (ZZ SINDBIS)	—	302
FUhLucW (ZZ SINDBIS)	Anti P-Glycoprotein	1667
FUhLucW (m168)	—	203
FUhLucW (m168)	Anti P-Glycoprotein	1295

†In vivo transduction by systemic virus injection

—	—	<200*	<19
FUhLucW (m168)	control antibody	405	<19
FUhLucW (m168)	control antibody	233	<19
FUhLucW (m168)	control antibody	296	<19
FUhLucW (m168)	Anti P-Glycoprotein	2737	87
FUhLucW (m168)	Anti P-Glycoprotein	2397	50
FUhLucW (m168)	Anti P-Glycoprotein	3104	65
FUhLucW (ZZ SINDBIS)	Anti P-Glycoprotein	1834	77
FUhLucW (ZZ SINDBIS)	Anti P-Glycoprotein	115	<19

Cells are harvested and analyzed for firefly luciferase expression and copy number of vector as described in materials and methods.
§The value of RLU for in vitro transduction is Relative Luciferase Unit/10⁴cells.
†The value of RLU for in vivo transduction is Relative Luciferase Unit/10³cells.
*The values of background (uninfected cells) ranged from 100 to 200.

The tumor cells were first marked in vitro by transducing with a vector expressing Renilla luciferase. This allowed us to differentially identify the location of vector expression in the tumor cells. The localization of vector expression and tumor cells in the mice was visualized using different substrates for the two luciferase genes, Firefly and Renilla, respectively (FIG. 7). Following injection, the tumor cells migrate to the lungs and can be visualized by CCCD imaging for Renilla luciferase. The virus bearing m168 and anti P-gp antibody was injected via the tail vein. Vectors injected in the absence of anti P-gp antibody, show no signal for Firefly luciferase. In contrast, when virus is pseudotyped with m168 bearing anti P-Gp antibody, the luciferase expression of Firefly luciferase (m168 virus vector) co-localizes in the lung with that of Renilla luciferase (tumor melanoma cells).
The co-localization in the lungs of Firefly and Renilla luciferase expression representing tumor and virus infection, respectively, was confirmed to be a result of infection of the melanoma cells by the targeting vector. Lung tissue was isolated and melanoma cells cultured. Firefly luciferase activity, representing expression from the vector, was observed predominately in those tumor cells isolated from animals in which anti P-gp targeted virus was used for the infection (Table 3). Quantitative real time PCR analysis confirmed these results. Interestingly, m168 pseudotype vectors demonstrate a higher level of infection in melanoma cells in vivo compared to the parental ZZ SINDBIS, most likely due to less nonspecific trapping in other mouse tissues.
The targeting of micrometastatic tumors was also visualized by immunohistochemistry (see, FIG. 10). Tumor micro-nodules are observed in the lungs at Day 6 following transplant with morphologic characteristics of melanoma and positive for melanoma antigen S-10037. About 1% of these nodules were also positive for EGFP, consistent with the previous PCR analysis (see, Table 2 of K. Morizono et al., Nature Med (2005) 11:346-352, hereby incorporated herein by reference in its entirety for all purposes).
Rare transduced cells in the spleen and liver were identified as macrophages and related Kupffer cells, respectively, by flow cytometry and immunohistochemistry (FIGS. 11, 12 a and 12 b).

Targeting of Established Melanoma Tumors.

In another set of experiments, we tested the ability of the m168 vector to target established tumors. The same protocols as above were utilized except that tumors were allowed to form for 12 days prior to intravenous injection of the targeting vector. In this model system, visible tumors are evident at 8 days after inoculation and death occurs within 16 days after inoculation. Animals were visualized by CCCD imaging 3 days following intravenous injection for both the location of tumors and the specificity of targeting. Specific targeting to the tumors in the lungs of the animals was observed only following intravenous injection with m168 pseudotypes plus P-gp antibody (see, FIG. 13 a). No non-specific infection was observed in the lungs in the absence of tumor and the infection to tumors in the lungs was dependent upon the presence of P-gp antibody. The transduction of organs was confirmed by isolation of specific organs following sacrifice (see FIG. 13 b). The reduced signal intensity in lungs of this experiment relative to targeting of micrometastatic cells (compare mice of FIG. 13 a with mice of FIG. 7) is due to limited growth of transduced cells (3 days versus 12 days after transduction) prior to imaging. For comparison, intravenous injection of VSVG pseudotypes show infection of a broad number of tissues without specificity for the tumors consistent with previously published studies (Sawai and Meruelo, Biochem Biophys Res Commun (1998) 248:315-323).

Discussion

We developed a gene therapy targeting strategy that for the first time allows production of a high titer virus that can be directed to specific cells and tissues. Most importantly, the high titer and specificity of this vector system makes it suitable for applications within living animals.
We took advantage of several aspects of the Sindbis virus envelope in designing our vector system. The Sindbis envelope consists of a cell derived lipid bilayer embedded with two integral membrane glycoproteins, E1 and E2, which mediate membrane fusion and receptor binding, respectively. Following binding of E2 to its receptor and endocytosis, E1 leads to fusion in a pH dependent fashion independent of E2. E1 and E2 are anchored in the cell membrane independently via transmembrane domains; an attribute that likely accounts for the high level of envelope stability and maintenance of function in chimeric molecules. Previous studies indicated that the Sindbis virus E2 envelope protein could be modified substantially yet retain infectivity (Dubuisson and Rice, Journal of Virology 67, 3363-3374 (1993)). Sindbis virus vectors with chimeric E2 envelopes were capable of targeting cells in vitro (Ohno et al., Nat. Biotechnol. 15, 763-767 (1997)).
Although Sindbis is an RNA virus, we previously created a DNA vector expressing the Sindbis envelope and demonstrated that it could be used to express functional envelope and form pseudotypes with both the HIV-1- and MuLV-based vectors (Morizono et al., J. Virol., September; 75.(17.):8015.-20. 75, 8016-8020 (2001)). When the Sindbis virus envelope is modified to encode the ZZ domain of protein A, monoclonal antibodies directed to cell surface antigens can be used to redirect the target specificity of the retroviral vectors. Here, we substantially modified the Sindbis E2 envelope to further increase the specificity of infectivity to a degree sufficient to achieve the high level of specificity required for in vivo infection. In such a context, the virus would encounter multiple cell types and thus, an increased potential for non-specific infectivity. Although the parental (first generation) ZZ SINDBIS pseudotyped vector retains infectivity in the liver and spleen, the pseudotypes bearing modified Sindbis virus envelope show a substantially decreased level of infectivity in these organs.
Although we have not investigated the specific cellular receptors responsible for the non-specific infectivity of the parental ZZ SINDBIS virus, our results indicate that background infectivity is likely due to changes within the Sindbis envelope domains and not the ZZ domain. Some of the mutations we characterized are known to abolish binding of the Sindbis virus envelope to heparin sulfate and thus, are likely responsible for the decreased nonspecific infectivity and resultant enhanced selectivity of these viruses (Klimstra et al., J. Virol. 73, 6299-6306 (1999); Byrnes and Griffin, J. Virol. 74, 644-651 (2000)). The phenotypes of these mutants are consistent with a previous report that characterized the role of the heparin sulfate binding domain in non-specific transduction of a targeting adenovirus vector in mice (Smith et al., Hum. Gene Ther. 14, 777-787 (2003); Koizumi et al., J. Viral. 77, 13062-13072 (2003)). By reducing the non-specific infectivity, it was possible for us to redirect the target cell specificity of the virus to a specific human tumor cell antigen, P-gp, which is expressed on the surface of murine melanoma cells.
Once a melanoma acquires the ability to invade tissues, continue to proliferate and escape immune surveillance metastatic spread is likely to occur. Metastatic competent tumor cells migrate from the site of the primary lesion and subsequently grow at distant anatomical sites including the liver and lungs. Pulmonary metastases are the most common site of visceral metastasis with between 15% and 35% of recurrence occurring in this location (Allen and Coit, Curr. Opin. Oncol. 14, 221-226 (2002)). Only 4% of patients with pulmonary metastases survive 5 years. The murine melanoma model we chose to evaluate the specificity of our mutants mimics the progression of human melanoma to a metastatic stage often found in the lung. This system was ideal for testing specific targeting of our modified ZZ virus vectors to metastatic tumor cells by directly injecting them into the bloodstream of mice.
Targeting P-gp as a tumor antigen can be useful not only for metastatic melanoma, but for many other tumors, which express this gene and are thus rendered resistant to multiple chemotherapeutic drugs (Ambudkar et al., Oncogene. 22, 7468-7485 (2003)). However, P-gp is also expressed on some normal cells, thus the targeting of tumor cells that express P-gp would be most successful in those situations where the P-gp was significantly over-expressed in the tumor cells.
Although non-covalent interactions via the protein A ZZ domain would be useful in ex vivo applications, in an animal or patient with an immunocompetent humoral immune system, the presence of circulating antibodies would compete for the monoclonal antibodies of the targeting vector. Thus, clinical in vivo applications use chimeric, recombinant single chain antibody sequences or specific ligand and/or peptide sequences. Human chorionic gonadotropin sequences have been successfully recombined into chimeric Sindbis envelope to target Sindbis virus based vectors (Sawai and Meruelo, Biochem. Biophys. Res. Commun. 248, 315-323 (1998)). To date, we have tested these pseudotypes with over ten specific monoclonal antibodies. Any specific ligand or affinity reagent incorporated into the Sindbis envelope can be used to target a cell surface molecule specific to a given cell or tissue type.
The applications of a specific targeting gene therapy vector are broad. In the melanoma model, for example, one could introduce specific suicide genes to kill tumor cells and/or immunomodulatory genes to enhance immune response directed to metastatic legions. Early treatment of metastatic cells is of significant therapeutic value. In theory, metastases could be targeted well before they grow to a size to be visualized by current technologies. Residual tumor cells following localized treatment with radiation and/or surgery could also be targeted and eliminated.
The targeting of gene therapy vectors to specific cells and tissues at specific sites in the body has numerous applications. Current applications of gene therapy require either ex vivo purification of cells followed by transduction of the purified target cells and/or injection directly into localized sites, both of which require extensive technical manipulation (Kohn et al., Nat. Med. 1, 1017-1023 (1995); Cavazzana-Calvo et al., Science 288, 669-672 (2000)). Direct injection into the bloodstream and infection to specified regions would facilitate the application of gene therapy to many diseases. Since most diseases, both acquired and hereditary, either originate in specific cells or manifest their clinical phenotypes in specific tissues, the gene therapeutic vectors could be delivered where they would be most effective. For example, gene therapy utilizing hematopoeitic progenitor cells currently require purification of the hematopoeitic stem cells followed by transduction ex vivo. Specific targeting vectors can be developed that target antigens specific for hematopoeitic stem cells and thus, allow direct introduction of therapeutic genes into the stem cells through bone marrow and/or systemic injection after progenitor cell mobilization. As evidenced by our ability to target the melanoma tumor cells prior to establishment of visible tumors in the lungs, targeting vectors that circulate and home to specific cells could allow early therapeutic intervention in the case of diseases such as cancer, and residual cells of chronic or latent infections by infectious agents. This system could also be applied to treatment of pulmonary diseases such as cystic fibrosis and alpha-1 antitrypsin deficiency, caused by mutations in the CFTR (CF transmembrane conductance regulator) and alpha-1 antitrypsin genes respectively (West and Rodman, Chest 119, 613-617 (2001)). In principle, the CFTR and alpha-1 anti trypsin genes could be delivered efficiently to lung cells by a simple intravenous injection.
Finally, targeting of specific cells and tissues would greatly enhance the safety of gene therapeutic applications. Inappropriate expression due to inadvertent infection of irrelevant cells or tissues is one cause for concern in gene therapy applications and has resulted in serious adverse effects in some clinical trials (Lehrman, S., Nature 401, 517-518 (1999)). Targeting to specific cells would lessen the possibility of adverse side effects. In addition, insertional mutagenesis of the retroviral vector, if it does occur, would be limited to a much smaller subset of cells, thus diminishing the possibility of events leading to the initiation and/or progression of malignant transformation (Hacein-Bey-Abina et al., Science 302, 415-419 (2003)). It is important to note that this targeting system has broad applicability for use with other retroviral vectors. Although we utilized lentiviral vectors in this study, we previously demonstrated that the Sindbis ZZ pseudotypes will also form readily with MuLV vectors, more commonly utilized in most existing gene therapy clinical applications for a variety of diseases.

Example 2

Targeting Prostate Cancer Cells through the Prostate Stem Cell Antigen (PSCA)

Prostate cancer is the most common cancer diagnosis and the second leading cause of cancer-related death in American men. Prostate cancer mortality frequently results from metastasis to bone and hormone-independent tumor growth. Physiologically relevant prostate cancer models exist, such as the LAPC-9 xenograft model (see, Craft, et al., Cancer Res (2000) 60:2541-2546). LAPC-9 cells were derived from a human bone metastasis, and are able to form a prostate cancer xenograft that can be propagated in SCID mice, and expresses prostate specific antigen and wild-type androgen receptor (Id.). Hormone independent outgrowths can be selected after castration of the mice, and micrometastasis can eventually be detected in half of the mice, recapitulating the clinical progression of human prostate cancer (Klein, et al., Nature Med (1997) 3:402-408).
We generated vectors that specifically deliver genes to prostate cancer in a living animal, and validated our vectors in the LAPC-9 model system. First, we found a candidate surface molecule in prostate cancer cells that our engineered Sindbis envelopes could target. Prostate stem cell antigen (PSCA) is a prostate-specific gene with 30% homology to stem cell antigen 2, a member of the Thy-1/Ly-6 family of glycosylphosphatidylinositol (GPI)-anchored cell surface antigens. PSCA encodes a 123-aa protein with an amino-terminal signal sequence, a carboxyl-terminal GPI-anchoring sequence, and multiple N-glycosylation sites (Gu, et al., Oncogene (2000) 19:1288-96; and Reiter, et al., Proc Natl Acad Sci USA (1998) 95:1735-1740). PSCA mRNA expression is prostate-specific in normal male tissues and is highly up-regulated in both androgen-dependent and -independent prostate cancer xenografts. PSCA is expressed in over 80% of prostate cancers, among them the LAPC-9 xenograft (Saffran, et al., Proc Natl Acad Sci (2001) 98:2658-2663), and is a promising therapeutic target. Thus, we targeted Sindbis pseudotyped lentiviral vectors with an anti-PSCA mAb, 1G8 (Saffran, supra). Although PSCA is widely expressed in human prostate cancers, expression is very low or undetectable in prostate cancer cell lines. We obtained a LNCaP derivative cell line stably transfected with PSCA (R. Reiter, UCLA), LPSCA4, and analyzed the ability of 1G8 to mediate infection of FUGW (that expresses EGFP from ubiquitin C promoter) pseudotyped with m168 (FIG. 14). LPSCA4 was very effectively infected by FUGW with both αHLA and 1G8 antibodies, whereas the parental LNCaP cells could only be infected with αHLA. 1G8 did not mediate infection into LNCaP cells, as levels were comparable to background infection in the absence of targeting antibody.

Example 3

Combining Cell Surface Targeting with Selective Cell to Increase Efficiency of Specific Targeting

The ubiquitin-C promoter in the FUGW lentiviral vector (Morizono, et al., Nature Medicine (2005) 11:346-352; and Lois, et al., Science (2002) 295:868-872), with a chimeric prostate specific antigen (PSA) promoter, designated (PSE-BC), to produce the construct FPGW. The key regulatory elements of the PSA enhancer include a proximal promoter (−541 to +12) comprising two binding sites for the androgen receptor (AREI and II) and a distal enhancer, which contains a 390-bp androgen responsive core region (Schuur, et al., J Biol Chem (1996) 8:1416-1426; and Cleutjens, et al., J Biol Chem (1996) 271:6379-6388). The core region contains a cluster of closely spaced androgen response elements (AREs) and sites for other transcription factors. The androgen receptor (AR) binds cooperatively to the enhancer and mediates synergistic transcription, and other factors within and outside of the enhancer contribute to prostate specificity (Reid, et al., J Biol Chem (2001) 276:2943-2952); and Huang, et al., (1999) J Biol Chem (1999) 274: 25756-25768). The PSE-BC promoter was generated by duplication of the PSA enhancer core and insertion of this duplicated element closer to the proximal promoter (200 bp upstream). After these modifications PSE-BC produced 20-fold higher expression levels than the parental construct, yet retained androgen inducibility and tissue specificity (Wu, et al, Gene Ther (2001) 8:1416-1426).
To assess the specificity of expression we infected prostate and non-prostate cell lines and primary cells with either FUGW or FPGW. Expression from the PSE-BC promoter was potent as the ubiquitin-C promoter in prostate cell lines, and specific to prostate cells, although some background expression could be detected in a hepatoma cell line (HepG2), primary fibroblasts and endothelial cells (FIG. 15). Of note, no expression from the PSE-BC promoter could be detected in primary macrophages in vitro.

Example 4

Targeting CNS Tissue By Conjugation To Anti-Transferrin Receptor Antibody

Successfully Targeted Transduction of Human Umbilical Vein Endothelial Cells (HUVEC) via TfR using TfR Monoclonal Antibodies.
Transferrin receptor (TfR) is highly expressed on brain capillary endothelial cells and has been used by Pardridge and co-workers as a means to deliver therapeutic reagents into the brain (Pardridge, Neuron (2002) 36:555-558; and Pardridge, Nat Rev Drug Discov (2002) 1:131-139. We determined that TfR could serve as a receptor for targeted infection by testing infection with m168 pseudotypes conjugated with antibodies directed to human TfR expressed on human umbilical vein endothelial cells (HUVEC). There are several available monoclonal antibodies directed to different or unknown epitopes of TfR (Panaccio, et al., Immunol Cell Biol (1987) 65:461-472; Esserman, et al., Blood (1989) 74:2718-2729; and Takahashi, et al, Blood (1991) 77:826-832). Our results demonstrate successful infection of HUVEC with TfR antibody, but not in the absence of TfR antibody. However the levels of infectivity were low compared to targeting to other cell surface molecules such as CD4, HLA, and P-gp in other cell types. (FIG. 16)
It was reported that a single mutation within the E1 envelope protein renders Sindbis virus replication to be independent of a requirement for cholesterol (Lu, et al., J Virol (1999) 73:4272-4278). A similar mutation was also identified in Semliki Forest virus (Vashishtha, et al., J Cell Biol (1998) 140:91-99). The mechanism of this cholesterol independent replication is unclear. Since the E1 protein is responsible for fusion of Sindbis envelope to induce entry into the cell, we reasoned that this mutation in the context of our targeting vector would work in concert with antibody mediated binding to enhance the infectivity of the targeting viruses. Our results show that this is the case. Introduction of the cholesterol independent mutation (E1 AK226-227SG) into the targeting Sindbis envelope (termed 2.2) enhanced infectivity of lentiviral pseudotypes 8-fold over that of m168 pseudotypes targeted to TfR (FIG. 16). These results demonstrate that efficient targeting to TfR can be obtained in cell culture.

Targeting to the CNS in Living Mice.

Using the modified vector described above we tested its ability to target TfR, particularly TfR expressing cells of the brain capillary endothelium. Mice were injected intravenously with anti-TfR conjugated vector through the tail vein. Five (5) days after injection mice were analyzed for location of transduced cells by optical imaging for expression of the luciferase reporter gene. We observed a distribution of luciferase activity in the body consistent with successful targeting to the CNS. Intense optical signals were observed in regions corresponding to the brain and spinal column. These results were confirmed after sacrifice by removing the skin and muscle from the back of the animals confirming luciferase expression from the brain and spinal column (FIG. 17). Control mice injected with vector in the absence of TfR antibody did not show a signal in the CNS, consistent with typical control animals utilized in the experiments targeting P-gp on melanoma (Morizono, et al, supra). It is noteworthy that although TfR is expressed on multiple cells and tissues in the body (Gatter, et al., J Clin Pathol (1983) 36:539-45; Lu, et al., Acta Pathol Jpn (1989) 39:759-764; and Soyer, et al., J Cutan Pathol (1987) 14:1-5), the major sites of transduction were observed in the regions corresponding to the central nervous system. Without being bound to any theory, this may be due to a higher density of transferrin receptor and/or enhanced rates of internalization of transferrin receptor in these regions (Pardridge, Neuron, supra; and Pardridge, Nat Rev Drug Discov, supra).
It is understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and scope of the appended claims. All publications, patents, and patent applications cited herein are hereby incorporated by reference in their entirety for all purposes.

Claims

1. A pseudotyped, targeted retroviral vector comprising:

a) a mutated Sindbis envelope comprising Sindbis envelope proteins E1, E2, and E3, wherein at least one of E1, E2, or E3 is mutated as compared to a wild-type sequence;

b) a targeting moiety linked to the Sindbis envelope.

2. The vector of claim 1, further comprising a retroviral-based nucleic acid genome.

3. The vector of claim 1, wherein the vector nucleic acid comprises a heterologous gene operably linked to a promoter.

4. The vector of claim 3, wherein the promoter is a tissue-specific promoter.

5. The vector of claim 4, wherein the tissue-specific promoter is a PSE-BC promoter.

6. The vector of claim 1, wherein the targeting moiety specifically binds to a target protein selected from the group consisting of P-glycoprotein, Her2/Neu, erythropoietin (EPO), epidermal growth factor receptor (EGFR), vascular endothelial growth factor receptor (VEGF-R), cadherin, carcinoembryonic antigen (CEA), CD4, CD8, CD19, CD20, CD33, CD34, CD45, CD117 (c-kit), CD133, HLA-A, HLA-B, HLA-C, chemokine receptor 5 (CCR5), stem cell marker ABCG2 transporter, ovarian cancer antigen CA125, an integrin, prostate specific antigen (PSA), prostate stem cell antigen (PSCA), dendritic cell-specific intercellular adhesion molecule 3-grabbing nonintegrin (DC-SIGN), thyroglobulin, granulocyte-macrophage colony stimulating factor (GM CSF), myogenic differentiation promoting factor-1 (MyoD-1), Leu-7 (CD57), LeuM-1, cell proliferation-associated human nuclear antigen defined by the monoclonal antibody Ki-67 (Ki-67), HIV gp120, and transferrin receptor.

7. The vector of claim 6, wherein the targeting moiety is an antibody.

8. The vector of claim 7, wherein the targeting moiety is an antibody directed against prostate stem cell antigen (PSCA).

9. The vector of claim 7, wherein the targeting moiety is an antibody directed against P-glycoprotein (P-gp).

10. The vector of claim 7, wherein the targeting moiety is an antibody directed against a transferrin receptor.

11. The vector of claim 1, wherein the targeting moiety is covalently linked to the Sindbis envelope.

12. The vector of claim 1, wherein the targeting moiety is non-covalently linked to the Sindbis envelope.

13. The vector of claim 1, wherein the targeting moiety is covalently linked to the E2 or the E3 protein of the Sindbis envelope.

14. The vector of claim 1, wherein the targeting moiety is non-covalently linked to the E2 or the E3 protein of the Sindbis envelope.

15. The vector of claim 14, wherein the targeting moiety is non-covalently linked to the E2 protein Sindbis envelope via the ZZ domain of protein A.

16. The vector of claim 1, wherein E2 protein is mutated at one amino acid position.

17. The vector of claim 1, wherein E2 protein is mutated at two or more amino acid positions.

18. The vector of claim 1, wherein E3 protein is mutated at one amino acid position.

19. The vector of claim 1, wherein E3 protein is mutated at two or more amino acid positions.

20. The vector of claim 1, wherein the mutated Sindbis envelope is encoded by a sequence listed in Table 1.

21. The vector of claim 1, wherein the mutated Sindbis envelope is encoded by m168 which has a mutation in Sindbis virus envelope protein E2.

22. The vector of claim 21, further comprising a mutation in Sindbis envelope protein E1.

23. A packaging system comprising a cell comprising nucleic acids encoding the pseudotyped, targeted retroviral vector of claim 1.

24. The packaging system of claim 23, wherein the vector further comprises a retroviral-based nucleic acid genome.

25. The packaging system of claim 24, wherein the Sinbis envelope proteins E1, E2, and E3 and the retroviral-based nucleic acid genome are encoded on the same nucleic acid.

26. The packaging cell of claim 24, wherein the Sinbis envelope proteins E1, E2, and E3 and the retroviral-based nucleic acid genome are encoded on separate nucleic acids.

27. An expression vector comprising a nucleic acid encoding Sindbis envelope proteins E1, E2, and E3, wherein at least one of E, E2, or E3 is mutated as compared to a wild-type sequence.

28. A method of making the pseudotyped, targeted retroviral vector of claim 1, the method comprising the step of expressing in a cell a nucleic acid comprising Sindbis envelope proteins E1, E2, and E3.

29. The method of claim 28, wherein the vector further comprises a retroviral-based nucleic acid genome.

30. The method of claim 29, wherein the Sindbis envelope proteins E1, E2, and E3 and the retroviral based nucleic acid genome are encoded on the same nucleic acid.

31. The method of claim 29, wherein the Sindbis envelope proteins E1, E2, and E3 and the retroviral based nucleic acid genome are encoded on separate nucleic acids.

32. The method of claim 28, further comprising the step of isolating a virus particle from the cell.

33. A method of transducing cells with a heterologous gene, the method comprising the step of contacting the cell with the pseudotyped, targeted retroviral vector of claim 1.

34. The method of claim 33, wherein the cells are in a subject and the vector is administered intravenously.

35. The method of claim 33, wherein the cells are transduced ex vivo.

36. The method of claim 33, wherein the cells are transduced in vivo.

37. The method of claim 33, wherein the cells are transduced in vitro.

38. A method of treating or preventing a disease state, the method comprising the step of contacting a cell with the pseudotyped, targeted retroviral vector of claim 1.

39. The method of claim 38, wherein the cell is contacted in vivo.

40. The method of claim 38, wherein the cell is contacted ex vivo.

41. The method of claim 38, wherein the cell is contacted in vitro.

42. A method of diagnosing a disease state, the method comprising the step of contacting a cell with the pseudotyped, targeted retroviral vector of claim 1.

43. The method of claim 42, wherein the cell is contacted in vivo.

44. The method of claim 42, wherein the cell is contacted ex vivo.

45. The method of claim 42, wherein the cell is contacted in vitro.

46. A method of delivering a pseudotyped, targeted retroviral vector across the blood brain barrier in a subject, the method comprising the step of contacting a cell with the pseudotyped, targeted retroviral vector of claim 10.