# Patent

## Title
Targeted particles comprising landscape phage fusion proteins and heterologous nucleic acid

## Abstract

Disclosed are targeted particles comprising or consisting of a plurality of landscape phage fusion proteins complexed with heterologous nucleic acid, the landscape phage fusion proteins displaying a heterologous peptide and the targeted particle binding specifically to a target site. The particles may be utilized in methods for modulating expression of genes in target cells.

## Background
CROSS REFERENCE TO RELATED APPLICATION
The present application is the U.S. national stage application of International Application PCT/US2011/035390, filed May 5, 2011, which international application was published on Nov. 10, 2011, as International Publication WO2011/140365, in the English Language. The International Application claims priority of U.S. Provisional Application No. 61/331,583, filed May 5, 2010, the contents of which are incorporated herein by reference in their entireties.


STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
This invention was made with government support under grant number 5R01 CA125063 awarded by the National Institutes of Health. The government has certain rights in the invention.


BACKGROUND
The field of the invention relates to targeted delivery of nucleic acid. In particular, the field of the invention relates to targeted delivery of nucleic acid such as small inhibitory ribonucleic acid (siRNA) via landscape phage fusion proteins.
The Ff class of filamentous phage includes three strains referred to as fl, fd, and M13. These phages are thread-like particles approximately 1000 nm long and 7 nm in diameter. The majority of the tubular capsid consists of 2700 identical, largely alpha-helical subunits of the  ̃50-residue pVIII major coat protein. Viral DNA of varying sizes, including recombinant genomes with foreign DNA inserts, can be accommodated in the filamentous capsid whose length is altered to match the size of the enclosed DNA by adding proportionally fewer or more pVIII subunits during phage assembly. Additional phage coat proteins include pIII, pVI, pVII, and pIX. One tip of the phage outer tube is capped with five copies each of the minor coat proteins pVII and pIX and another tip with the minor coat proteins pIII and pVI.
In phage display constructs and libraries formed therefrom, heterologous or foreign coding sequences are spliced in-frame into one of the five phage coat protein genes, so that the ‘guest’ peptide, encoded by that sequence, is fused to the coat protein to form a fusion protein which displays the guest peptide on the surface of the virion. A phage display library is a collection of such fusion phage clones, each harboring a different foreign coding sequence, and therefore displaying a different guest peptide on their surface. When a foreign coding sequence is spliced into the major coat protein's gene (pVIII), the guest peptide is displayed on every pVIII subunit increasing the virion's total mass by up to 20%. Such particles are generally referred to as “landscape phage” to emphasize the dramatic change in surface architecture caused by arraying thousands of copies of the foreign peptide in a dense, repeating pattern around the viral capsid. A landscape library refers to a large population of such phages, encompassing billions of clones with different surface structures and biophysical properties. Landscape libraries may be screened to identify phage that bind specifically to selected targets such as cancer cells. The fusion proteins isolated from the selected phage can be utilized to target liposomes specifically to these targets. (See U.S. Patent Publication No. U.S. 2007-0077291; and Bedi et al., Nanomedicine 2010 Nov. 2 [Epub ahead of print], PMID:21050894; the contents of which are incorporated herein by reference in their entireties).
Delivery of nucleic acid to target cells holds considerable promise as a therapeutic approach to treating various diseases, for example, via gene therapy or via regulating gene expression. In particular, RNA interference (RNAi) holds considerable promise as a therapeutic approach to silence disease-causing genes. Here, a nanotechnological platform for delivering nucleic acid to target cells is proposed. This platform utilizes the unique propensity of phage proteins to self-assemble in the presence of nucleic acids and to form particles mimicking the structure of the phage capsid.
SUMMARY
Disclosed are targeted particles comprising or consisting of a plurality of landscape phage fusion proteins complexed with heterologous nucleic acid, the landscape phage fusion proteins displaying a heterologous peptide and the targeted particle binding specifically to a target site. The targeted particles may comprise a filamentous phage protein, such as a pVIII major coat protein displaying the heterologous peptide, for example, where the filamentous phage protein and heterologous peptide form a fusion protein. The heterologous peptide is relatively small, for example no more than about 12, 11, 10, 9, or 8 amino acids in length. The disclosed targeted particles may be nanoparticulate with respect to size and having one or more dimensions such as effective diameter or length between about 1 nm and 1000 nm. The complexed nucleic acid may be relatively short in length, for example 10-50 nucleotides in length, and may include siRNA.
The disclosed particles are targeted to specific cellular targets. For example, the disclosed particles may be targeted to one or more cell surface molecules. In some embodiments, the disclosed particles bind specifically to cancer cells or a specific tissue type (e.g., breast cancer cells) but do not bind to non-cancerous cells of the same specific tissue type (e.g., non-cancerous breast cancer cells).
The disclosed particles comprise heterologous nucleic acid such as siRNA for modulating expression of one or more genes in a cell to which the particles are specifically targeted. In some embodiments, the siRNA inhibits expression of one or more genes that are associated with cancer or the risk of developing cancer, or one or more genes that are associated with a cancer cell's resistance to treatment with one or more chemotherapeutic agents. In some embodiments, the targeted particle comprises siRNA that inhibits gene expression of a gene selected from PARP1, MDR1/Pgp, MRP1, and BCRP.
The disclosed particles may be formulated as part of a pharmaceutical composition comprising the targeted particles and a pharmaceutical carrier, excipient, or diluent. The disclosed particles may be used for preparing a pharmaceutical composition for modulating expression of one or more genes in a patient in need thereof. In some embodiments, the disclosed particles are used for preparing a pharmaceutical composition for treating cancer in a patient in need thereof, which may include but is not limited to breast cancer. In further embodiments, the cancer may be refractory or resistant to treatment with a chemotherapeutic agent.
Also contemplated herein are kits that include a pharmaceutical composition comprising the presently disclosed particles and further including a pharmaceutical composition comprising a chemotherapeutic agent. Suitable chemotherapeutic agents for the kits may include, but are not limited to doxyorubicin liposomal.
The presently disclosed particles may be utilized in methods for modulating expression of a gene in a cell (e.g., inhibiting expression of the gene in the cell via promoting degradation of mRNA for the gene). The methods may be performed in vitro or in vivo. The contemplated methods may include methods for inhibiting expression of a gene in a cell, the methods including contacting the cell with the presently disclosed particles where the particles bind specifically to the cell and the particles include an siRNA that inhibits expression of the gene.
The presently disclosed particles may be utilized in methods for treating or preventing a disease or disorder in patient in need thereof. For example, the disclosed particles may be formulated as a pharmaceutical composition for treating or preventing cancer or a proliferative disorder in a patient in need thereof. The pharmaceutical compositions comprising the disclosed particles may be administered to a patient in a treatment regimen with a chemotherapeutic agent, which may be administered to the patient prior, concurrently with, or after the pharmaceutical compositions comprising the disclosed particles are administered to the patient.
Also contemplated herein are methods of making the disclosed particles. In some embodiments, the methods include the following steps: (a) obtaining bacteriophage comprising or consisting of a plurality of fusion proteins displaying a binding peptide for a desired target site (e.g., landscape bacteriophage); (b) treating the bacteriophage with a denaturing agent; (c) isolating or purifying the phage fusion protein from the treating bacteriophage (e.g., removing phage DNA and other components); (d) preparing a mixture of the isolated or purified phage fusion protein and heterologous nucleic acid to form the targeted particle; and (e) isolating or purifying the targeted particle from the mixture. Suitable denaturing agents include detergents. Typically, the targeted particles are formed from a mixture that comprises a molar excess of fusion proteins relative to nucleic acid. In other embodiments, the disclosed particles may be prepared by: (a) preparing a mixture of (i) a solution of isolated or purified landscape phage fusion proteins and (ii) a solution of isolated or purified heterologous nucleic acid where the targeted particle forms in the mixture; and (b) isolating or purifying the targeted particle from the mixture.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1. is a schematic representation of an siRNA molecule: a  ̃19-21 basepair RNA core duplex that is followed by a 2 nucleotide 3′ overhang on each strand. OH: 3′ hydroxyl; P: 5′ phosphate.
FIG. 2. illustrates a recombinant phage particle library formed from pVIII fusion proteins that display a “guest peptide.”
FIG. 3. illustrates that the selected tumor-specific phage can be converted into the siRNA-phage protein complex by their self-assembly, resembling phages.
FIG. 4. atomic force microscopy analysis illustrating a dense layer of siRNA-nanophage complexes (scan size: A=3 μm, B=500 nm, C=1.5 μm, D=250 nm). The cross sections belong to image B and D.
FIG. 5. illustrates tumor-targeted phage-like nanoparticles with entrapped siRNA. siRNA is depicted as a double helix. Fusion pVIII proteins are depicted as alpha-helixes with disordered fused tumor-specific peptides.
FIG. 6. illustrates selectivity of phage VEEGGYIAA (SEQ ID NO:7) towards breast cancer cells MCF-7 in comparison with normal breast cells MCF-10A and hepatocellularcarcinoma HepG2. Unrelated phage bearing the peptide VPEGAFSS (SEQ ID NO:8) was used as a control.
FIG. 7. illustrates the analysis of the complex of siRNA with phage protein. The complex was analyzed by gel-electrophoresis (1% agarose, SIBR green). 1: siRNA control; 2: phage protein-siRNA (molar ratio 80:1), 3: Proteinase K-mediated release of siRNA from protein-siRNA complex.
FIG. 8. illustrates the cellular localization of phage-siRNA complex inside MCF-7 cells by fluorescence microscopy. Cells incubated with protein-siRNA complex (80:1) for 24 hrs were fixed, permeabilized, stained with anti-fd phage antibody followed by Alexa fluor 488 goat anti rabbit antibody (Upper, left (no filter), right (FITC filter), or incubated with protein-Alexa fluor 488-labelled siRNA for 24 hours and were trypsinized washed and viewed (Lower, left (no filter), right (FITC-filter).
FIG. 9. illustrates RT-PCR analysis of gene transcription in MCF-7 cells treated with phage-siRNA complexes, including transcription level of the target gene in cells treated with: 1. PRDM14-targeted phage-siRNA; 2. phage-siRNA scrambled; 3. PRDM14-targeted siRNA-lipofectamine, 4. Scrambled siRNA-lipofectamine, 5. Control (no treatment).
FIG. 10. A. illustration of RT-PCR analysis of relative GAPDH gene transcription levels in cells treated with VEEGGYIAA (SEQ ID NO:7) phage-siRNA complexes or siRNA-lipofectamine: No Treatment (1), 20 nM complex (2), 40 nM complex (3), 80 nM complex (4) and 160 nM complex (5), 80 nM siRNA-lipofectamine (6), 80 nM scrambled siRNA-lipofectamine. Relative transcription level of GAPDH gene transcription in MCF-10A cells treated with 80 nM complex (8); and 100 nM complex (9).
FIG. 11. Analysis of GAPDH protein expression in MCF-7 or MCF-10A cells by Western blot. (A). Relative level of protein synthesis in cells treated with: 1. VEEGGYIAA phage-siRNA complex in MCF-7 cells; 2. control VEEGGYIAA phage-NesiRNA in MCF-7 cells; 3. Control non-treated MCF7-cells, 4. VEEGGYIAA phage-siRNA complex in MCF-10A cells; 5. Control non-treated MCF10A-cells. (B). Western blot band intensities quantified using Image J software (NIH). All data represent the mean±S. D.*P<0.05, student-t-test.



DETAILED DESCRIPTION
The present invention is described herein using several definitions, as set forth below and throughout the application.
Unless otherwise specified or indicated by context, the terms “a”, “an”, and “the” mean “one or more.” For example, “a targeted particle” should be interpreted to mean “one or more targeted particles.”
As used herein, “about,” “approximately,” “substantially,” and “significantly” will be understood by persons of ordinary skill in the art and will vary to some extent on the context in which they are used. If there are uses of these terms which are not clear to persons of ordinary skill in the art given the context in which they are used, “about” and “approximately” will mean plus or minus ≦10% of the particular term and “substantially” and “significantly” will mean plus or minus >10% of the particular term.
As used herein, the terms “include” and “including” have the same meaning as the terms “comprise” and “comprising.” For example, a “pharmaceutical composition that includes a targeted particle” should be interpreted to mean “a pharmaceutical composition that comprises a targeted particle.”
In some embodiments, the targeted particles disclosed herein may have one or more dimensions (e.g., dimensions such as length and/or effective diameter) that are between about 1 nm and 1000 nm. As such, the targeted particles may be referred to as “targeted nanoparticles.”
The targeted particles disclosed herein typically include a plurality of landscape phage fusion proteins. Although the term “plurality” should be interpreted to mean more than one, typically, herein the term “plurality” means several hundred or thousand (e.g., at least about 100, 200, 300, 400, 500, 1000, 2000, 3000, or 4000).
Suitable landscape phage fusion proteins for the targeted particles disclosed herein may include pVIII major coat protein either in precursor or mature form, or mutants, variants, or fragments thereof. As used herein, “pVIII” refers to the major coat protein of the filamentous phage fl, fd, and M13 that belong to the Ff family. The completed coding sequence of a filamentous phage display vector f8-1 is deposited at GenBank under accession number AF218734.1 and encodes a major coat protein pVIII mutant precursor having an amino acid sequence MKKSLVLKASVAVATLVPMLSFAAEGEDPAKAAFDSLQASATEYIGYAWAMVV VIVGATIGIKLFKKFTSKAS (SEQ ID NO:1). The complete coding sequence of a filamentous phage display vector f8-5 is deposited at GenBank under accession number AF464138.1 and major coat protein pVIII precursor also having an amino acid sequence MKKSLVLKASVAVATLVPMLSFAAEGEDPAKAAFDSLQASATEYIGYAWAMVV VIVGATIGIKLFKKFTSKAS (SEQ ID NO:1). The vector f8-5 was constructed by engineering several single-base-pair substitutions into filamentous phage cloning vector f8-1 and is intended as a phage-display vector. The vector 18-5 has PstI, BamHI, NheI and MluI cloning sites in gene VIII and confers tetracycline resistance to the host Escherichia coli cells. ‘Stiffers’ between these cloning sites can be replaced with degenerate coding sequences to create libraries of phage displaying different random peptides in exposed area of all 4000 copies of the major coat protein pVIII. The vector f8-5 then may be utilized to create a phage library which may be screened as described herein to isolate phage that bind specifically to a target.
The presently disclosed particles, compositions, kits, and methods contain and/or utilize a plurality of landscape phage fusion proteins complexed with heterologous nucleic acid, the landscape phage fusion proteins displaying a heterologous peptide and the targeted particle binding specifically to a target site. As utilized herein, a protein, polypeptide, and peptide refer to a molecule comprising a chain of amino acid residues joined by amide linkages. The term “amino acid residue,” includes but is not limited to amino acid residues contained in the group consisting of alanine (Ala or A), cysteine (Cys or C), aspartic acid (Asp or D), glutamic acid (Glu or E), phenylalanine (Phe or F), glycine (Gly or G), histidine (His or H), isoleucine (Ile or I), lysine (Lys or K), leucine (Leu or L), methionine (Met or M), asparagine (Asn or N), proline (Pro or P), glutamine (Gln or Q), arginine (Arg or R), serine (Ser or S), threonine (Thr or T), valine (Val or V), tryptophan (Trp or W), and tyrosine (Tyr or Y) residues.
The terms “protein,” “polypeptide,” and “peptide” may be referred to interchangeably herein. However, the terms may be distinguished as follows. A “protein” typically refers to the end product of transcription, translation, and post-translation modifications in a cell. Accordingly, a protein typically exhibits a biological function. A polypeptide is typically an amino acid chain of length ≧50 amino acids (Garrett & Grisham, Biochemistry, 2nd edition, 1999, Brooks/Cole, 110, which is incorporated herein by reference in its entirety). A polypeptide, as contemplated herein, may comprise, but is not limited to, 50, 100, 101, 102, 103, 104, 105, about 110, about 120, about 130, about 140, about 150, about 160, about 170, about 180, about 190, about 200, about 210, about 220, about 230, about 240, about 250, about 275, about 300, about 325, about 350, about 375, about 400, about 425, about 450, about 475, about 500, about 525, about 550, about 575, about 600, about 625, about 650, about 675, about 700, about 725, about 750, about 775, about 800, about 825, about 850, about 875, about 900, about 925, about 950, about 975, about 1000, about 1100, about 1200, about 1300, about 1400, about 1500, about 1750, about 2000, about 2250, about 2500 or more amino acid residues. A peptide, in contrast to a polypeptide, typically is a short polymer of amino acids, of a length typically of 20 or less amino acids (Garrett & Grisham, Biochemistry, 2nd edition, 1999, Brooks/Cole, 110, which is incorporated herein by reference in its entirety). In some embodiments, a peptide as contemplated herein may include no more than about 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acids.
As contemplated herein, “a mutant or variant” of a reference protein, polypeptide, or peptide, typically has an amino acid sequence that is at least about 50% identical (preferably at least about 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, or 99% identical) to the reference protein, polypeptide, or peptide. For example, a mutant or variant of the major coat protein pVIII typically has an amino acid sequence that is at least about 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, or 99% identical to the amino acid sequence of major coat protein pVIII. Preferably, the mutant or variant retains at least one or more biological functions of the reference protein, polypeptide, or peptide. For example, where the reference protein is the major coat protein pVIII, preferably a mutant or variant thereof retains at least one biological function of the major coat protein pVIII precursor such as the biological function of binding to nucleic acid and/or the biological function of assembling into a higher order phage particle.
The landscape phage fusion protein of the presently disclosed targeted particles displays a heterologous peptide. As used herein, “heterologous peptide” may be interpreted to mean a peptide inserted into a landscape phage protein to provide the landscape phage fusion protein having an inserted amino acid sequence with respect to the landscape phage protein. A “heterologous peptide” may have an artificial amino acid sequence or a naturally occurring amino acid sequence not normally present in the landscape phage protein. As used herein, a “heterologous peptide” may refer to a “guest peptide.”
Nucleic acid as contemplated herein includes ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) which may be single- or double-stranded (i.e., ssRNA, ssDNA, dsRNA, dsDNA). Double stranded nucleic acid may be fully or partially double-stranded and may include single-stranded overhangs at one or both ends of the nucleic acid molecule. RNA may include small inhibitory ribonucleic acid (siRNA).
In the disclosed particles, the nucleic acid complexed with the landscape phage fusion proteins may be heterologous. As used herein, “heterologous nucleic acid” may be interpreted to mean non-phage nucleic acid. A heterologous nucleic acid with respect to the landscape phage fusion proteins may be interpreted to mean a nucleic acid having a nucleic acid sequence derived from a species other than the phage from which the landscape phage proteins are derived or a nucleic acid having a nucleic acid sequence not present in the phage genome from which the landscape phage protein are derived. In addition, a “heterologous nucleic acid” may have an artificial nucleic acid sequence or a naturally occurring nucleic acid sequence not normally present in the phage genome from which the landscape phage protein.
A “fragment” of a protein or a polypeptide as contemplated herein refers to a contiguous portion of the amino acid sequence of the protein or polypeptide. A fragment of a protein or polypeptide refers to less than a full-length amino acid sequence of the protein or polypeptide (e.g., where the full-length amino acid sequence is truncated at the N-terminus, the C-terminus, or both termini). For example, a fragment of a protein or polypeptide may comprise or consist of a 5-200, 5-150, 5-100, 5-50, 5-25, 5-15, 10-200, 10-150, 10-100, 10-50, 10-25, or 10-15 contiguous amino acid sequence of the full-length protein or polypeptide. The major coat protein pVIII may be expressed as a precursor which subsequently is processed to provide a fragment of the precursor. For example, the major coat protein pVIII precursor may have a sequence MKKSLVLKASVAVATLVPMLSFAAEGEDPAKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKAS (SEQ ID NO: 1) which subsequently is processed at its N-terminus to remove a 23 amino acid leader sequence and provide a mature fragment having an amino acid sequence AEGEDPAKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKAS (SEQ ID NO:2). Mutants or variants of the mature fragment of major coat protein pVIII precursor may have an amino acid sequence AXXXXXXXXDPAKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKAS (SEQ ID NO:3), where amino acids 2-4 of SEQ ID NO:2 are replaced by a peptide have a random amino acid sequence that is 8 residues in length (i.e., X8). Mutants or variants of the mature fragment of major coat protein pVIII precursor may have an amino acid sequence AXXXXXXXXXPAKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKAS (SEQ ID NO:4), where amino acids 2-5 of SEQ ID NO:2 are replaced by a peptide have a random amino acid sequence that is 9 residues in length (i.e., X9).
The targeted particles disclosed herein may include heterologous nucleic acid that is relatively small in size. For example, in some embodiments the heterologous nucleic acid has a nucleic acid sequence that is about 10-50 nucleotides in length (or about 15-30 nucleotides in length, or about 20-25 nucleotides in length). The nucleic acid may be partially or fully double-stranded and may include single-stranded overhangs at one or both ends of the nucleic acid molecule. The targeted particles may include one type of heterologous nucleic acid (i.e., a single type of nucleic acid molecule) or may include a plurality of different types of heterologous nucleic acid. For example, the targeted particles may include a mixture of different RNA and/or DNA molecules (e.g., a mixture of different siRNAs). Where the targeted particles include a mixture of different nucleic acid molecules, “size” may be determined as “average size,” in which case, the heterologous nucleic acid may have a nucleic acid sequence that is about, on average, 10-50 nucleotides in length (or about 15-30 nucleotides in length, or about 20-25 nucleotides in length).
In some embodiments, the targeted particles disclosed herein may include a plurality of small interfering RNA (siRNA) molecules which may be the same or different. Small interfering RNA (siRNA) is a class of double-stranded RNA (dsRNA) molecules, typically 20-25 nucleotides (nt) in length that are involved in the RNA interference (RNAi) pathway, where it interferes with the expression of a specific gene (e.g., by inducing degradation of mRNA associated with the gene). The structure of siRNAs typically is a dsRNA molecule typically about 19-21 nt in length with 2-nt 3′ overhangs on either end. (See FIG. 1). Each strand of the dsRNA has a 5′ phosphate group and a 3′ hydroxyl group, the result of processing by dicer, an enzyme that converts long dsRNAs or small hairpin RNAs into siRNAs. siRNAs can be transfected into cells by various methods to bring about the specific knockdown of a gene of interest. Generally, any gene whose sequence is known can, thus, be targeted based on sequence complementarity with an appropriately tailored siRNA.
The targeted particles disclosed herein may include siRNA that is targeted to a gene selected from the genes listed in Table 1 which discloses a representative list of genes associated with cancer or associated with resistance to chemotherapeutic treatment of cancer (e.g., drug resistance genes such as PARP-1, MDR1/Pgp, MRP1, and BRCP). For example, the siRNA may modulate the expression of one or more genes listed in Table 1. As used herein, “modulating expression” should be interpreted to mean inhibiting expression or increasing expression. Typically, the siRNA present in the disclosed particles inhibits expression of one or more genes listed in Table 1.
The disclosed particles may be prepared by a method that includes (a) obtaining bacteriophage comprising a plurality of fusion proteins displaying a binding peptide for a desired target site; (b) treating the bacteriophage with a denaturing agent (e.g., a detergent which may include an ionic detergent); (c) preparing a mixture of the treated bacteriophage and heterologous nucleic acid to form the targeted particle; and (d) isolating or purifying the targeted particle from the mixture (e.g., via centrifugation and/or a separation method such as filtration chromatography which may include high pressure liquid chromatography (HPLC)). Typically, the targeted particles are formed from a mixture that comprises a molar excess of fusion proteins relative to nucleic acid (e.g., at least a 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100-fold molar excess). In some embodiments, the targeted particles are formed from a mixture that comprises a 10-80 molar excess of fusion proteins relative to nucleic acid. In other embodiments, the disclosed particles may be prepared by a method that includes: (a) preparing an mixture of (i) a solution of isolated or purified landscape phage fusion proteins (e.g., non-assembled landscape phage fusion proteins or disassembled landscape fusion proteins) and (ii) a solution of isolated or purified heterologous nucleic acid where the targeted particle forms in the mixture; and (b) isolating or purifying the targeted particle from the mixture. In the methods of preparing the targeted particles, the landscape phage fusion proteins may be obtained from recombinant phage or from other recombinant expression systems. Alternatively, the landscape phage fusion proteins may be chemically synthesized. In the methods of preparing the targeted particles, the heterologous nucleic acid may be obtained from recombinant expression systems. Alternatively, the heterologous nucleic may be chemically synthesized.
Proteins, polypeptides, peptides, and nucleic acid may be synthesized by any technique known to those of skill in the art, including the expression of proteins, polypeptides, peptides, and nucleic acid through standard molecular biological techniques, the isolation of proteins, polypeptides, peptides, and nucleic acid from natural sources, or the chemical synthesis of proteins, polypeptides, peptides, or nucleic acid. For example, proteins, polypeptides, peptides may be prepared using synthetic organic chemistry methods, such as solid phase synthesis where an amino acid's carboxylic acid is activated for amide bond formation with dicyclohexyl carbodiimide (Garrett & Grisham, Biochemistry, 2nd edition, 1999, Brooks/Cole, 150).
Proteins, polypeptides, and peptides as contemplated herein may be further modified to include non-amino acid moieties. Modifications may include but are not limited to acylation (e.g., O-acylation (esters), N-acylation (amides), S-acylation (thioesters)), acetylation (e.g., the addition of an acetyl group, either at the N-terminus of the protein or at lysine residues), formylation lipoylation (e.g., attachment of a lipoate, a C8 functional group), myristoylation (e.g., attachment of myristate, a C14 saturated acid), palmitoylation (e.g., attachment of palmitate, a C16 saturated acid), alkylation (e.g., the addition of an alkyl group, such as an methyl at a lysine or arginine residue), isoprenylation or prenylation (e.g., the addition of an isoprenoid group such as farnesol or geranylgeraniol), amidation at C-terminus, glycosylation (e.g., the addition of a glycosyl group to either asparagine, hydroxylysine, serine, or threonine, resulting in a glycoprotein). Distinct from glycation, which is regarded as a nonenzymatic attachment of sugars, polysialylation (e.g., the addition of polysialic acid), glypiation (e.g., glycosylphosphatidylinositol (GPI) anchor formation, hydroxylation, iodination (e.g., of thyroid hormones), and phosphorylation (e.g., the addition of a phosphate group, usually to serine, tyrosine, threonine or histidine).
As used herein, the terms “isolated” or “purified” mean removed from a natural source and/or separated from natural or other components. For example, a solution of an isolated or purified landscape phage fusion protein means a solution comprising a landscape phage fusion protein that is removed from a natural source (e.g., recombinant phage) and/or separated from natural or other components. A solution of an isolated or purified landscape phage fusion protein may be interpreted to mean a solution in which the landscape phage fusion protein represents at least about 90% (w/w) of the solubilized or protein components in the solution (preferably at least about 95%, 96%, 97%, 98%, or 99% of the solubilized or protein components in the solution). A solution of an isolated or purified landscape phage fusion protein may be interpreted to mean a solution in which the landscape phage fusion protein represents at least about 90% (w/w) of the solute of the solution (preferably at least about 95%, 96%, 97%, 98%, or 99% of the solute of the solution). Similarly, a solution of an isolated or purified nucleic acid may be interpreted to mean a solution in which the nucleic acid represents at least about 90% (w/w) of the solubilized or nucleic acid components in the solution (preferably at least about 95%, 96%, 97%, 98%, or 99% of the solubilized or nucleic acid components in the solution). A solution of an isolated or purified nucleic acid may be interpreted to mean a solution wherein the nucleic acid represents at least about 90% (w/w) of the solute of the solution (preferably at least about 95%, 96%, 97%, 98%, or 99% of the solution).
The targeted particles comprise or consist of a plurality of landscape phage fusion proteins complexed with heterologous nucleic acid. The landscape phage fusion protein and the heterologous nucleic acid may represent the sole components of the targeted particles. As such, the targeted particles may consist of the plurality of landscape phage fusion proteins complexed with heterologous nucleic acid. In some embodiments, the landscape phage fusion proteins complexed with heterologous nucleic acid together represent the major components of the targeted particles. For example, the landscape phage fusion proteins complexed with heterologous nucleic acid together may represent at least about 50% (w/w) of the targeted particles (or at least 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, or 99% (w/w) of the targeted particles.
Surprisingly, the disclosed targeted particles can bind to a targeted cell and be taken into the cell without the targeted particles comprising liposomal or micelle components. As such, the disclosed targeted particles may be prepared without liposomal or micelle components and need not include liposomal or micelle components. For example, in some embodiments the disclosed targeted particles do not include amphipathic lipid molecules such as phospholipids. For example, the targeted particles may comprise no more than 5% (w/w) phospholipids (or no more than 4%, 3%, 2%, or 1% (w/w) phospholipids).
The presently disclosed particles may be formulated in pharmaceutical compositions that comprise an “effective amount” of the particles as a therapeutic agent. As used herein, the phrase “effective amount” shall mean that dosage that provides the specific pharmacological response for which the agent is administered in a significant number of patients in need of such treatment. An effective amount of an agent that is administered to a particular patient in a particular instance will not always be effective in treating the conditions/diseases described herein, even though such dosage is deemed to be a therapeutically effective amount by those of skill in the art.
As used herein, a “patient” may be interchangeable with “subject” and means an animal, which may be a human or non-human animal, in need of treatment. Non-human animals may include dogs, cats, horses, cows, pigs, sheep, and the like.
A “patient in need thereof” may include a patient having or at risk for developing a cell proliferative disease or disorder. A patient having or at risk for developing a cell proliferative disease or disorder, such as cancer, may include a patient having or at risk for developing Acute Lymphoblastic Leukemia (ALL), Acute Myeloid Leukemia (AML), Adrenocortical Carcinoma, AIDS-Related Cancers such as Kaposi Sarcoma and Lymphoma, Anal Cancer, Appendix Cancer, Astrocytomas, Atypical Teratoid/Rhabdoid Tumor, Childhood, Central Nervous System, Basal Cell Carcinoma, Bile Duct Cancer such as Extrahepatic Bile Duct Cancer, Bladder Cancer, Bone Cancer such as Osteosarcoma and Malignant Fibrous Histiocytoma, Brain Stem Glioma, Brain-Related Tumors (e.g., Astrocytomas, Brain and Spinal Cord Tumors, Brain Stem Glioma, Central Nervous System Atypical Teratoid/Rhabdoid Tumor, Central Nervous System Embryonal Tumors, Craniopharyngioma, Ependymoblastoma, Ependymoma, Medulloblastoma, Medulloepithelioma, Pineal Parenchymal Tumors of Intermediate Differentiation, and Supratentorial Primitive Neuroectodermal Tumors and Pineoblastoma), Breast Cancer (e.g., female or male), Bronchial Tumors, Burkitt Lymphoma (i.e., Non-Hodgkin Lymphoma), Carcinoid Tumor such as Gastrointestinal Carcinoid Tumors, Central Nervous System (CNS)-Related Tumors (e.g., Atypical Teratoid/Rhabdoid Tumors, Embryonal Tumors, and Primary Lymphomas of the CNS), Cervical Cancer, Chordoma, Chronic Lymphocytic Leukemia (CLL), Chronic Myelogenous Leukemia (CML), Chronic Myeloproliferative Disorders, Colon Cancer, Colorectal Cancer, Craniopharyngioma, Cutaneous T-Cell Lymphoma (e.g., Mycosis Fungoides and Sézary Syndrome), Ductal Carcinoma In Situ (DCIS), Endometrial Cancer, Ependymoblastoma, Ependymoma, Esophageal Cancer, Esthesioneuroblastoma, Ewing Sarcoma Family of Tumors, Extracranial Germ Cell Tumor, Extragonadal Germ Cell Tumor, Eye Cancer (e.g., Intraocular Melanoma and Retinoblastoma), Gallbladder Cancer, Gastric (Stomach) Cancer, Gastrointestinal Stromal Tumors (GIST), Germ Cell Tumor (e.g., Extracranial, Extragonadal, and Ovarian Tumors), Gestational Trophoblastic Tumor, Hairy Cell Leukemia, Head and Neck Cancer, Heart Cancer, Hepatocellular (Liver) Cancer, Histiocytosis such as Langerhans Cell Histiocytosis, Hodgkin Lymphoma, Hypopharyngeal Cancer, Islet Cell Tumors (Endocrine Pancreas), Kidney Cancer (e.g., Renal Cell Cancer), Laryngeal Cancer, Lip and Oral Cavity Cancer, Lobular Carcinoma In Situ (LCIS), Lung Cancer (e.g., Non-Small Cell Lung Cancer or Small Cell Lung Cancer), Macroglobulinemia (e.g., Waldenström Macroglobulinemia, Medulloblastoma, Medulloepithelioma, Melanoma, Merkel Cell Carcinoma, Malignant Mesothelioma, Metastatic Squamous Neck Cancer with Occult Primary, Mouth Cancer, Multiple Endocrine Neoplasia Syndromes, Multiple Myeloma/Plasma Cell Neoplasm, Myelodysplastic Syndromes, Myelodysplastic/Myeloproliferative Neoplasms, Nasal Cavity and Paranasal Sinus Cancer, Nasopharyngeal Cancer, Neuroblastoma, Oral Cancer, Oropharyngeal Cancer, Ovarian Cancer (e.g., Epithelial, Germ Cell Tumor, and Low Malignant Potential Tumor), Pancreatic Cancer (e.g., Islet Cell Tumors), Papillomatosis, Paraganglioma, Parathyroid Cancer, Penile Cancer, Pharyngeal Cancer, Pheochromocytoma, Pineal Parenchymal Tumors of Intermediate Differentiation, Pineoblastoma and Supratentorial Primitive Neuroectodermal Tumors, Pituitary Tumor, Plasma Cell Neoplasm/Multiple Myeloma, Pleuropulmonary Blastoma, Childhood, Prostate Cancer, Rectal Cancer, Renal Pelvis and Ureter Transitional Cell Cancer, Respiratory Tract Cancer with Chromosome 15 Changes, Rhabdomyosarcoma, Salivary Gland Cancer, Skin Cancer, Small Intestine Cancer, Squamous Cell Carcinoma, Stomach (Gastric) Cancer, Supratentorial Primitive Neuroectodermal Tumors, Testicular Cancer, Throat Cancer, Thymoma and Thymic Carcinoma, Thyroid Cancer, Trophoblastic Tumor, Urethral Cancer, Uterine Cancer (Endometrial), Uterine Sarcoma, Vaginal Cancer, Vulvar Cancer, or Wilms Tumor. In some embodiments, the patient has or is at risk for developing breast cancer.
As contemplated herein, a patient may include a patient having or at risk for developing cancer and who has been administered a chemotherapeutic agent. Chemotherapeutic agents may include agents selected from a group consisting of F13-cis-Retinoic Acid, 2-CdA, 2-Chlorodeoxyadenosine, 5-Azacitidine, 5-Fluorouracil, 5-FU, 6-Mercaptopurine, 6-MP, 6-TG, 6-Thioguanine, Abraxane, Accutane®, Actinomycin-D, Adriamycin®, Adrucil®, Afinitor®, Agrylin®, Ala-Cort®, Aldesleukin, Alemtuzumab, ALIMTA, Alitretinoin, Alkaban-AQ®, Alkeran®, All-transretinoic Acid, Alpha Interferon, Altretamine, Amethopterin, Amifostine, Aminoglutethimide, Anagrelide, Anandron®, Anastrozole, Arabinosylcytosine, Ara-C, Aranesp®, Aredia®, Arimidex®, Aromasin®, Arranon®, Arsenic Trioxide, ArzerraTM, Asparaginase, ATRA, Avastin®, Azacitidine, BCG, BCNU, Bendamustine, Bevacizumab, Bexarotene, BEXXAR®, Bicalutamide, BiCNU, Blenoxane®, Bleomycin, Bortezomib, Busulfan, Busulfex®, C225, Calcium Leucovorin, Campath®, Camptosar®, Camptothecin-11, Capecitabine, CaracTM, Carboplatin, Carmustine, Carmustine Wafer, Casodex®, CC-5013, CCI-779, CCNU, CDDP, CeeNU, Cerubidine®, Cetuximab, Chlorambucil, Cisplatin, Citrovorum Factor, Cladribine, Cortisone, Cosmegen®, CPT-11, Cyclophosphamide, Cytadren®, Cytarabine, Cytarabine Liposomal, Cytosar-U®, Cytoxan®, Dacarbazine, Dacogen, Dactinomycin, Darbepoetin Alfa, Dasatinib, Daunomycin, Daunorubicin, Daunorubicin Hydrochloride, Daunorubicin Liposomal, DaunoXome®, Decadron, Decitabine, Delta-Cortefg, Deltasone®, Denileukin Diftitox, DepoCytTM, Dexamethasone, Dexamethasone Acetate, Dexamethasone Sodium Phosphate, Dexasone, Dexrazoxane, DHAD, DIC, Diodex, Docetaxel, Doxil®, Doxorubicin, Doxorubicin Liposomal, DroxiaTM, DTIC, DTIC-Dome®, Duralone®, Efudex®, EligardTM, EllenceTM, EloxatinTM, Elspar®, Emcyt®, Epirubicin, Epoetin Alfa, Erbitux, Erlotinib, Erwinia L-asparaginase, Estramustine, Ethyol, Etopophos®, Etoposide, Etoposide Phosphate, Eulexin®, Everolimus, Evista®, Exemestane, Fareston®, Faslodex®, Femara®, Filgrastim, Floxuridine, Fludara®, Fludarabine, Fluoroplex®, Fluorouracil, Fluorouracil (cream), Fluoxymesterone, Flutamide, Folinic Acid, FUDR®, Fulvestrant, G-CSF, Gefitinib, Gemcitabine, Gemtuzumab ozogamicin, Gemzar, GleevecTM, Gliadel® Wafer, GM-CSF, Goserelin, Granulocyte-Colony Stimulating Factor, Granulocyte Macrophage Colony Stimulating Factor, Halotestin®, Herceptin®, Hexadrol, Hexylen®, Hexamethylmelamine, HMM, Hycamtin®, Hydrea®, Hydrocort Acetate®, Hydrocortisone, Hydrocortisone Sodium Phosphate, Hydrocortisone Sodium Succinate, Hydrocortone Phosphate, Hydroxyurea, Ibritumomab, Ibritumomab Tiuxetan, Idamycin®, Idarubicin, Ifex®, IFN-alpha, Ifosfamide, IL-11, IL-2, Imatinib mesylate, Imidazole Carboxamide, Interferon alfa, Interferon Alfa-2b (PEG Conjugate), Interleukin-2, Interleukin-11, Intron A® (interferon alfa-2b), Iressa®, Irinotecan, Isotretinoin Ixabepilone IxempraTM, Kidrolase (t), Lanacort®, Lapatinib, L-asparaginase, LCR, Lenalidomide, Letrozole, Leucovorin, Leukeran, LeukineTM, Leuprolide, Leurocristine, LeustatinTM, Liposomal Ara-C, Liquid Pred®, Lomustine, L-PAM, L-Sarcolysin, Lupron®, Lupron Depot®, Matulane®, Maxidex, Mechlorethamine, Mechlorethamine Hydrochloride, Medralone®, Medrol®, Megace®, Megestrol, Megestrol Acetate, Melphalan, Mercaptopurine, Mesna, MesnexTM, Methotrexate, Methotrexate Sodium, Methylprednisolone, Meticorten®, Mitomycin, Mitomycin-C, Mitoxantrone, M-Prednisol®, MTC, MTX, Mustargen®, Mustine, Mutamycin®, Myleran®, MylocelTM, Mylotarg®, Navelbine®, Nelarabine, Neosar®, NeulastaTM, Neumega®, Neupogen®, Nexavar®, Nilandron®, Nilotinib, Nilutamide, Nipent®, Nitrogen Mustard, Novaldex®, Novantrone®, Nplate, Octreotide, Octreotide acetate, Ofatumumab, Oncospar®, Oncovin®, Ontak®, OnxalTM, Oprelvekin, Orapred®, Orasone®, Oxaliplatin, Paclitaxel, Paclitaxel Protein-bound, Pamidronate, Panitumumab, Panretin®, Paraplatin®, Pediapred®, PEG Interferon, Pegaspargase, Pegfilgrastim, PEG-INTRONTM, PEG-L-asparaginase, PEMETREXED, Pentostatin, Phenylalanine Mustard, Platinol®, Platinol-AQ®, Prednisolone, Prednisone, Prelone®, Procarbazine, PROCRIT®, Proleukin®, Prolifeprospan 20 with Carmustine Implant, Purinethol®, Raloxifene, Revlimid®, Rheumatrex®, Rituxan®, Rituximab, Roferon-A® (Interferon Alfa-2a), Romiplostim, Rubex®, Rubidomycin hydrochloride, Sandostatin®, Sandostatin LAR®, Sargramostim, Solu-Cortef®, Solu-Medrol®, Sorafenib, SPRYCELTM, STI-571, Streptozocin, SU11248, Sunitinib, Sutent®, Tamoxifen, Tarceva®, Targretin®, Tasigna®, Taxol®, Taxotere®, Temodar, Temozolomide, Temsirolimus, Teniposide, TESPA, Thalidomide, Thalomid®, TheraCys®, Thioguanine, Thioguanine Tabloid®, Thiophosphoamide, Thioplex®, Thiotepa, TICE®, Toposar, Topotecan, Toremifene, Torisel®, Tositumomab, Trastuzumab, Treanda®, Tretinoin, TrexallTM, Trisenox®, TSPA, TYKERB®, VCR, VectibixTM, Velban®, Velcade®, VePesid®, Vesanoid®, ViadurTM, Vidaza®, Vinblastine, Vinblastine Sulfate, Vincasar Pfs®, Vincristine, Vinorelbine, Vinorelbine tartrate, VLB, VM-26, Vorinostat, VP-16, Vumon®, Xeloda®, Zanosar®, ZevalinTM, Zinecard®, Zoladex®, Zoledronic acid, Zolinza, and Zometa®. In some embodiments, the patient is refractory.
The presently disclosed particles formulated as pharmaceutical compositions may be administered to a patient in need thereof together with a chemotherapeutic agent. The chemotherapeutic agent may have been administered to the patient prior to when the pharmaceutical compositions comprising the disclosed particles are administered to the patient. In other embodiments, the chemotherapeutic agent is administered to the patient concurrently or after the pharmaceutical compositions comprising the disclosed particles are administered to the patient.
The targeted particles utilized in the methods disclosed herein may be formulated as pharmaceutical compositions that include: (a) a therapeutically effective amount of the targeted particles as disclosed herein; and (b) one or more pharmaceutically acceptable carriers, excipients, or diluents. The pharmaceutical compositions may be administered prophylactically or therapeutically. In prophylactic administration, the compositions may be administered in an amount sufficient to induce a response for protecting against disease. In therapeutic applications, the compositions are administered to a patient in an amount sufficient to elicit a therapeutic effect (e.g., a response which cures or at least partially arrests or slows symptoms and/or complications of disease (i.e., a “therapeutically effective dose”)).
The pharmaceutical composition disclosed herein may be delivered via a variety of routes. However, typical delivery routes involve parental administration (e.g., intravenous, intradermal, intramuscular or subcutaneous delivery). Pharmaceutical compositions adapted for parenteral administration include aqueous and non-aqueous sterile injection solutions which may contain anti-oxidants, buffers, bacteriostats and solutes which render the formulation isotonic with the blood of the intended recipient; and aqueous and non-aqueous sterile suspensions which may include suspending agents and thickening agents. The formulations may be presented in unit-dose or multi-dose containers, for example sealed ampoules and vials, and may be stored in a freeze-dried (lyophilized) condition requiring only the addition of the sterile liquid carrier, for example water for injections, immediately prior to use. Extemporaneous injection solutions and suspensions may be prepared from sterile powders, granules and tablets.
The pharmaceutical compositions may include a carrier. For example, the carrier may be selected from the group consisting of proteins, carbohydrates, sugar, talc, magnesium stearate, cellulose, calcium carbonate, and starch-gelatin paste.
The pharmaceutical compositions may include a diluent. Suitable diluents may include pharmaceutically acceptable aqueous and non-aqueous sterile injection solutions, inert fillers, such as microcrystalline cellulose, lactose, dibasic calcium phosphate, saccharides, and mixtures of any of the foregoing. Examples of diluents include microcrystalline cellulose, such as Avicel® PH101 and Avicel® PH102; lactose such as lactose monohydrate, lactose anhydrous, and Pharmatose® DCL21; dibasic calcium phosphate such as Emcompress®; mannitol; starch; sorbitol; sucrose; and glucose.
The pharmaceutical compositions may include an excipient. Suitable excipients include lightly crosslinked polyvinyl pyrrolidone, corn starch, potato starch, maize starch, and modified starches, croscarmellose sodium, cross-povidone, sodium starch glycolate, and mixtures thereof.
EXAMPLES
The following Examples are illustrative and are not intended to limit the scope of the claimed subject matter.
Example 1
Targeted Delivery of siRNA Via Phage Fusion Protein
Abstract
RNA interference (RNAi) holds considerable promise as a therapeutic approach to silence disease-causing genes. The primary obstacles in achieving the addressed delivery of small interfering RNA (siRNA) in vivo include, non-competitive cells uptake by non-target cells, degradation by nucleases and endosomal trapping. A new challenge in the targeted delivery of siRNA, is development of highly selective, stable, active and physiologically acceptable ligands that would navigate the encapsulated drugs to the site of the disease and control their unloading inside the cancer cells. Here, a nanotechnological platform for breast tumor-targeted siRNA delivery is proposed. This platform utilizes the unique propensity of phage proteins to self-assemble in the presence of nucleic acids and to form particles mimicking the structure of the phage capsid.
Introduction
Selective oncogene silencing, mediated by siRNA shows promise for cancer treatment. However, the obstacles in successfully delivering siRNA hinder the therapeutic viability of this treatment. Various viral and non-viral methods are used to overcome the challenge of delivery of siRNA into the cells including liposomes9, cell penetrating peptides4,5 and cell-targeting ligands. Phage display has emerged as a robust technology for identifying cell-targeting ligands10. Here, landscape phage display is proposed to provide a source of targeting ligands. The major principle of the proposed innovative idea is that the gene silencing siRNAs are encapsulated into targeted phage proteins that protect them against degradation and deliver to the receptors, cells, tissues and organs that have been used for selection of the precisely targeting phage. The tumor-specific peptides genetically fused to all 4,000 copies of the phage's major coat protein pVIII6 have been affinity selected from multibillion clone libraries (see FIG. 2) by their ability to bind very specifically cancer cells, penetrate into the cells or accumulate in the tumor-surrounding vasculature. The landscape phage fusion proteins can be isolated from these phage, mixed with siRNA such that the landscape phage fusion proteins and siRNA self-assemble into phage-like particles. (See FIGS. 3-5). In FIG. 4, the diameter of the single complex is larger than the determined values because of the tip broadening effect. The presence of a dense layer was confirmed with nanolithography experiments (not shown). In FIG. 4, single siRNA-nanophage complexes can be seen beside the scratched hole (left and right). The holes on the surrounding area are defects in the APTES layer.
Experimental Methods and Results
Landscape Phage Clones for Breast Cancer Cells
Highly selective and specific landscape phage ligands for human breast carcinoma cells MCF-7 and ZR-75-1 were selected using landscape phage libraries f8/8 and f8/910,21 (also see Example 2 below) and earlier developed biopanning procedure14. Individual phage clones identified by DNA sequencing were propagated, purified and tested for binding with target MCF-7 or ZR-75-1 cells in comparison with control normal epithelial cells MCF-10A and hepatocellular carcinoma cells HepG2 (FIG. 6). Phage harboring peptide VEEGGYIAA (SEQ ID NO:7) was identified as being one of the most selective binders to MCF-7 cells, which was also able to penetrate into the cells. Control phage bearing the unrelated peptide VPEGAFSS (SEQ ID NO:8) and the “wild-type” vector phage f8-5 demonstrated negligible binding to cells.
siRNAs Targeted to MCF-7 Cells by Phage Protein.
Fusion protein of phage VEEGGYIAA (SEQ ID NO:7) was isolated in octameric form by size exclusion chromatography of cholate-solubilized phage17. This inexpensive procedure allows obtaining 10-20 mg of a pure target-specific phage coat protein from 1 L of culture and can be optimized and scaled up. A complex of the phage protein with AlexaFluor-488-labeled siRNA (molar ratio 80:1) was obtained by gradual decrease of concentration of cholate by ultrafiltration. Encapsulation of siRNA and its release after digestion of the protein by protease K was controlled by agarose gel electrophoresis (FIG. 7). When the complex was incubated with MCF-7 cells for 24 hrs, internalization of siRNA was observed by fluorescence microscopy (FIG. 8). The silencing effect of protein-targeted siRNA was tested on MCF-7 cells using proline rich domain-14 (PRDM 14) gene as a model. Protein-targeted PRDM-14-specific siRNA down-regulated PRDM-14 gene expression by 40% as compared to targeted scrambled siRNA (FIG. 9). Gene specificity and cell targeting potential of complexes of phage proteins with siRNA was also demonstrated using another model-gene glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in cancer and normal cells MCF-7 and MCF-10A (FIGS. 10 and 11).
MCF-7 cells were treated with phage-siRNAs comprising siRNA targeted to GADPH. FIG. 10 illustrates RT-PCR analysis of GAPDH gene transcription cells treated with VEEGGYIAA (SEQ ID NO:7) phage-siRNA complexes or siRNA-lipofectamine. FIG. 11 illustrates an analysis of GAPDH protein expression by Western blot. MCF-7 or MCF-100A cells were treated with VEEGGYIAA phage-siRNA complex (80/1) (50 nM siRNA) or control VEEGGYIAA phage-NesiRNA (50 nM siRNA) and incubated for 72 h. Cells were lysed and portion of cell extract was run on 4-20% Tris-HCl gel, transferred to PVDF membrane and probed with monoclonal anti-GAPDH antibody (1:2000 dilution) followed by incubation with peroxidase-conjugated Affinipure Goat Anti-mouse IgG (1:5000). The bands corresponding to GAPDH were visualized using chemiluminescent substrate solution. Membranes were treated with the Western blot stripping buffer and probed with polyclonal anti-β-Actin antibody (1:2000) followed by incubation with peroxidase-conjugated Affinipure Goat Anti-rabbit IgG (1:5000). The bands corresponding to actin were visualized using chemiluminescent substrate solution.
These data can justify the idea of using phage protein-targeted siRNA as breast cancer-specific therapeutics. The results show that siRNAs targeted to the breast cancer cells MCF-7 via their encapsulation by phage fusion proteins down-regulated targeted gene expression and inhibited protein synthesis in MCF-7 cells.
Conclusion
The landscape phage bearing MCF-7-specific peptide, VEEGGYIAA (SEQ ID NO:7) was selected from a landscape library f8/8 and a biopanning protocol against MCF-7 cells. Phage fusion protein-siRNA complex was formed by self-assembly of VEEGGYIAA (SEQ ID NO:7) phage protein and PRDM14 or GAPDH specific siRNAs. Delivery of gene specific siRNAs via the complex downregulated their corresponding gene expression in MCF-7 cells but not in MCF-10A cells, demonstrating that pVIII coat protein displaying cancer cell-targeting peptides can be effectively used to deliver siRNA into the target cells and silence target specific genes.
Example 2
Targeted Delivery of siRNA into Breast Cancer Cells Via Landscape Phage Fusion Proteins
Abstract
Chemotherapy plays a minimal role in recurrent settings of breast cancer where the tumor is in the chemotherapy refractory state. The resistance of breast cancer cells to cytotoxic drugs is acquired mainly due to the overproduction of some proteins, such as MDR1/Pgp, MRP1, BRCP and PARP, which protect the cells in different ways against cytotoxic anti-tumor agents, such as doxorubicin. Effectiveness of chemotherapy can be increased by supplementing chemotherapy with siRNA that inhibits the synthesis of drug-resistance proteins. Although unprotected “naked” siRNAs have demonstrated significant specific effect in some model systems, a systemic use of naked siRNA medicines is hindered by their fast destruction in physiological liquids, insufficient tissue bioavailability and poor cellular uptake. A challenge for clinical use of siRNAs as anti-breast cancer drugs is development of tumor selective, stable, active and physiologically stable targeting carriers that would make stable complexes with siRNA, protect them from degradation, deliver them to the tumors and control their unloading inside the cancer cells. Disclosed here are phage-fusion protein-siRNA-nanoparticles, “phage-siRNAs”, in which siRNAs are encapsulated and targeted to breast tumors by phage fusion proteins with high selectivity, affinity and stability. It is hypothesized that silencing of genes that relate to tumor drug resistance by targeting of siRNAs via breast cancer specific phage proteins may significantly enhance the sensitivity of tumor cells to chemotherapy.
Introduction
Breast cancer is the most common cancer and the second leading cause of cancer death in American women. Despite advances in early detection and understanding of breast cancer mechanisms, about 30% of cured patients with early-stage breast cancer have recurrent disease. Their treatment may require systemic chemotherapy using cytotoxic, hormonal, and immunotherapeutic agents. In general, systemic agents are effective at the beginning of therapy in 90% of primary breast cancers and 50% of metastases1. However, after a certain period, progression occurs. At that point, tumor cells become resistant to systematic therapy. It was shown that resistance of breast cancer cells to chemotherapy can be eliminated or essentially decreased by the use of small (short) interfering RNAs (siRNAs) that inhibit synthesis of proteins related to tumor drug resistance2. However, a systematic use of siRNAs is hindered by their instability in physiological liquids, limited tissue bioavailability and poor cellular uptake. Cellular delivery and bioavailability of siRNA can be increased by their encapsulation into nanoparticulate carriers3, or association with cell penetrating peptides (CPP)4,5,6. Efficacy of siRNA nanomedicines can be further enhanced by their conjugation with cell-targeting ligands (CTL) that bind to cancer-specific cellular receptors7,8. The availability of combinatorial peptide libraries adds another availing dimension to the concept of the targeted antitumor pharmaceuticals8,9. They provide a rich source of peptides targeted to specific tissue, cell, receptor or cellular compartments.
A new challenge, within the frame of the emerging concept of targeted siRNA delivery is development of highly selective, stable, active and physiologically acceptable ligands that would protect siRNAs against degradation in the blood stream, navigate them to the site of disease and provide a means for their penetration into the target cancer cells. To respond to this challenge, siRNA-nanoparticles are proposed, in which siRNA is encapsulated and targeted to the breast tumor cells by phage fusion proteins having high selectivity, affinity and stability. The tumor-specific fusion phage proteins can be isolated from phage particles affinity selected from multibillion clone libraries by their ability to bind cancer cells very specifically and penetrate into the cells or accumulate in the tumor-surrounding vasculature. Phage proteins can be converted then into siRNA-phage protein complexes, named “phage-siRNAs”, by their self-assembly, as illustrated in FIGS. 3-5. Gene silencing siRNA may be encapsulated and protected in the phage-siRNA particle and can be targeted to cells, tissues and organs via a binding peptide on the phage (e.g., presented by the pVIII major coat protein) for selective delivery of gene silencing siRNA.
Phage display technology is based on a genetic fusion of phage coat proteins with foreign peptides to achieve their surface display on a viable and infective virion16. Foreign peptides have been displayed on the pVIII protein and the pill minor coat protein9,10. In the pVIII display format (landscape phage), the guest peptide is fused to every pVIII subunit, increasing the virion's mass by up to 20%. Such particles retain their ability to infect host E. coli bacteria and form phage progeny. Landscape phage and their isolated fusion proteins have been shown to serve as substitutes for antibodies against various antigens and receptors, including cancer cells, in drug/gene-delivery vehicles and biosensors11,16. Recent studies have shown that landscape phage proteins can serve as ligands that target doxorubicin-containing liposomes (Doxil) to cancer cells and enhance their cytotoxic effects12,19.
Landscape phage represents an attractive platform for targeted siRNA delivery due to its unique characteristics: a) the phage capsid formed by  ̃4,000 domains of the coat protein associated with phage DNA is very stable and is resistant to stressful aggressive media and high temperature13,14; b) reproduction of phage relies on powerful and natural mechanisms of phage infection, biosynthesis and self-assembly; and c) tumor-targeted landscape phages can be affinity selected from multibillion clone libraries due to their ability to bind very specifically to cancer cells, penetrate into the cells or accumulate in the tumor-surrounding vasculature. Importantly, selection of phage that binds or internalizes into cancer cells can be designed, so that only phage capable of internalizing and escaping endosomes are selected20, where endosomal escape of siRNA from the vehicle carrying the siRNA is desirable for biological activity of the siRNA; d) targeted fusion phages are able to penetrate into mammalian cells, survive inside cellular compartments and deliver gene into target cells15,16. In view of these properties of phage as an efficient natural delivery system, the phage-like platform may provide a superior vehicle for siRNA delivery, for example to cancer cells such as breast cancer cells. The proposed new strategy of siRNA delivery to breast cancer cells explores the unique propensity of phage proteins to self-assemble in the presence of nucleic acids and to form particles mimicking the structure of the phage capsid15,16. Owing to high stability of assembled phage proteins in stressful environments and their tight association with nucleic acid, siRNA may be shielded and protected from serum endonucleases and other distressing environmental factors. At the same time, phage capsid becomes unstable when phage interacts with cellular membranes which may enable a release of encapsulated siRNA inside the cells. Furthermore, phage fusion protein can target siRNA specifically not only to a target cell but can navigate it further to a specific cytoplasmic destination. Therefore, phage-siRNAs may provide a highly selective, stable, active and physiologically acceptable breast cancer nanomedicine.
Furthermore, complexes of siRNAs with breast cancer-specific phage fusion proteins may significantly enhance the sensitivity of tumor cells to chemotherapy where the siRNA silences genes related to tumor drug resistance. For example, silencing of breast cancer-specific genes in patients may be achieved by administering to the patients preparations of siRNAs self-assembled with phage proteins that are targeted to breast cancer cells. The phage proteins may protect siRNAs against degradation and mediate their efficient internalization into the breast cancer cells, thereby inducing siRNA-specific gene silencing. The proposed technique may be tested and optimized using model doxorubicin-resistant breast cancer cells MDA-MB-231 and representative gene PARP-1 encoding poly(ADP-ribose) polymerase-1. Doxorubicin induces expression of the PARP-1 gene which subsequently causes resistance of the cells to treatment with doxorubicin. Inhibition of PARP-1 gene expression potentiates the effect of doxorubicin18 suggesting that PARP-1 gene expression has an active role in development of chemoresistant status in breast cancer cells. The MDA-MB-231/PARP-1 model may demonstrate specificity and selectivity of targeted nanomedicines both in vitro which subsequently may be confirmed in vivo using a mice xenograft models.
Accordingly, landscape phage libraries f8/8 and f8/910,21 may be used to select phage binding to MDA-MB-231 cells. Four rounds of selection may be performed and the isolated clones may be identified by their DNA sequence. Binding specificity of the phage may be determined in a phage capture assay12. Phage fusion proteins may be isolated by stripping the phage and may be purified from viral DNA and traces of other proteins by size-exclusion chromatography. PARP-1-targeted siRNAs or scrambled siRNAs may be mixed with increasing concentrations of phage proteins, to provide phage protein/siRNA complexes. Complexes with optimized compositions of siRNAs and proteins may be purified by size-exclusion chromatography and analyzed by electrophoresis. Size distribution of the phage protein/siRNA complexes may be analyzed by dynamic light scattering. Efficacy of intracellular delivery of fluorescent siRNA may be determined using microscopy.
The cytotoxic potential of doxorubicin and Doxil may be studied in combination with phage-siRNAs (targeted to PARP-1) and control complexes, as described below. Activation of gene PARP-1 by doxorubicin and effect of the phage-siRNAs on PARP-1 mRNA and protein levels may be determined by RT-PCR and western blot analysis. Stability, uptake, and antitumor effect of phage-siRNA complexes in comparison with control preparations may be tested in mice with xenografts of MDA-MB-231 cells, as described in detail below.
Methods
Phage Libraries and Selection Procedures.
Cancer cell-binding phages may be obtained using established selection protocols14. An aliquot of the library ( ̃1011 virions) in a washing/blocking buffer may be added to an empty depletion flask and incubated for 1 h at 20° C. Non-bound phages may be transferred to another depletion flask treated with serum, and then to a depletion flask containing non-target cells MCF-10A. Cell surface-bound phage may be retrieved with acid elution buffer. The eluate may be neutralized and concentrated by ultrafiltration. To recover cell-penetrating phage, cells may be scraped, pelleted by centrifugation and lysed in 2% sodium deoxycholate buffer. Both phage fractions (eluted fraction and lysis fraction) may be amplified separately and used in subsequent rounds of selection. Phage input/output ratio may be followed by phage titering. Following the 4-6th round, a segment of phage gene VIII DNA from 100 individual clones may be amplified by PCR and sequenced to reveal the protein sequences responsible for binding to the cells.
Binding specificity and selectivity of phages may be determined in a phage capture assay adapted for 96-well culture plate format12. Selectivity of phages may be determined by measuring their binding to target cancer cells in comparison with serum, control normal and other cancer cells. Briefly, amplified test phages and control phages may be incubated with MDA-MB-231 target cells, control epithelial MCF-10A cells, unrelated hepatocellular carcinoma HepG2 cancer cells and control serum-treated wells. Unbound phages may be washed away and bound phages may be recovered with CHAPS buffer. The amount of phage in fractions may be determined by its titering in E. coli K91 BlueKan host bacterial cells. Phage recovery may be expressed as a ratio of input to output phage. To determine a localization of phages in the cells, cell-associated phages may be eluted with acid buffer. Next, the cells may be washed with neutral buffer and finally with CHAPS buffer for recovery of cell-penetrated phage particles, To determine a role of cell metabolism in association of the phage with live cells, the incubation of phage with cells may be carried out at 20° C. and at 37° C. with and without serum.
Fusion Phage Proteins.
Phage fusion 55- or 56-mer coat proteins with general formula AXXXXXXXXDPAKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKAS (SEQ ID NO:3), where X is a random amino acid or AXXXXXXXXXPAKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKAS (SEQ ID NO:4), may be prepared by stripping phage virions in cholate22. Briefly, the mixture (1:2 v/v) of phage in TBS buffer ( ̃1 mg/ml), 120 mM cholate in 10 mM Tris-HCl, 0.2 mM EDTA, pH 8.0, and 5% chloroform may be incubated overnight at 37° C. on rotator. The protein may be purified by size-exclusion chromatography using a Sepharose 6B-CL column (1 cm×45 cm), eluted with 100 mM cholate in 10 mM Tris-HCl, 0.2 mM EDTA pH 8.0. The chromatographic profile may be controlled by Econo UV monitor. The isolated protein typically is an aggregate with molecular weight  ̃46 KDa (8-mer) determined by chromatography on a calibrated column. Concentration of proteins may be measured spectrophotometrically using their molar extinction calculated using PROTEAN program (DNA STAR Inc., Madison, Wis.).
Preparation and Characterization of Targeted Phage-siRNA Preparations.
PARP-1-targeted siRNAs (sense 5′-GGAUGAUCUUCGACGUGGA-3′ (SEQ ID NO:5), antisense 5′-UCCACGUCGAAGAUCAUCC-3′ (SEQ ID NO:6)) or scrambled siRNAs (200 nM; Invitrogen, Carlsbad, Calif.) may be mixed with 10-80-fold molar excess of phage proteins and centrifuged in 30 Kda Amicon unit and washed two times with 10 mM TrisHCl buffer to remove the detergent and form a complex comprising phage proteins and siRNA. The complex may be analyzed by: (1) agarose gel analysis with SIBR-green staining; and (2) size-exclusion chromatography. Size distribution will analyzed by the dynamic light scattering using a Beckman Coulter N4 Plus Particle analyzer (Beckman Coulter, Inc., Fullerton, Calif.).
Analysis of PARP-1 Gene Activation in MDA-MB-231 Cells.
MDA-MB-231 cells grown during 24 h in a 6-well plate/well may be treated with Doxil (10-200 μg/ml) for 1 hr. Total RNA may be extracted using Micro RNA isolation kit (Qiagen, GmbH, Hilden, Germany) and RT-PCR may be performed to determine the level of PARP-1 gene expression. To determine a level of PARP-1 protein synthesis, cells may be lysed with 70 μL of RIPA buffer (Sigma) containing protease inhibitor cocktail (7 μL) and 2 mM PMSF. The protein concentration in whole cell lysate may be measured by Biorad DC protein assay. Cell extract may be separated by gel-electrophoresis (4-20%; Biorad) and transferred to PVDF membrane. The membrane may be blocked in wash buffer (PBS, 5% nonfat dry milk) at 20° C. for 1 h; incubated overnight at 4° C. with polyclonal anti-PAR-1 antibody (1:500 dilution) (Trivegen); washed with PBS/0.5% Tween-20 four times; incubated with peroxidase-conjugated Affinipure Goat Anti-rabbit IgG (1:5000) (Jackson Immunoresearch) at 20° C. for 1 h; washed with PBS/0.5% Tween-20 four times; incubated with 5 ml of West Pico Luminol/Enhancer Solution and 5 ml West Pico Stable Peroxide Solution (Pierce Super Signal West Pico Biotin detection Kit) for 10 min; stripped using the western blot stripping buffer for 10 min; probed with monoclonal anti-PARP-1 antibody (1:2000) for 1 hr; loaded on to a cassette and exposed to radiographic film for 1-2 min. Images may be scanned using a scanner and quantified by NIH image J software.
Knockdown of Target Gene.
MDA-MB-231 cells grown in a 6-well plate may be treated with Doxil (10-200 g/ml) for 1 hr. Media may be replaced with fresh media containing complexes of a) phage proteins with siRNAs targeted to PARP-1; b) phage protein with scrambled siRNA, c) non-related phage protein with siRNA targeted to PARP-1; or d) complex of lipofectamine with siRNA targeted to PARP-1. Plates may be incubated for 24 hr in DMEM supplemented with 10% FBS at 37° C. in a humidified 5% CO2 incubator. Total RNA may be extracted at 24-72 h time points using Micro RNA isolation kit (Qiagen, GmbH, Hilden, Germany), and the knockdown of PARP-1 gene by phage protein-siRNA or siRNA-lipofectamine preparations may be determined by RT-PCR using One step Access RT-PCR kit (Promega). A level of PARP-1 protein synthesis will be analyzed by western blot as describe above.
Cytotoxicity Assay.
Cells may be grown in 96-well plates to  ̃75% confluence to obtain  ̃5×105 cells/well. The plates may be washed twice with serum-free DMEM media and treated with Doxil (10-200 μg/ml) for 1 hr. After 1 hr, media may be replaced and fresh media containing complexes of a) phage proteins with siRNA targeted to PARP-1, b) phage protein with scrambled siRNA, non-related phage-protein with siRNA targeted to PARP-1, or c) lipofectamine with siRNA targeted to PARP-1. After incubation for 24-72 h in DMEM supplemented with 10% FBS at 37° C. in a humidified 5% CO2 incubator, the plates may be washed 3 times with serum-free DMEM media, and incubated with CellTiter 96® Aqueous One solution for 1-4 hrs at 37° C., 5% CO2. The cell survival rate may be estimated by measuring the absorbance of the MTS degradation product at 492 nm using the Tecan SpectraFluor Plus plate reader (Tecan Systems, Inc., San Jose, Calif.).
Tumor Inoculation in Mice.
The experiments may be performed in BALB/c/nu/nu (nude) mice (n=15; Charles River Laboratories, Wilmington, Mass.). The protocol may be approved by Institutional animal care and use committee (I-COOK committee) of Auburn University and Northeastern University. MDA-MB-231 cells may be grown in the logarithmic phase, centrifuged (100 r/min, 5 min) and the supernatant removed. Each nude mouse may be injected with 0.2 ml (i.e., 5×106 cells) cell suspension in the subcutaneous layer in the right lower back using a 1-ml syringe. Tumors may be grown while keeping animals in aseptic conditions for 7-10 days until the tumor can be discovered by direct palpation. There may be at least 5 animals in each group. Experimental mice bearing a tumor xenograft may be treated at chosen times with Doxil and protein/siRNA formulations intravenously. Complex formulations and controls may be given twice per week for a total of 5 weeks. The mice may be monitored daily for tumor size. Tumor measurements may be performed using calipers to measure the tumor in two dimensions, at the longest and widest points at approximately 90° C. to each other. Tumor volume may be calculated as: Volume=(width2×length)/2. Antitumor activity may be assessed according to the guidelines established by the National Cancer Institute. Microscopic postmortem tumor tissue examination may be performed using a standard hematoxylyn/eosin staining.
Accumulation of Phage-siRNAs in Tumors.
The experiments may be performed in nude mice following the above-described protocol, which may be approved by the Institutional Animal Care and Use Committee. The mice may be injected with targeted phage-siRNAs in the tail vein (approx. 10 days after tumor inoculation). At 1, 3, 6, and 24 h post injection, mice may be sacrificed by CO2 euthanasia. Tumors may be removed, imbedded in paraffin and sectioned. Tumor sections may be incubated with anti-fd phage antibody (1:500) and visualized under microscope.
Assessment of Therapeutic Anticancer Effect of Phase-siRNAs.
Mice inoculated with MDA-MB-231 tumor cells (5 mice per group) may be treated twice weekly with a) Doxil, b) Doxil and phage-siRNAs (targeted to PARP-1) preparation, c) Doxil and phage-siRNAs (scrambled), d) Doxil and non-related phage-siRNA (targeted to PARP-1), or e) siRNA alone for 7 weeks through intravenous injection. The dosing regimen may be adjusted based on the analysis of the intratumoral drug accumulation, as described. The mice may be monitored on alternate days for tumor size for 5 weeks depending on the tumor type and examined routinely for tumor appearance. Tumor measurements may be performed as described above. Microscopic postmortem tumor tissue examination may be performed using a standard hemato-xylyn/eosin staining, apoptotic staining using TUNEL kit (ApoAlert, BD Biosciences) and immunohistochemistry using phospho-Ser473 Akt antibody (Cell Signaling) with VectaStain IHC peroxidase kit (Vector Labs). Angiogenesis in the tumors may be assessed by assessment of microvessel density following staining of the tumor sections with anti-CD31 antibody (Santa Cruz).
Statistical Treatment of the Data to be Obtained.
The choice of statistical tests, as well as of group size for both in vitro and in vivo experiments may be made according to the principles formulated by Siegel23. Each in vitro experiment will include 4-5 points for each measurement, and each animal experiment will include 5-6 mice and may be repeated twice. In vitro data may be analyzed using the Student's t-test for two independent samples and two-way ANOVA analysis with Tukey's HSD Post-Hoc test for three or more independent samples. These tests may be analyzed using Kaliedagraph® software, version 3.6 (Synergy Software, Reading, Pa.). Non-parametric, Wilcoxon rank sum test may be used to evaluate the results on the tumor accumulation and inhibition for various formulations. The exact probability values under the randomization test may be computed with the aid of the software RS1. P<0.05 may be considered significant. If required, the survival data may be analyzed by log rank Kaplan-Meier method using GraphPad P.
REFERENCES


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In the foregoing description, it will be readily apparent to one skilled in the art that varying substitutions and modifications may be made to the invention disclosed herein without departing from the scope and spirit of the invention. The invention illustratively described herein suitably may be practiced in the absence of any element or elements, limitation or limitations which is not specifically disclosed herein. The terms and expressions which have been employed are used as terms of description and not of limitation, and there is no intention that in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the invention. Thus, it should be understood that although the present invention has been illustrated by specific embodiments and optional features, modification and/or variation of the concepts herein disclosed may be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this invention.
Citations to a number of patent and non-patent references are made herein. The cited references are incorporated by reference herein in their entireties. In the event that there is an inconsistency between a definition of a term in the specification as compared to a definition of the term in a cited reference, the term should be interpreted based on the definition in the specification.








TABLE 1







ABL1
v-abl Abelson murine leukemia viral oncogene homolog 1


ABL2
v-abl Abelson murine leukemia viral oncogene homolog 2


ACSL3
acyl-CoA synthetase long-chain family member 3


AF15Q14
AF15q14 protein


AF1Q
ALL1-fused gene from chromosome 1q


AF3p21
SH3 protein interacting with Nck, 90 kDa (ALL1 



fused gene from 3p21)


AF5q31
ALL1 fused gene from 5q31


AKAP9
A kinase (PRKA) anchor protein (yotiao) 9


AKT1
v-akt murine thymoma viral oncogene homolog 1


AKT2
v-akt murine thymoma viral oncogene homolog 2


ALDH2
aldehyde dehydrogenase 2 family (mitochondrial)


ALK
anaplastic lymphoma kinase (Ki-1)


ALO17
KIAA1618 protein


APC
adenomatous polyposis of the colon gene


ARHGEF12
RHO guanine nucleotide exchange factor (GEF) 



12 (LARG)


ARHH
RAS homolog gene family, member H (TTF)


ARID1A 
AT rich interactive domain 1A (SWI-like)


ARNT
aryl hydrocarbon receptor nuclear translocator


ASPSCR1
alveolar soft part sarcoma chromosome region,



candidate 1


ASXL1
additional sex combs like 1


ATF1
activating transcription factor 1


ATIC
5-aminoimidazole-4-carboxamide ribonucleotide 



formyltransferase/IMP cyclohydrolase


ATM
ataxia telangiectasia mutated


ATRX
alpha thalassemia/mental retardation syndrome X-linked


BAP1
BRCA1 associated protein-1 (ubiquitin 



carboxy-terminal hydrolase)


BCL10
B-cell CLL/lymphoma 10


BCL11A
B-cell CLL/lymphoma 11A


BCL11B
B-cell CLL/lymphoma 11B (CTIP2)


BCL2
B-cell CLL/lymphoma 2


BCL3
B-cell CLL/lymphoma 3


BCL5
B-cell CLL/lymphoma 5


BCL6
B-cell CLL/lymphoma 6


BCL7A
B-cell CLL/lymphoma 7A


BCL9
B-cell CLL/lymphoma 9


BCR
breakpoint cluster region


BHD
folliculin, Birt-Hogg-Dube syndrome


BIRC3
baculoviral IAP repeat-containing 3


BLM
Bloom Syndrome


BMPR1A
bone morphogenetic protein receptor, type IA


BRAF
v-raf murine sarcoma viral oncogene homolog B1


BRCA1
familial breast/ovarian cancer gene 1


BRCA2
familial breast/ovarian cancer gene 2


BRCP
breast cancer resistance protein


BRD3
bromodomain containing 3


BRD4
bromodomain containing 4


BRIP1
BRCA1 interacting protein C-terminal helicase 1


BTG1
B-cell translocation gene 1, anti-proliferative


BUB1B
BUB1 budding uninhibited by benzimidazoles 



1 homolog beta (yeast)


C12orf9
chromosome 12 open reading frame 9


C15orf21
chromosome 15 open reading frame 21


C15orf55
chromosome 15 open reading frame 55


C16orf75
chromosome 16 open reading frame 75


CANT1
calcium activated nucleotidase 1


CARD11
caspase recruitment domain family, member 11


CARS
cysteinyl-tRNA synthetase


CBFA2T1
core-binding factor, runt domain, alpha subunit 2; 



translocated to, 1 (ETO)


CBFA2T3
core-binding factor, runt domain, alpha subunit 2; 



translocated to, 3 (MTG-16)


CBFB
core-binding factor, beta subunit


CBL
Cas-Br-M (murine) ecotropic retroviral transforming


CBLB
Cas-Br-M (murine) ecotropic retroviral transforming



sequence b


CBLC
Cas-Br-M (murine) ecotropic retroviral transforming



sequence c


CCNB1IP1
cyclin B1 interacting protein 1, E3 ubiquitin protein ligase


CCND1
cyclin D1


CCND2
cyclin D2


CCND3
cyclin D3


CD273
programmed cell death 1 ligand 2


CD274
CD274 molecule


CD74
CD74 molecule, major histocompatibility complex, 



class II invariant chain


CD79A
CD79a molecule, immunoglobulin-associated alpha


CD79B
CD79b molecule, immunoglobulin-associated beta


CDH1
cadherin 1, type 1, E-cadherin (epithelial) (ECAD)


CDH11
cadherin 11, type 2, OB-cadherin (osteoblast)


CDK4
cyclin-dependent kinase 4


CDK6
cyclin-dependent kinase 6


CDKN2A -
cyclin-dependent kinase inhibitor 2A (p16(INK4a)) gene


p16(INK4a)



CDKN2A-
cyclin-dependent kinase inhibitor 2A- p14ARF protein


p14ARF



CDKN2C
cyclin-dependent kinase inhibitor 2C (p18,



inhibits CDK4)


CDX2
caudal type homeo box transcription factor 2


CEBPA
CCAAT/enhancer binding protein (C/EBP), alpha


CEP1
centrosomal protein 1


CHCHD7
coiled-coil-helix-coiled-coil-helix domain containing 7


CHEK2
CHK2 checkpoint homolog (S. pombe)


CHIC2
cysteine-rich hydrophobic domain 2


CHN1
chimerin (chimaerin) 1


CIC
capicua homolog (Drosophila)


CIITA
class II, major histocompatibility complex, transactivator


CLTC
clathrin, heavy polypeptide (Hc)


CLTCL1
clathrin, heavy polypeptide-like 1


CMKOR1
chemokine orphan receptor 1


COL1A1
collagen, type I, alpha 1


COPEB
core promoter element binding protein (KLF6)


COX6C
cytochrome c oxidase subunit VIc


CREB1
cAMP responsive element binding protein 1


CREB3L1
cAMP responsive element binding protein 3-like 1


CREB3L2
cAMP responsive element binding protein 3-like 2


CREBBP
CREB binding protein (CBP)


CRLF2
cytokine receptor-like factor 2


CRTC3
CREB regulated transcription coactivator 3


CTNNB1
catenin (cadherin-associated protein), beta 1


CYLD
familial cylindromatosis gene


D10S170
DNA segment on chromosome 10 (unique) 170, 



H4 gene (PTC1)


DAXX
death-domain associated protein


DDB2
damage-specific DNA binding protein 2


DDIT3
DNA-damage-inducible transcript 3


DDX10
DEAD (Asp-Glu-Ala-Asp) box polypeptide 10


DDX5
DEAD (Asp-Glu-Ala-Asp) box polypeptide 5


DDX6
DEAD (Asp-Glu-Ala-Asp) box polypeptide 6


DEK
DEK oncogene (DNA binding)


DICER1
dicer 1, ribonuclease type III


DNMT3A
DNA (cytosine-5-)-methyltransferase 3 alpha


DUX4
double homeobox, 4


EBF1
early B-cell factor 1


EGFR
epidermal growth factor receptor (erythroblastic leukemia 



viral (v-erb-b) oncogene homolog, avian)


EIF4A2
eukaryotic translation initiation factor 4A, isoform 2


ELF4
E74-like factor 4 (ets domain transcription factor)


ELK4
ELK4, ETS-domain protein (SRF accessory protein 1)


ELKS
ELKS protein


ELL
ELL gene (11-19 lysine-rich leukemia gene)


ELN
elastin


EML4
echinoderm microtubule associated protein like 4


EP300
300 kd E1A-Binding protein gene


EPS15
epidermal growth factor receptor pathway substrate 



15 (AF1p)


ERBB2
v-erb-b2 erythroblastic leukemia viral oncogene 



homolog 2, neuro/glioblastoma 



derived oncogene homolog (avian)


ERCC2
excision repair cross-complementing rodent repair



deficiency, complementation group 2 



(xeroderma pigmentosum D)


ERCC3
excision repair cross-complementing rodent repair 



deficiency, complementation group 3 (xeroderma



pigmentosum group B complementing)


ERCC4
excision repair cross-complementing rodent repair 



deficiency, complementation group 4


ERCC5
excision repair cross-complementing rodent 



repair deficiency, complementation group 5 



(xeroderma pigmentosum, complementation 



group G (Cockayne syndrome))


ERG
v-ets erythroblastosis virus E26 oncogene like (avian)


ETV1
ets variant gene 1


ETV4
ets variant gene 4 (E1A enhancer binding protein, E1AF)


ETV5
ets variant gene 5


ETV6
ets variant gene 6 (TEL oncogene)


EVI1
ecotropic viral integration site 1


EWSR1
Ewing sarcoma breakpoint region 1 (EWS)


EXT1
multiple exostoses type 1 gene


EXT2
multiple exostoses type 2 gene


EZH2
enhancer of zeste homolog 2


FACL6
fatty-acid-coenzyme A ligase, long-chain 6


FANCA
Fanconi anemia, complementation group A


FANCC
Fanconi anemia, complementation group C


FANCD2
Fanconi anemia, complementation group D2


FANCE
Fanconi anemia, complementation group E


FANCF
Fanconi anemia, complementation group F


FANCG
Fanconi anemia, complementation group G


FBXW7
F-box and WD-40 domain protein 7 



(archipelago homolog, Drosophila)


FCGR2B
Fc fragment of IgG, low affinity IIb, receptor for (CD32)


FEV
FEV protein - (HSRNAFEV)


FGFR1
fibroblast growth factor receptor 1


FGFR1OP
FGFR1 oncogene partner (FOP)


FGFR2
fibroblast growth factor receptor 2


FGFR3
fibroblast growth factor receptor 3


FH
fumarate hydratase


FHIT
fragile histidine triad gene


FIP1L1
FIP1 like 1 (S. cerevisiae)


FLI1
Friend leukemia virus integration 1


FLJ27352
BX648577, FLJ27352 hypothetical LOC145788


FLT3
fms-related tyrosine kinase 3


FNBP1
formin binding protein 1 (FBP17)


FOXL2
forkhead box L2


FOXO1A
forkhead box O1A (FKHR)


FOXO3A
forkhead box O3A


FOXP1
forkhead box P1


FSTL3
follistatin-like 3 (secreted glycoprotein)


FUS
fusion, derived from t(12;16) malignant liposarcoma


FVT1
follicular lymphoma variant translocation 1


GAS7
growth arrest-specific 7


GATA1
GATA binding protein 1 (globin transcription factor 1)


GATA2
GATA binding protein 2


GATA3
GATA binding protein 3


GMPS
guanine monphosphate synthetase


GNA11
guanine nucleotide binding protein (G protein), 



alpha 11 (Gq class)


GNAQ
guanine nucleotide binding protein (G protein), 



q polypeptide


GNAS
guanine nucleotide binding protein (G protein), 



alpha stimulating activity polypeptide 1


GOLGA5
golgi autoantigen, golgin subfamily a, 5 (PTC5)


GOPC
golgi associated PDZ and coiled-coil motif containing


GPC3
glypican 3


GPHN
gephyrin (GPH)


GRAF
GTPase regulator associated with focal adhesion 



kinase pp125(FAK)


HCMOGT-1
sperm antigen HCMOGT-1


HEAB
ATP_GTP binding protein


HEI10
enhancer of invasion 10 - fused to HMGA2


HERPUD1
homocysteine-inducible, endoplasmic reticulum stress-



inducible, ubiquitin-like domain member 1


HIP1
huntingtin interacting protein 1


HISTIH4I
histone I, H4i (H4FM)


HLF
hepatic leukemia factor


HLXB9
homeo box HB9


HMGA1
high mobility group AT-hook 1


HMGA2
high mobility group AT-hook 2 (HMGIC)


HNRNPA2B1
heterogeneous nuclear ribonucleoprotein A2/B1


HOOK3
hook homolog 3


HOXA11
homeo box A11


HOXA13
homeo box A13


HOXA9
homeo box A9


HOXC11
homeo box C11


HOXC13
homeo box C13


HOXD11
homeo box D11


HOXD13
homeo box D13


HRAS
v-Ha-ras Harvey rat sarcoma viral oncogene homolog


HRPT2
hyperparathyroidism 2


HSPCA
heat shock 90 kDa protein 1, alpha


HSPCB
heat shock 90 kDa protein 1, beta


IDH1
isocitrate dehydrogenase 1 (NADP+), soluble


IDH2
socitrate dehydrogenase 2 (NADP+), mitochondrial


IGH@
immunoglobulin heavy locus


IGK@
immunoglobulin kappa locus


IGL@
immunoglobulin lambda locus


IKZF1
IKAROS family zinc finger 1


IL2
interleukin 2


IL21R
interleukin 21 receptor


IL6ST
interleukin 6 signal transducer (gp130, oncostatin 



M receptor)


IRF4
interferon regulatory factor 4


IRTA1
immunoglobulin superfamily receptor translocation 



associated 1


ITK
IL2-inducible T-cell kinase


JAK1
Janus kinase 1


JAK2
Janus kinase 2


JAK3
Janus kinase 3


JAZF1
juxtaposed with another zinc finger gene 1


JUN
jun oncogene


KDM5A
lysine (K)-specific demethylase 5A, JARID1A


KDM5C
lysine (K)-specific demethylase 5C (JARID1C)


KDM6A
lysine (K)-specific demethylase 6A, UTX


KDR
vascular endothelial growth factor receptor 2


KIAA1549
KIAA1549


KIT
v-kit Hardy-Zuckerman 4 feline sarcoma viral 



oncogene homolog


KLK2
kallikrein-related peptidase 2


KRAS
v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog


KTN1
kinectin 1 (kinesin receptor)


LAF4
lymphoid nuclear protein related to AF4


LASP1
LIM and SH3 protein 1


LCK
lymphocyte-specific protein tyrosine kinase


LCP1
lymphocyte cytosolic protein 1 (L-plastin)


LCX
leukemia-associated protein with a CXXC domain


LHFP
lipoma HMGIC fusion partner


LIFR
leukemia inhibitory factor receptor


LMO1
LIM domain only 1 (rhombotin 1) (RBTN1)


LMO2
LIM domain only 2 (rhombotin-like 1) (RBTN2)


LPP
LIM domain containing preferred translocation 



partner in lipoma


LYL1
lymphoblastic leukemia derived sequence 1


MADH4
Homolog of Drosophila Mothers Against 



Decapentaplegic 4 gene


MAF
v-maf musculoaponeurotic fibrosarcoma 



oncogene homolog


MAFB
v-maf musculoaponeurotic fibrosarcoma oncogene 



homolog B (avian)


MALT1
mucosa associated lymphoid tissue lymphoma 



translocation gene 1


MAML2
mastermind-like 2 (Drosophila)


MAP2K4
mitogen-activated protein kinase kinase 4


MDM2
Mdm2 p53 binding protein homolog


MDM4
Mdm4 p53 binding protein homolog


MDR1/Pgp
Multi-drug resistance protein/P-glycoprotein


MDS1
myelodysplasia syndrome 1


MDS2
myelodysplastic syndrome 2


MECT1
mucoepidermoid translocated 1


MEN1
multiple endocrine neoplasia type I gene


MET
met proto-oncogene (hepatocyte growth factor receptor)


MHC2TA
MHC class II transactivator


MITF
microphthalmia-associated transcription factor


MKL1
megakaryoblastic leukemia (translocation) 1


MLF1
myeloid leukemia factor 1


MLH1
E. coli MutL homolog gene


MLL
myeloid/lymphoid or mixed-lineage leukemia



(trithorax homolog, Drosophila)


MLL2
myeloid/lymphoid or mixed-lineage leukemia 2


MLL3
myeloid/lymphoid or mixed-lineage leukemia 3


MLLT1
myeloid/lymphoid or mixed-lineage leukemia (trithorax



homolog, Drosophila); translocated to, 1 (ENL)


MLLT10
myeloid/lymphoid or mixed-lineage leukemia (trithorax



homolog, Drosophila); translocated to, 10 (AF10)


MLLT2
myeloid/lymphoid or mixed-lineage leukemia (trithorax



homolog, Drosophila); translocated to, 2 (AF4)


MLLT3
myeloid/lymphoid or mixed-lineage leukemia (trithorax



homolog, Drosophila); translocated to, 3 (AF9)


MLLT4
myeloid/lymphoid or mixed-lineage leukemia (trithorax



homolog, Drosophila); translocated to, 4 (AF6)


MLLT6
myeloid/lymphoid or mixed-lineage leukemia (trithorax



homolog, Drosophila); translocated to, 6 (AF17)


MLLT7
myeloid/lymphoid or mixed-lineage leukemia (trithorax



homolog, Drosophila); translocated to, 7 (AFX1)


MN1
meningioma (disrupted in balanced translocation) 1


MPL
myeloproliferative leukemia virus oncogene, 



thrombopoietin receptor


MRP1
multiple drug resistance protein 1


MSF
MLL septin-like fusion


MSH2
mutS homolog 2 (E. coli)


MSH6
mutS homolog 6 (E. coli)


MSI2
musashi homolog 2 (Drosophila)


MSN
moesin


MTCP1
mature T-cell proliferation 1


MUC1
mucin 1, transmembrane


MUTYH
mutY homolog (E. coli)


MYB
v-myb myeloblastosis viral oncogene homolog


MYC
v-myc myelocytomatosis viral oncogene homolog (avian)


MYCL1
v-myc myelocytomatosis viral oncogene homolog 1,



lung carcinoma derived (avian)


MYCN
v-myc myelocytomatosis viral related oncogene,



neuroblastoma derived (avian)


MYD88
myeloid differentiation primary response gene (88)


MYH11
myosin, heavy polypeptide 11, smooth muscle


MYH9
myosin, heavy polypeptide 9, non-muscle


MYST4
MYST histone acetyltransferase (monocytic leukemia) 



4 (MORF)


NACA
nascent-polypeptide-associated complex alpha 



polypeptide


NBS1
Nijmegen breakage syndrome 1 (nibrin)


NCOA1
nuclear receptor coactivator 1


NCOA2
nuclear receptor coactivator 2 (TIF2)


NCOA4
nuclear receptor coactivator 4 - PTC3 (ELE1)


NF1
neurofibromatosis type 1 gene


NF2
neurofibromatosis type 2 gene


NFE2L2
nuclear factor (erythroid-derived 2)-like 2 (NRF2)


NFIB
nuclear factor I/B


NFKB2
nuclear factor of kappa light polypeptide gene



enhancer in B-cells 2 (p49/p100)


NIN
ninein (GSK3B interacting protein)


NKX2-1
NK2 homeobox 1


NONO
non-POU domain containing, octamer-binding


NOTCH1
Notch homolog 1, translocation-associated



(Drosophila) (TAN1)


NOTCH2
Notch homolog 2


NPM1
nucleophosmin (nucleolar phosphoprotein B23, numatrin)


NR4A3
nuclear receptor subfamily 4, group A, member 3 (NOR1)


NRAS
neuroblastoma RAS viral (v-ras) oncogene homolog


NSD1
nuclear receptor binding SET domain protein 1


NTRK1
neurotrophic tyrosine kinase, receptor, type 1


NTRK3
neurotrophic tyrosine kinase, receptor, type 3


NUMA1
nuclear mitotic apparatus protein 1


NUP214
nucleoporin 214 kDa (CAN)


NUP98
nucleoporin 98 kDa


NUT
nuclear protien in testis


OLIG2
oligodendrocyte lineage transcription factor 2 (BHLHB1)


OMD
osteomodulin


P2RY8
purinergic receptor P2Y, G-protein coupled, 8


PAFAH1B2
platelet-activating factor acetylhydrolase, isoform Ib, 



beta subunit 30 kDa


PALB2
partner and localizer of BRCA2


PARP-1
poly [ADP-ribose] polymerase 1


PAX3
paired box gene 3


PAX5
paired box gene 5 (B-cell lineage specific activator



protein)


PAX7
paired box gene 7


PAX8
paired box gene 8


PBRM1
polybromo 1


PBX1
pre-B-cell leukemia transcription factor 1


PCM1
pericentriolar material 1 (PTC4)


PCSK7
proprotein convertase subtilisin/kexin type 7


PDE4DIP
phosphodiesterase 4D interacting protein (myomegalin)


PDGFB
platelet-derived growth factor beta polypeptide



(simian sarcoma viral (v-sis) oncogene homolog)


PDGFRA
platelet-derived growth factor, alpha-receptor


PDGFRB
platelet-derived growth factor receptor, beta polypeptide


PER1
period homolog 1 (Drosophila)


PHOX2B
paired-like homeobox 2b


PICALM
phosphatidylinositol binding clathrin assembly protein 



(CALM)


PIK3CA
phosphoinositide-3-kinase, catalytic, alpha polypeptide


PIK3R1
phosphoinositide-3-kinase, regulatory subunit 1 (alpha)


PIM1
pim-1 oncogene


PLAG1
pleiomorphic adenoma gene 1


PML
promyelocytic leukemia


PMS1
PMS1 postmeiotic segregation increased 1 (S. cerevisiae)


PMS2
PMS2 postmeiotic segregation increased 2 (S. cerevisiae)


PMX1
paired mesoderm homeo box 1


PNUTL1
peanut-like 1 (Drosophila)


POU2AF1
POU domain, class 2, associating factor 1 (OBF1)


POU5F1
POU domain, class 5, transcription factor 1


PPARG
peroxisome proliferative activated receptor, gamma


PPP2R1A
protein phosphatase 2, regulatory subunit A, alpha


PRCC
papillary renal cell carcinoma (translocation-associated)


PRDM1
PR domain containing 1, with ZNF domain


PRDM16
PR domain containing 16


PRF1
perforin 1 (pore forming protein)


PRKAR1A
protein kinase, cAMP-dependent, regulatory, type I, 



alpha (tissue specific extinguisher 1)


PRO1073
PRO1073 protein (ALPHA)


PSIP2
PC4 and SFRS1 interacting protein 2 (LEDGF)


PTCH
Homolog of Drosophila Patched gene


PTEN
phosphatase and tensin homolog gene


PTPN11
protein tyrosine phosphatase, non-receptor type 11


RAB5EP
rabaptin, RAB GTPase binding effector protein 1 



(RABPT5)


RAD51L1
RAD51-like 1 (S. cerevisiae) (RAD51B)


RAF1
v-raf-1 murine leukemia viral oncogene homolog 1


RALGDS
ral guanine nucleotide dissociation stimulator


RANBP17
RAN binding protein 17


RAP1GDS1
RAP1, GTP-GDP dissociation stimulator 1


RARA
retinoic acid receptor, alpha


RB1
retinoblastoma gene


RBM15
RNA binding motif protein 15


RECQL4
RecQ protein-like 4


REL
v-rel reticuloendotheliosis viral oncogene



homolog (avian)


RET
ret proto-oncogene


ROS1
v-ros UR2 sarcoma virus oncogene homolog 1 (avian)


RPL22
ribosomal protein L22 (EAP)


RPN1
ribophorin I


RUNDC2A
RUN domain containing 2A


RUNX1
runt-related transcription factor 1 (AML1)


RUNXBP2
runt-related transcription factor binding protein 2



(MOZ/ZNF220)


SBDS
Shwachman-Bodian-Diamond syndrome protein


SDH5
chromosome 11 open reading frame 79


SDHB
succinate dehydrogenase complex, subunit B, 



iron sulfur (Ip)


SDHC
succinate dehydrogenase complex, subunit C, 



integral membrane protein, 15 kDa


SDHD
succinate dehydrogenase complex, subunit D, 



integral membrane protein


SEPT6
septin 6


SET
SET translocation


SETD2
SET domain containing 2


SFPQ
splicing factor proline/glutamine rich(polypyrimidine 



tract binding protein associated)


SFRS3
splicing factor, arginine/serine-rich 3


SH3GL1
SH3-domain GRB2-like 1 (EEN)


SIL
TAL1 (SCL) interrupting locus


SLC45A3
solute carrier family 45, member 3


SMARCA4
SWI/SNF related, matrix associated, actin dependent 



regulator of chromatin, subfamily a, member 4


SMARCB1
SWI/SNF related, matrix associated, actin dependent 



regulator of chromatin, subfamily b, member 1


SMO
smoothened homolog (Drosophila)


SOCS1
suppressor of cytokine signaling 1


SOX2
SRY (sex determining region Y)-box 2


SRGAP3
SLIT-ROBO Rho GTPase activating protein 3


SS18
synovial sarcoma translocation, chromosome 18


SS18L1
synovial sarcoma translocation gene on 



chromosome 18-like 1


SSH3BP1
spectrin SH3 domain binding protein 1


SSX1
synovial sarcoma, X breakpoint 1


SSX2
synovial sarcoma, X breakpoint 2


SSX4
synovial sarcoma, X breakpoint 4


STK11
serine/threonine kinase 11 gene (LKB1)


STL
Six-twelve leukemia gene


SUFU
suppressor of fused homolog (Drosophila)


SUZ12
suppressor of zeste 12 homolog (Drosophila)


SYK
spleen tyrosine kinase


TAF15
TAF15 RNA polymerase II, TATA box binding protein



(TBP)-associated factor, 68 kDa


TAL1
T-cell acute lymphocytic leukemia 1 (SCL)


TAL2
T-cell acute lymphocytic leukemia 2


TCEA1
transcription elongation factor A (SII), 1


TCF1
transcription factor 1, hepatic (HNF1)


TCF12
transcription factor 12 (HTF4, helix-loop-helix 



transcription factors 4)


TCF3
transcription factor 3 (E2A immunoglobulin enhancer 



binding factors E12/E47)


TCL1A
T-cell leukemia/lymphoma 1A


TCL6
T-cell leukemia/lymphoma 6


TET2
tet oncogene family member 2


TFE3
transcription factor binding to IGHM enhancer 3


TFEB
transcription factor EB


TFG
TRK-fused gene


TFPT
TCF3 (E2A) fusion partner (in childhood Leukemia)


TFRC
transferrin receptor (p90, CD71)


THRAP3
thyroid hormone receptor associated protein 3 (TRAP150)


TIF1
transcriptional intermediary factor 1 (PTC6, TIF1A)


TLX1
T-cell leukemia, homeobox 1 (HOX11)


TLX3
T-cell leukemia, homeobox 3 (HOX11L2)


TMPRSS2
transmembrane protease, serine 2


TNFAIP3
tumor necrosis factor, alpha-induced protein 3


TNFRSF14
tumor necrosis factor receptor superfamily, member 



14 (herpesvirus entry mediator)


TNFRSF17
tumor necrosis factor receptor superfamily, member 17


TNFRSF6
tumor necrosis factor receptor superfamily, 



member 6 (FAS)


TOP1
topoisomerase (DNA) I


TP53
tumor protein p53


TPM3
tropomyosin 3


TPM4
tropomyosin 4


TPR
translocated promoter region


TRA@
T cell receptor alpha locus


TRB@
T cell receptor beta locus


TRD@
T cell receptor delta locus


TRIM27
tripartite motif-containing 27


TRIM33
tripartite motif-containing 33 (PTC7, TIF1G)


TRIP11
thyroid hormone receptor interactor 11


TSC1
tuberous sclerosis 1 gene


TSC2
tuberous sclerosis 2 gene


TSHR
thyroid stimulating hormone receptor


TTL
tubulin tyrosine ligase


USP6
ubiquitin specific peptidase 6 (Tre-2 oncogene)


VHL
von Hippel-Lindau syndrome gene


WAS
Wiskott-Aldrich syndrome


WHSC1
Wolf-Hirschhorn syndrome candidate 1(MMSET)


WHSC1L1
Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)


WIF1
WNT inhibitory factor 1


WRN
Werner syndrome (RECQL2)


WT1
Wilms tumour 1 gene


WTX
family with sequence similarity 123B (FAM123B)


XPA
xeroderma pigmentosum, complementation group A


XPC
xeroderma pigmentosum, complementation group C


ZNF145
zinc finger protein 145 (PLZF)


ZNF198
zinc finger protein 198


ZNF278
zinc finger protein 278 (ZSG)


ZNF331
zinc finger protein 331


ZNF384
zinc finger protein 384 (CIZ/NMP4)


ZNF521
zinc finger protein 521


ZNF9
zinc finger protein 9 (a cellular retroviral 



nucleic acid binding protein)


ZNFN1A1
zinc finger protein, subfamily 1A, 1 (Ikaros)

## Claims

1. A targeted particle comprising:
(a) a plurality of landscape phage fusion proteins comprising a filamentous phage pVIII major coat protein displaying a heterologous peptide, the heterologous peptide capable of directing binding of the targeted particle to a specific target site,
(b) a heterologous nucleic acid that is 10-50 nucleotides in length, and
(c) no more than 5% (w/w) phospholipids,
wherein the targeted particle comprises a molar excess of the landscape fusion proteins relative to the heterologous nucleic acid within a range of 60-fold to 100-fold, and
wherein the targeted particle is formed by self-assembly in vitro of complexes formed between the plurality of landscape phage fusion proteins and the heterologous nucleic acid, such that the landscape phage fusion proteins encapsulate the nucleic acid in the particle so as to protect the nucleic acid from degradation and allow delivery of the heterologous nucleic acid to the target site.

2. The targeted particle of claim 1, wherein the heterologous nucleic acid is siRNA.

3. The targeted particle of claim 1, wherein the heterologous peptide comprises no more than 9 amino acids.

4. The targeted particle of claim 1, wherein the targeted particle binds specifically to cancer cells.

5. The targeted particle of claim 4, wherein the cancer cells are breast cancer cells.

6. The targeted particle of claim 1, wherein the heterologous nucleic acid is siRNA that inhibits expression of a gene selected from a group consisting of ABI1, ABL2, ACSL6, AF1Q, AF5Q31, AKT1, AKT2, ARNT, ASPSCR1, ATF1, ATIC, BCL10, BCRP, BFHD, BIRC3, BMPR1A, BTG1, CBFA2T1, CBFA2T3, CBFB, CCND1, CDC2, CDK4, CHIC2, CHN1, COPEB, COX6C, CTNNB1, CYLD, DDB2, DDIT3, DEK, Eif4a, EIF4A2, EPS15, ERBB2, ERCC2, ERCC3, ERCC5, ERG, ETV4, ETV6, EWSR1, EXT1, EXT2, FANCC, FANCG, EGER1OP, FGFR3, FH, FIP1L1, FUS, GAS7, GATA1, GMPS, GOLGA5, GPC (gene), GPHN, HIST1H4I, HRAS, HSPCA, IL21R, IIRF4, KRAS2, LASP1, LCP1, LHFP, LMO2, LYL1, MADH4, MDR1/Pgp, MEIS1, MLF1, MLH1, MLLT3, MLLT6, MNAT1, MRP1, MSF, MSH2, MSN, MUTYH, MYC, MYCL1, MYCN, NCOA4, NF2, NPM1, NRAS, PARP1, PAX8, PCBD, PDGFB, PHOX2B, PIM1, PLK2, PNUTL1, POU2F1, PPARG, PRCC, PRKACB, PRKAR1A, PTEN, PTPN11, RABEP1, RAD51L1, RAP1GDS1, RARA, RBI, REL, RET, RHOH, RPL22, SBDS, SDHB, SEPTIN6, SET, SH3GL1, SS18L1, SSX1, SSX2, SSX4, STAT3, TAF15, TCF12, TCL1A, TFE3, TFEB, TFG, TFPT, TFRC, TNFRSF6, TP53, TPM3, TPM4, TRIP11, VHL, WAS, WT1, ZNF198, ZNF278, ZNF384, and ZNFN1A.

7. The targeted particle of claim 1, wherein the heterologous nucleic acid is siRNA that inhibits gene expression of a gene selected from PARP1, MDR1/Pgp, MRP1, and BCRP.

8. A pharmaceutical composition comprising:
(a) the targeted particle of claim 1; and
(b) a pharmaceutical carrier, excipient, or diluent.

9. A method for inhibiting expression of a gene in a cell comprising contacting the cell with the targeted particle of claim 1, the targeted particle binding specifically to the cell and comprising a siRNA that inhibits expression of the gene.

10. A method for forming the targeted particle of claim 1, the method comprising:
(a) obtaining bacteriophage comprising a plurality of fusion proteins displaying a binding peptide for a desired target site;
(b) treating the bacteriophage with a denaturing agent and isolating or purifying the fusion proteins from the treated bacteriophage;
(c) preparing a mixture of the isolated or purified fusion proteins and a heterologous nucleic acid that is 10-50 nucleotides in length to form the targeted particle; and
(d) purifying the targeted particle from the mixture.

11. A method for forming the targeted particle of claim 1, the method comprising:
(a) preparing a mixture of
(i) a solution of isolated or purified landscape phage fusion proteins displaying a binding peptide for a desired target site, wherein the fusion proteins are in non-assembled form and
(ii) a solution of isolated or purified heterologous nucleic acid that is 10-50 nucleotides in length, wherein the targeted particle forms in the mixture; and

(b) isolating or purifying the targeted particle from the mixture.

12. The method of claim 10, wherein the heterologous nucleic acid is siRNA.

13. The method of claim 12, wherein the mixture comprises at east a 10-fold molar excess of the fusion proteins relative to the siRNA.

14. A targeted particle consisting of:
(a) a plurality of landscape phage fusion proteins consisting of a filamentous phage pVIII major coat protein displaying a heterologous peptide, the heterologous peptide capable of directing binding of the particle to a specific target site, and
(b) a heterologous nucleic acid that is 10-50 nucleotides in length,
wherein the targeted particle comprises a molar excess of the landscape fusion protein relative to the heterologous nucleic acid within a range of 60-fold to 100-fold, and
wherein the targeted particle is formed by self-assembly in vitro of complexes formed between the plurality of landscape phage fusion proteins and the heterologous nucleic acid, such that the landscape phage fusion proteins encapsulate the nucleic acid in the particle so as to protect the nucleic acid from degradation and allow delivery of the heterologous nucleic acid to the target site.

15. A targeted particle consisting of:
(a) a plurality of landscape phage fusion proteins consisting of a filamentous phage pVIII major coat protein displaying a heterologous peptide, the heterologous peptide capable of directing binding of the particle to a specific target site, and
(b) siRNA that is 15-50 nucleotides in length,
wherein the targeted particle the targeted particle comprises a molar excess of the landscape fusion protein relative to the siRNA within a range of 60-fold to 100-fold, and
wherein the targeted particle is formed by self-assembly in vitro of complexes formed between the plurality of landscape phage fusion proteins and the siRNA, such that the landscape phage fusion proteins encapsulate the siRNA in the particle so as to protect the siRNA from degradation and allow delivery of the siRNA to the target site.