# Patent

## Title
Polynucleotides encoding therapeutic inhibitors of PAI-1

## Abstract

The invention relates to mammalian PAI-I ligands and modulators. In particular, the invention relates to polypeptides, polypeptide compositions and polynucleotides that encode polypeptides that are ligands and/or modulators of PAI-I. The invention also relates to polyligands that are homopolyligands or heteropolyligands that modulate PAI-I activity. The invention also relates to ligands and polyligands localized to a region of a cell. The invention also relates to localization tethers and promoter sequences that can be used to provide spatial control of the PAI-I ligands and polyligands. The invention also relates to inducible gene switches that can be used to provide temporal control of the PAI-I ligands and polyligands. The invention also relates to methods of treating or preventing atherosclerosis. The invention also relates to methods of treating or preventing fibrosis.

## Background
This application is a divisional of U.S. application Ser. No. 12/812,127, filed Sep. 1, 2010, now U.S. Pat. No. 8,431,363, which is the U.S. National Stage of International Application No. PCT/US2009/000155, filed Jan. 9, 2009, and which claims priority benefit of U.S. Provisional Application Nos. 61/020,127, filed Jan. 9, 2008, and 61/080,640, filed Jul. 14, 2008.


REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY VIA EFS-WEB
This application includes a “Sequence_Listing_ascii.txt,” 145,037 bytes, created on Jun. 17, 2013, and submitted electronically via EFS-Web, which is hereby incorporated by reference in its entirety.
BACKGROUND OF THE INVENTION
1. Field of the Invention
The invention relates to modified PAI-1 proteins and nucleic acids. The invention also relates to mammalian PAI-1 ligands and modulators. In particular, the invention relates to polypeptides, polypeptide compositions and polynucleotides that encode polypeptides that are ligands and/or modulators of PAI-1. The invention also relates to polyligands that are homopolyligands or heteropolyligands that modulate PAI-1 activity. The invention also relates to ligands and polyligands localized to a region of a cell. The invention also relates to localization tethers and promoter sequences that can be used to provide spatial control of the PAI-1 ligands and polyligands. The invention also relates to inducible gene switches that can be used to provide temporal control of the PAI-1 ligands and polyligands. The invention also relates to methods of treating or preventing atherosclerosis. The invention also relates to methods of treating or preventing fibrosis.
BACKGROUND OF THE INVENTION
Plasminogen activator inhibitor-1 (PAI-1) is a serine protease inhibitor of tissue plasminogen activator (tPA) and urokinase plasminogen activator (uPA), agents that convert the proenzyme plasminogen to the fibrinolytic enzyme plasmin. Regulation of fibrinolysis by PAI-1 is an important control point for normal vascular function, as the accumulation of fibrin can lead to blood clots, while an excessive decrease in fibrin can lead to hemorrhage. PAI-1 also plays an important role in tissue fibrosis by inactivating matrix metalloproteinases as well as plasmin generation (Takeshita, K, et al., American Journal of Physiology, 2004(2):449-456), and studies that modulated PAI-1 expression in animal models have implicated PAI-1 in the pathogenesis of fibrosis after chemical or immune-mediated injury (Weisberg. A D et al., Arterioscler. Thromb. Vasc. Biol., 2005, 25:365-371).
PAI-1 has also been implicated in the pathophysiology of renal, pulmonary, cardiovascular, and metabolic diseases (Cale, J M and Lawrence, D A. Curr Drug Targets, 2007, 8(9):971-81), as well as cancer. A number of investigations have supported a role for PAI-1 in the development of heart disease. For example, pharmacologic inhibition of PAI-1 was demonstrated to protect against antiotensin-II-induced aortic remodeling (Weisberg. A D et al., Arterioscler. Thromb. Vasc. Biol., 2005, 25:365-371). Further, attenuated development of cardiac fibrosis was observed in PAI-deficient mice after myocardial infarction compared to wild-type (Takesita, K, et al., American Journal of Pathology, 2004, 164(2):449-455. Several studies (reviewed in Sobel, B E et al., Arterioscler. Thromb. Vasc. Biol., 2003, 23:1979-1989) suggest altered expression of PAI-1 in vessel walls might contribute to coronary atherogenesis.
New reagents and methods for manipulating PAI-1 expression in heart would advance research into its role in heart disease. Further, there is a need in this area for novel reagents, treatments, and methods for inhibiting PAI-1 activity.
SUMMARY OF THE INVENTION
One object of the invention is to provide mammalian PAI-1 ligands, polyligands, and/or modulators.
Another object of the invention is to provide mammalian PAI-1 ligands, polyligands, and/or modulators linked to a localization tether.
Another object of the invention is to provide mammalian PAI-1 ligands, polyligands, and/or modulators linked to a tissue-specific promoter.
Another object of the invention is to provide mammalian PAI-1 ligands, polyligands, and/or modulators linked to an inducible gene switch.
Another object of the invention is to provide a method for achieving spatial control of a mammalian PAI-1 ligand, polyligand, and/or modulator by linking the ligand, polyligand, and/or modulator to a localization tether or a tissue-specific promoter.
Another object of the invention is to provide a method for achieving temporal control of a mammalian PAI-1 ligand, polyligand, and/or modulator by linking the ligand, polyligand, and/or modulator to an inducible gene switch.
Another object of the invention is to provide localization tethers that can be used with a PAI-1 ligand, polyligand, and/or modulator to provide spatial control.
Another object of the invention is to provide tissue-specific promoters that can be used with a PAI-1 ligand, polyligand, and/or modulator to provide spatial control.
Another object of the invention is to provide inducible gene switches that can be used with a PAI-1 ligand, polyligand, and/or modulator to provide temporal control.
Another object of the invention is to provide polynucleotides encoding mammalian PAI-1 ligands, polyligands, and/or modulators.
Another object of the invention is to provide gene constructs comprising a polynucleotide encoding a mammalian PAI-1 ligand, polyligand, and/or modulator and a localization tether or tissue-specific promoter.
Another objection of the invention is to provide vectors comprising polynucleotides encoding mammalian PAI-1 ligands, polyligands, and/or modulators.
Another object of the invention is to provide host cells comprising polynucleotides encoding mammalian PAI-1 ligands, polyligands, and/or modulators.
Another object of the invention is to provide transgenic organisms comprising polynucleotides encoding mammalian PAI-1 ligands, polyligands, and/or modulators.
Another object of the invention is to provide methods of treating or preventing a cardiovascular disease using mammalian PAI-1 ligands, polyligands, and/or modulators.
Another object of the invention is to provide methods of treating or preventing a fibrotic condition using mammalian PAI-1 ligands, polyligands, and/or modulators.
Another object of the invention is a method for transferring a polynucleotide encoding a PAI-1 ligand, polyligand, and/or modulator to cardiovascular tissue.
Another embodiment of the invention is to provide a method for assessing the function of PAI-1 in the formation of unstable plaques.
Another object of the invention is to provide methods of treating or preventing atherosclerosis using monocytes modified to express an inhibitor of the fibrinolytic pathway.
Another object of the invention is to provide methods of treating or preventing a fibrotic condition using monocytes modified to express an inhibitor of the fibrinolytic pathway.
Another object of the invention is to provide a fusion protein comprising PAI-1 protein linked to a degron.
Another object of the invention is to provide a fusion protein comprising PAI-1 linked to a localization signal.
It is another object of the invention to provide a PAI-1 polynucleotide sequence that has been optimized for vector insertion.
Another object of the invention is to provide a PAI-1 polynucleotide sequence that has been optimized for vector insertion, that is optionally linked to a polynucleotide sequence encoding a degron.
Another object of the invention is to provide a PAI-1 polynucleotide sequence that has been optimized for vector insertion, that is optionally linked to a polynucleotide sequence encoding a localization signal.
Another object of the invention is to provide gene constructs containing a PAI-1 polynucleotide sequence that has been optimized for vector insertion, optionally linked to a polynucleotide sequence encoding a degron and/or a localization signal.
Another object of the invention is to provide vectors containing gene constructs containing a PAI-1 polynucleotide sequence that has been optimized for vector insertion, optionally linked to a polynucleotide sequence encoding a degron and/or a localization signal.
Another object of the invention is to provide host cells containing vectors containing gene constructs containing a PAI-1 polynucleotide sequence that has been optimized for vector insertion, optionally linked to a polynucleotide sequence encoding a degron and/or a localization signal.
Another object of the invention is to provide transgenic organisms containing a PAI-1 polynucleotide sequence that has been optimized for vector insertion, optionally linked to a polynucleotide sequence encoding a degron and/or a localization signal.
Another object of the invention is to provide gene constructs containing a PAI-1 polynucleotide sequence that has been optimized for vector insertion, optionally linked to a polynucleotide sequence encoding a degron and/or a localization signal, that include a ubiquitous, tissue-specific, cell-specific, or inducible promoter.
Another object of the invention is to provide vectors containing gene constructs containing a PAI-1 polynucleotide sequence that has been optimized for vector insertion, optionally linked to a polynucleotide sequence encoding a degron and/or a localization signal, that include a ubiquitous, tissue-specific, cell-specific, or inducible promoter.
Another object of the invention is to provide host cells containing vectors containing gene constructs containing a PAI-1 polynucleotide sequence that has been optimized for vector insertion, optionally linked to a polynucleotide sequence encoding a degron and/or a localization signal, that include a ubiquitous, tissue-specific, cell-specific, or inducible promoter.
Another object of the invention is to provide transgenic organisms containing gene constructs containing a PAI-1 polynucleotide sequence that has been optimized for vector insertion, optionally linked to a polynucleotide sequence encoding a degron and/or a localization signal, that include a ubiquitous, tissue-specific, cell-specific, or inducible promoter.
Another object of the invention is to provide a method of altering the expression of PAI-1 in a host cell.
Another object of the invention is to provide a method of altering expression of PAI-1 in heart tissue.
Another object of the invention is to provide a method of creating a transgenic subject with altered PAI-1 expression.
Another object of the invention is to provide mammalian PAI-1 ligands, polyligands, and/or modulators.
Another object of the invention is to provide mammalian PAI-1 ligands, polyligands, and/or modulators linked to a degron.
Another object of the invention is to provide mammalian PAI-1 ligands, polyligands, and/or modulators linked to a localization signal
Another object of the invention is to provide polynucleotides encoding mammalian PAI-1 ligands, polyligands, and/or modulators, optionally linked to an epitope, reporter, degron and/or a localization signal.
Another object of the invention is to provide gene constructs containing polynucleotides encoding mammalian PAI-1 ligands, polyligands, and/or modulators, optionally linked to an epitope, reporter, degron and/or a localization signal.
Another object of the invention is to provide vectors containing gene constructs containing polynucleotides encoding mammalian PAI-1 ligands, polyligands, and/or modulators, optionally linked to an epitope, reporter, degron and/or a localization signal.
Another object of the invention is to provide host cells containing vectors containing gene constructs containing polynucleotides encoding mammalian PAI-1 ligands, polyligands, and/or modulators, optionally linked to an epitope, reporter, degron and/or a localization signal.
Another object of the invention is to provide transgenic organisms containing polynucleotides encoding mammalian PAI-1 ligands, polyligands, and/or modulators, optionally linked to an epitope, reporter, degron and/or a localization signal.
Another object of the invention is to provide gene constructs containing polynucleotides encoding mammalian PAI-1 ligands, polyligands, and/or modulators, optionally linked to an epitope, reporter, degron and/or a localization signal, that include a ubiquitous, tissue-specific, cell-specific, or inducible promoter.
Another object of the invention is to provide vectors containing gene constructs containing polynucleotides encoding mammalian PAI-1 ligands, polyligands, and/or modulators, optionally linked to an epitope, reporter, degron and/or a localization signal, that include a ubiquitous, tissue-specific, cell-specific, or inducible promoter.
Another object of the invention is to provide host cells containing vectors containing gene constructs containing polynucleotides encoding mammalian PAI-1 ligands, polyligands, and/or modulators, optionally linked to an epitope, reporter, degron and/or a localization signal, that include a ubiquitous, tissue-specific, cell-specific, or inducible promoter.
Another object of the invention is to provide transgenic organisms containing gene constructs containing polynucleotides encoding mammalian PAI-1 ligands, polyligands, and/or modulators, optionally linked to an epitope, reporter, degron and/or a localization signal, that include a ubiquitous, tissue-specific, cell-specific, or inducible promoter.
Another object of the invention is to provide methods of inhibiting PAI-1 in a host cell.
Another object of the invention is to provide methods of inhibiting PAI-1 in heart tissue.
Another object of the invention is to provide methods of creating a transgenic subject with reduced PAI-1 activity.
DESCRIPTION OF POLYPEPTIDE AND POLYNUCLEOTIDE SEQUENCES
SEQ ID NOS:1-30 represent examples of PAI-1 ligands and polyligands and polynucleotides encoding them. A diagram of each of the following ligands and polyligands that shows the architecture of their individual peptide components is shown in FIG. 9.
Specifically, the PAI-1 polyligand of SEQ ID NO:1 is encoded by SEQ ID NO:2, wherein codons are optimized for mammalian expression and vector insertion. The PAI-1 polyligand of SEQ ID NO:1 is an embodiment of a homopolyligand and is known herein as PAI1-DCY-94-1.
The PAI-1 polyligand of SEQ ID NO:3 is encoded by SEQ ID NO:4, wherein codons are optimized for mammalian expression and vector insertion. The PAI-1 polyligand of SEQ ID NO:3 is an embodiment of a monomeric ligand and is also known herein as PAI1-DCY-94-2.
The PAI-1 polyligand of SEQ ID NO:5 is encoded by SEQ ID NO:6, wherein codons are optimized for mammalian expression and vector insertion. The PAI-1 polyligand of SEQ ID NO:5 is an embodiment of a homopolyligand and is also known herein as PAI1-DCY-94-3.
The PAI-1 polyligand of SEQ ID NO:7 is encoded by SEQ ID NO:8, wherein codons are optimized for mammalian expression and vector insertion. The PAI-1 polyligand of SEQ ID NO:7 is an embodiment of a heteropolyligand and is also known herein as PAI1-DCY-94-4.
The PAI-1 polyligand of SEQ ID NO:9 is encoded by SEQ ID NO:10, wherein codons are optimized for mammalian expression and vector insertion. The PAI-1 polyligand of SEQ ID NO:9 is an embodiment of a monomeric ligand and is also known herein as PAI1-DCY-94-5.
The PAI-1 polyligand of SEQ ID NO:11 is encoded by SEQ ID NO:12, wherein codons are optimized for mammalian expression and vector insertion. The PAI-1 polyligand of SEQ ID NO:11 is an embodiment of a monomeric ligand and is also known herein as PAI1-DCY-94-6.
The PAI-1 polyligand of SEQ ID NO:13 is encoded by SEQ ID NO:14, wherein codons are optimized for mammalian expression and vector insertion. The PAI-1 polyligand of SEQ ID NO:13 is an embodiment of a heteropolyligand and is also known herein as PAI1-DCY-94-7.
The PAI-1 polyligand of SEQ ID NO:15 is encoded by SEQ ID NO:16, wherein codons are optimized for mammalian expression and vector insertion. The PAI-1 polyligand of SEQ ID NO:15 is an embodiment of a heteropolyligand and is also known herein as PAI1-DCY-94-8.
The PAI-1 polyligand of SEQ ID NO:17 is encoded by SEQ ID NO:18, wherein codons are optimized for mammalian expression and vector insertion. The PAI-1 polyligand of SEQ ID NO:17 is an embodiment of a heteropolyligand and is also known herein as PAI1-DCY-94-9.
The PAI-1 polyligand of SEQ ID NO:19 is encoded by SEQ ID NO:20, wherein codons are optimized for mammalian expression and vector insertion. The PAI-1 polyligand of SEQ ID NO:19 is an embodiment of a heteropolyligand and is also known herein as PAI1-DCY-94-10.
The PAI-1 polyligand of SEQ ID NO:21 is encoded by SEQ ID NO:22, wherein codons are optimized for mammalian expression and vector insertion. The PAI-1 polyligand of SEQ ID NO:21 is an embodiment of a heteropolyligand and is also known herein as PAI1-DCY-94-11.
The PAI-1 polyligand of SEQ ID NO:23 is encoded by SEQ ID NO:24, wherein codons are optimized for mammalian expression and vector insertion. The PAI-1 polyligand of SEQ ID NO:23 is an embodiment of a heteropolyligand and is also known herein as PAI1-DCY-94-12.
The PAI-1 polyligand of SEQ ID NO:25 is encoded by SEQ ID NO:26, wherein codons are optimized for mammalian expression and vector insertion. The PAI-1 polyligand of SEQ ID NO:25 is an embodiment of a heteropolyligand and is also known herein as PAI1-DCY-94-13.
The PAI-1 polyligand of SEQ ID NO:27 is encoded by SEQ ID NO:28, wherein codons are optimized for mammalian expression and vector insertion. The PAI-1 polyligand of SEQ ID NO:27 is an embodiment of a heteropolyligand and is also known herein as PAI1-DCY-94-14.
The PAI-1 polyligand of SEQ ID NO:29 is encoded by SEQ ID NO:30, wherein codons are optimized for mammalian expression and vector insertion. The PAI-1 polyligand of SEQ ID NO:29 is an embodiment of a heteropolyligand and is also known herein as PAI1-DCY-94-15.
SEQ ID NOS:31-36 represent examples of full length proteins used to construct ligands and polyligands. SEQ ID NO:31 is known as Homo sapiens plasminogen activator inhibitor 1 and has the public accession number AAA60009. SEQ ID NO:32 is known as Homo sapiens vitronectin and has the public accession number EAW51082. SEQ ID NO:33 is known as Homo sapiens kallikrein 2, prostatic isoform 1 and has the public accession number NP—005542. SEQ ID NO:34 is known as Homo sapiens tissue plasminogen activator and has the public accession number BAA00881. SEQ ID NO:35 is known as Homo sapiens toll-like receptor 3 and has the public accession number NP—003256. SEQ ID NO:36 is known as Homo sapiens urokinase plasminogen activator (uPA) and has the public accession number CAA01390.
SEQ ID NOS:37-51 represent examples of monomeric ligand peptides. Each of SEQ ID NOS:37-51 is represented in FIG. 9 with the name or abbreviated name of the parent protein, followed by the amino acid range of the parent protein that it represents, followed by any amino acid substitution mutation indicated by the convention: X#Z, where X is the one letter amino acid code of the amino acid to be replaced, # is the amino acid residue position or number within the parent protein, and Z is the one letter amino acid code of the new substituting amino acid.
SEQ ID NO:37 is a partial sequence of SEQ ID NO:31 and is represented in FIG. 9 as ‘PAI1 354-368’.
SEQ ID NO:38 is a partial sequence of SEQ ID NO:31 and is represented in FIG. 9 as ‘PAI1 300-309’.
SEQ ID NO:39 is a partial sequence of SEQ ID NO:31 and is represented in FIG. 9 as ‘PAI1 343-353’.
SEQ ID NO:40 is a partial sequence of SEQ ID NO:32 and is represented in FIG. 9 as ‘vitronectin 20-63’.
SEQ ID NO:41 is a partial sequence of SEQ ID NO:32 that comprises a F32L substitution mutation and is represented in FIG. 9 as ‘vitronectin 20-63 F32L’.
SEQ ID NO:42 is a partial sequence of SEQ ID NO:32 that comprises a T29A substitution mutation and is represented in FIG. 9 as ‘vitronectin 20-63 T29A’.
SEQ ID NO:43 is a partial sequence of SEQ ID NO:32 that comprises a E42A substitution mutation and is represented in FIG. 9 as ‘vitronectin 20-63 E42a’.
SEQ ID NO:44 is a partial sequence of SEQ ID NO:32 that comprises a L43A substitution mutation and is represented in FIG. 9 as ‘vitronectin 20-63 L43A’.
SEQ ID NO:45 is a partial sequence of SEQ ID NO:45 that comprises S23F, T52E, D53L, A56Y, and E57Y substitution mutations and is represented in FIG. 9 as ‘vitronectin 20-63 mutant’.
SEQ ID NO:46 is a partial sequence of SEQ ID NO:33 and is represented in FIG. 9 as ‘Kallikrein 2 (25-256)’.
SEQ ID NO:47 is a partial sequence of SEQ ID NO:33 and is represented in FIG. 9 as hK2 (25-44).
SEQ ID NO:48 is a partial sequence of SEQ ID NO:33 and is represented in FIG. 9 as ‘Kallikrein 2 (47-256)’.
SEQ ID NO:49 is a partial sequence of SEQ ID NO:34 and is represented in FIG. 9 as ‘tPA (301-308)’.
SEQ ID NO:50 is a partial sequence of SEQ ID NO:35 that comprises V55A, N57Y, T59N, S79K, D81K, and G83E substitution mutations and is represented in FIG. 9 as ‘Toll like receptor 3 29-121 (V55A, N57Y, T59N, S79K, D81K, G83E)’.
SEQ ID NO:51 is a partial sequence of SEQ ID NO:36 that comprises H224A, D275A, and S376A substitution mutations and is represented in FIG. 9 as ‘Urokinase Plasminogen Activator (179-415) H224A, D275A, S376A’.
SEQ ID NO:52 represents an example of a full-length protein used to create a natural spacer fragment. SEQ ID NO:52 is known as Humicola insolens exoglucanase-6A precursor (Exocellobiohydrolase 6A) (1,4-beta-cellobiohydrolase 6A) (Beta-glucancellobiohydrolase 6A) (Avicelase 2) and has the public accession number Q9C1S9.
SEQ ID NO:53 represents an example of a natural spacer fragment. SEQ ID NO:53 is a partial sequence of SEQ ID NO:52, and is represented in FIG. 9 as ‘16aa linker’.
SEQ ID NOS:54-56 represent examples of artificial spacers.
SEQ ID NOS:57-76 represent examples of class 1 localization tether polypeptides useful in the present invention. A diagram of each of the following class 1 localization tether polypeptides that shows the architecture of their individual peptide components is shown in FIGS. 14A-14B.
The class 1 localization tether of SEQ ID NO:57 is also known herein as 91-1.
The class 1 localization tether of SEQ ID NO:58 is also known herein as 91-2.
The class 1 localization tether of SEQ ID NO:59 is also known herein as 91-3.
The class 1 localization tether of SEQ ID NO:60 is also known herein as 91-4.
The class 1 localization tether of SEQ ID NO:61 is also known herein as 91-5.
The class 1 localization tether of SEQ ID NO:62 is also known herein as 91-6.
The class 1 localization tether of SEQ ID NO:63 is also known herein as 91-7.
The class 1 localization tether of SEQ ID NO:64 is also known herein as 91-8.
The class 1 localization tether of SEQ ID NO:65 is also known herein as 91-9.
The class 1 localization tether of SEQ ID NO:66 is also known herein as 91-10.
The class 1 localization tether of SEQ ID NO:67 is also known herein as 91-11.
The class 1 localization tether of SEQ ID NO:68 is also known herein as 91-12.
The class 1 localization tether of SEQ ID NO:69 is also known herein as 91-13.
The class 1 localization tether of SEQ ID NO:70 is also known herein as 91-14.
The class 1 localization tether of SEQ ID NO:71 is also known herein as 91-15.
The class 1 localization tether of SEQ ID NO:72 is also known herein as 91-16.
The class 1 localization tether of SEQ ID NO:73 is also known herein as 91-17.
The class 1 localization tether of SEQ ID NO:74 is also known herein as 91-18.
The class 1 localization tether of SEQ ID NO:75 is also known herein as 91-19.
The class 1 localization tether of SEQ ID NO:76 is also known herein as 91-20.
SEQ ID NOS:77-95 represent examples of polypeptide fragments used to construct class 1 localization tethers.
SEQ ID NO:96 represents an example of an epitope tag used as internal cargo to construct class 1 localization tethers, and is represented in FIGS. 14A-14B as ‘TAG’.
SEQ ID NOS:97-99 represent examples of spacers used to construct class 1 localization tethers.
SEQ ID NOS:100-111 represent examples of class 3 localization tether polypeptides useful in the present invention. A diagram of each of the following class 3 localization tether polypeptides that shows the architecture of their individual peptide components is shown in FIG. 15.
The class 3 localization tether of SEQ ID NO:100 is also known herein as 93-1.
The class 3 localization tether of SEQ ID NO:101 is also known herein as 93-2.
The class 3 localization tether of SEQ ID NO:102 is also known herein as 93-3.
The class 3 localization tether of SEQ ID NO:103 is also known herein as 93-4.
The class 3 localization tether of SEQ ID NO:104 is also known herein as 93-5.
The class 3 localization tether of SEQ ID NO:105 is also known herein as 93-6.
The class 3 localization tether of SEQ ID NO:106 is also known herein as 93-7.
The class 3 localization tether of SEQ ID NO:107 is also known herein as 93-8.
The class 3 localization tether of SEQ ID NO:108 is also known herein as 93-9.
The class 3 localization tether of SEQ ID NO:109 is also known herein as 93-10.
The class 3 localization tether of SEQ ID NO:110 is also known herein as 93-11.
The class 3 localization tether of SEQ ID NO:111 is also known herein as 93-12.
SEQ ID NOS:112-129 represent examples of polypeptide fragments used to construct class 3 localization tethers.
SEQ ID NO:130 represents an example of an epitope tag used as internal cargo to construct class 3 localization tethers, and is represented in FIG. 15 as ‘TAG’ or ‘TAG/IC’.
SEQ ID NO:131 represents an example of a synthetic TACE/ADAM17 cut site used to construct class 3 localization tethers.
SEQ ID NOS:132-139 represent examples of tissue specific promoter sequences useful in the present invention.
SEQ ID NO:132 is an example of an arterial smooth muscle-specific promoter and is also known herein as MOD 5306, the structure of which is depicted schematically in FIG. 10.
SEQ ID NO:133 is an example of a synthetic vascular smooth muscle cell-specific promoter and is also known herein as MOD 5309, the structure of which is depicted schematically in FIG. 11A.
SEQ ID NO:134 is an example of a synthetic vascular smooth muscle cell-specific promoter and is also known herein as MOD 5312, the structure of which is depicted schematically in FIG. 11B.
SEQ ID NO:135 is an example of a synthetic vascular smooth muscle cell-specific promoter and is also known herein as MOD 5315, the structure of which is depicted schematically in FIG. 11C.
SEQ ID NO:136 is an example of a endothelial cell-specific promoter and is also known herein as MOD 4012-ESM1, the structure of which is depicted schematically in FIG. 12A.
SEQ ID NO:137 is an example of a endothelial cell-specific promoter and is also known herein as MOD 4399-FLT1, the structure of which is depicted schematically in FIG. 12B.
SEQ ID NO:138 is an example of a synthetic endothelial cell-specific promoter and is also known herein as MOD 4790, the structure of which is depicted schematically in FIG. 13A.
SEQ ID NO:139 is an example of a synthetic endothelial cell-specific promoter and is also known herein as MOD 4791, the structure of which is depicted schematically in FIG. 13B.
Three letter amino acid codes and one letter amino acid codes are used herein as is commonly known in the art.



DESCRIPTION OF THE DRAWINGS
FIGS. 1A-1F show examples of homopolyligands with or without spacers.
FIGS. 2A-2J show examples of heteropolyligands with or without spacers.
FIGS. 3A-3H show examples of ligands and polyligands linked to localization signals.
FIGS. 4A-4G show examples of polyligands linked to epitopes or reporters.
FIGS. 5A-5I show examples of polyligands linked to localization signals and epitopes or reporters.
FIGS. 6A-6E show examples of gene constructs that include a ligand or polyligand optionally linked to an epitope, reporter, and/or a localization signal.
FIGS. 7A-7D show examples of vectors containing ligand gene constructs.
FIG. 8 shows an example of a sequential cloning process useful for combinatorial synthesis of polyligands.
FIG. 9 shows examples of ligands and polyligands and their PAI-1 inhibition mechanisms.
FIG. 10 shows an example of an arterial smooth muscle-specific promoter.
FIGS. 11A-11C show examples of synthetic vascular smooth muscle cell-specific promoters.
FIGS. 12A-12B show examples of endothelial cell-specific promoters.
FIGS. 13A-13B show examples of synthetic endothelial cell-specific promoters.
FIGS. 14A-14B show examples of class 1 localization tethers.
FIG. 15 shows examples of class 3 localization tethers.
FIG. 16 shows exemplary inhibition mechanisms of PAI-1 ligands and polyligands.
FIGS. 17A-17H show examples of PAI-1 linked to a degron and/or a localization signal.
FIGS. 18A-18I show examples of gene constructs that include an ULTRAVECTOR(UV)-enabled PAI-1 cDNA, optionally linked to a degron and/or a localization signal.
FIGS. 19A-19D show examples of vectors that contain ULTRAVECTOR(UV)-enabled PAI-1 gene constructs.
FIGS. 20A-20J show examples of ligands and homopolyligands with or without spacers linked to degrons.
FIGS. 21A-21H show examples of heteropolyligands with or without spacers linked to degrons.
FIGS. 22A-22F show examples of ligands and polyligands linked to degrons and localization signals.
FIGS. 23A-23G show examples of gene constructs that include a ligand or polyligand optionally linked to a degron and/or a localization signal.



DETAILED DESCRIPTION OF THE INVENTION
Terms used in the specification and claims have ordinary meanings understood in the art. For example, polynucleotide is used interchangeably with nucleic acid and includes single or double stranded DNA, RNA and polymeric analogs thereof.
The term chimeric means comprised of fragments that are not contiguous in their natural state. For example, a chimeric polynucleotide means a polynucleotide comprising fragments that are not contiguous in their natural state.
The terms polypeptide, peptide, and protein are used interchangeably and represent polymers of amino acids.
A synthetic gene (or portion of a gene) is a non-natural gene (or portion of a gene) that differs from a wildtype polynucleotide sequence. A synthetic gene (or portion of a gene) may contain one or more nucleic acid sequences not contiguous in nature (chimeric sequences), and/or may encompass substitutions, insertions, and deletions and combinations thereof.
A non-human organism encompasses, non-human primates, mammals, vertebrates, invertebrates, plants, and lower eukaryotic organisms including yeast and slime molds.
Restriction endonucleases are enzymes that cleave nucleic acids at recognition sequences within a nucleic acid molecule.
Host cells include but are not limited to commercial and non-commercial cell lines, such as those available from the ATCC (Manassas, Va.), primary cell cultures, stem cells, immune cells, blood cells, cells from any organism or tissue.
A vector refers to any vehicle for the cloning of and/or transfer of a nucleic acid into a host cell. A vector may be a replicon to which another DNA segment may be attached so as to bring about the replication of the attached segment. A replicon refers to any genetic element (e.g., plasmid, phage, cosmid, chromosome, virus) that functions as an autonomous unit of DNA replication in vivo, i.e., capable of replication under its own control. The term vector includes both viral and nonviral vehicles for introducing the nucleic acid into a cell in vitro, ex vivo or in vivo. A large number of vectors known in the art may be used to manipulate nucleic acids, incorporate response elements and promoters into genes, etc. Possible vectors include, for example, plasmids or modified viruses including, for example bacteriophages such as lambda derivatives, or plasmids such as pBR322 or pUC plasmid derivatives, or the Bluescript vector. Another example of vectors that are useful in the present invention is the UltraVectorTM Production System (Intrexon Corp., Blacksburg, Va.) as described in WO 2007/038276, incorporated herein by reference. For example, the insertion of the DNA fragments corresponding to response elements and promoters into a suitable vector can be accomplished by ligating the appropriate DNA fragments into a chosen vector that has complementary cohesive termini. Alternatively, the ends of the DNA molecules may be enzymatically modified or any site may be produced by ligating nucleotide sequences (linkers) into the DNA termini. Such vectors may be engineered to contain selectable marker genes that provide for the selection of cells that have incorporated the marker into the cellular genome. Such markers allow identification and/or selection of host cells that incorporate and express the proteins encoded by the marker.
Viral vectors, and particularly retroviral vectors, have been used in a wide variety of gene delivery applications in cells, as well as living animal subjects. Viral vectors that can be used include, but are not limited to, retrovirus, adeno-associated virus, pox, baculovirus, vaccinia, herpes simplex, Epstein-Barr, adenovirus, geminivirus, and caulimovirus vectors. Non-viral vectors include plasmids, liposomes, electrically charged lipids (cytofectins), DNA-protein complexes, and biopolymers. In addition to a nucleic acid, a vector may also comprise one or more regulatory regions, and/or selectable markers useful in selecting, measuring, and monitoring nucleic acid transfer results (transfer to which tissues, duration of expression, etc.).
The term plasmid refers to an extra-chromosomal element often carrying a gene that is not part of the central metabolism of the cell, and usually in the form of circular double-stranded DNA molecules. Such elements may be autonomously replicating sequences, genome integrating sequences, phage or nucleotide sequences, linear, circular, or supercoiled, of a single- or double-stranded DNA or RNA, derived from any source, in which a number of nucleotide sequences have been joined or recombined into a unique construction which is capable of introducing a promoter fragment and DNA sequence for a selected gene product along with appropriate 3′ untranslated sequence into a cell.
A cloning vector refers to a replicon which is a unit length of a nucleic acid, preferably DNA, that replicates sequentially and which comprises an origin of replication, such as a plasmid, phage or cosmid, to which another nucleic acid segment may be attached so as to bring about the replication of the attached segment. Cloning vectors may be capable of replication in one cell type and expression in another (shuttle vector). Cloning vectors may comprise one or more sequences that can be used for selection of cells comprising the vector and/or one or more multiple cloning sites for insertion of sequences of interest.
The term expression vector refers to a vector, plasmid or vehicle designed to enable the expression of an inserted nucleic acid sequence following transformation into the host. The cloned gene, i.e., the inserted nucleic acid sequence, is usually placed under the control of control elements such as a promoter, a minimal promoter, an enhancer, or the like. Initiation control regions or promoters, which are useful to drive expression of a nucleic acid in the desired host cell are numerous and familiar to those skilled in the art. Virtually any promoter capable of driving expression of these genes can be used in an expression vector, including but not limited to, viral promoters, bacterial promoters, animal promoters, mammalian promoters, synthetic promoters, constitutive promoters, tissue specific promoters, pathogenesis or disease related promoters, developmental specific promoters, inducible promoters, light regulated promoters; CYC1, HIS3, GAL1, GAL4, GAL10, ADH1, PGK, PHO5, GAPDH, ADC1, TRP1, URA3, LEU2, ENO, TPI, alkaline phosphatase promoters (useful for expression in Saccharomyces); AOX1 promoter (useful for expression in Pichia); Beta-lactamase, lac, ara, tet, trp, 1PL, 1PR, T7, tac, and trc promoters (useful for expression in Escherichia coli); light regulated-, seed specific-, pollen specific-, ovary specific-, cauliflower mosaic virus 35S, CMV 35S minimal, cassava vein mosaic virus (CsVMV), chlorophyll a/b binding protein, ribulose 1,5-bisphosphate carboxylase, shoot-specific, root specific, chitinase, stress inducible, rice tungro bacilliform virus, plant super-promoter, potato leucine aminopeptidase, nitrate reductase, mannopine synthase, nopaline synthase, ubiquitin, zein protein, and anthocyanin promoters (useful for expression in plant cells); animal and mammalian promoters known in the art including, but are not limited to, the SV40 early (SV40e) promoter region, the promoter contained in the 3′ long terminal repeat (LTR) of Rous sarcoma virus (RSV), the promoters of the E1A or major late promoter (MLP) genes of adenoviruses (Ad), the cytomegalovirus (CMV) early promoter, the herpes simplex virus (HSV) thymidine kinase (TK) promoter, a baculovirus IE1 promoter, an elongation factor 1 alpha (EF1) promoter, a phosphoglycerate kinase (PGK) promoter, a ubiquitin (Ubc) promoter, an albumin promoter, the regulatory sequences of the mouse metallothionein-L promoter and transcriptional control regions, the ubiquitous promoters (HPRT, vimentin, beta-actin, tubulin and the like), the promoters of the intermediate filaments (desmin, neurofilaments, keratin, GFAP, and the like), the promoters of therapeutic genes (of the MDR, CFTR or factor VIII type, and the like), pathogenesis or disease related-promoters, and promoters that exhibit tissue specificity and have been utilized in transgenic animals, such as the elastase I gene control region which is active in pancreatic acinar cells; insulin gene control region active in pancreatic beta cells, immunoglobulin gene control region active in lymphoid cells, mouse mammary tumor virus control region active in testicular, breast, lymphoid and mast cells; albumin gene, Apo AI and Apo AII control regions active in liver, alpha-fetoprotein gene control region active in liver, alpha 1-antitrypsin gene control region active in the liver, beta-globin gene control region active in myeloid cells, myelin basic protein gene control region active in oligodendrocyte cells in the brain, myosin light chain-2 gene control region active in skeletal muscle, and gonadotropic releasing hormone gene control region active in the hypothalamus, pyruvate kinase promoter, villin promoter, promoter of the fatty acid binding intestinal protein, promoter of the smooth muscle cell beta-actin, and the like. In addition, these expression sequences may be modified by addition of enhancer or regulatory sequences and the like.
Vectors may be introduced into the desired host cells by methods known in the art, e.g., transfection, electroporation, microinjection, transduction, cell fusion, DEAE dextran, calcium phosphate precipitation, lipofection (lysosome fusion), use of a gene gun, or a DNA vector transporter (see, e.g., Wu et al., J. Biol. Chem. 267:963 (1992); Wu et al., J. Biol. Chem. 263:14621 (1988); and Hartmut et al., Canadian Patent Application No. 2,012,311).
A polynucleotide according to the invention can also be introduced in vivo by lipofection. For the past decade, there has been increasing use of liposomes for encapsulation and transfection of nucleic acids in vitro. Synthetic cationic lipids designed to limit the difficulties and dangers encountered with liposome-mediated transfection can be used to prepare liposomes for in vivo transfection of a gene encoding a marker (Feigner et al., Proc. Natl. Acad. Sci. USA. 84:7413 (1987); Mackey et al., Proc. Natl. Acad. Sci. USA 85:8027 (1988); and Ulmer et al., Science 259:1745 (1993)). The use of cationic lipids may promote encapsulation of negatively charged nucleic acids, and also promote fusion with negatively charged cell membranes (Feigner et al., Science 337:387 (1989)). Particularly useful lipid compounds and compositions for transfer of nucleic acids are described in WO95/18863, WO96/17823 and U.S. Pat. No. 5,459,127. The use of lipofection to introduce exogenous genes into the specific organs in vivo has certain practical advantages. Molecular targeting of liposomes to specific cells represents one area of benefit. It is clear that directing transfection to particular cell types would be particularly preferred in a tissue with cellular heterogeneity, such as pancreas, liver, kidney, and the brain. Lipids may be chemically coupled to other molecules for the purpose of targeting (Mackey et al. 1988, supra). Targeted peptides, e.g., hormones or neurotransmitters, and proteins such as antibodies, or non-peptide molecules could be coupled to liposomes chemically.
Other molecules are also useful for facilitating transfection of a nucleic acid in vivo, such as a cationic oligopeptide (e.g., WO95/21931), peptides derived from DNA binding proteins (e.g., WO96/25508), or a cationic polymer (e.g., WO95/21931).
It is also possible to introduce a vector in vivo as a naked DNA plasmid (see U.S. Pat. Nos. 5,693,622, 5,589,466 and 5,580,859). Receptor-mediated DNA delivery approaches can also be used (Curiel et al., Hum. Gene Ther. 3:147 (1992); and Wu et al., J. Biol. Chem. 262:4429 (1987)).
The term transfection refers to the uptake of exogenous or heterologous RNA or DNA by a cell. A cell has been transfected by exogenous or heterologous RNA or DNA when such RNA or DNA has been introduced inside the cell. A cell has been transformed by exogenous or heterologous RNA or DNA when the transfected RNA or DNA effects a phenotypic change. The transforming RNA or DNA can be integrated (covalently linked) into chromosomal DNA making up the genome of the cell.
Transformation refers to the transfer of a nucleic acid fragment into the genome of a host organism, resulting in genetically stable inheritance. Host organisms containing the transformed nucleic acid fragments are referred to as transgenic or recombinant or transformed organisms.
In addition, the recombinant vector comprising a polynucleotide according to the invention may include one or more origins for replication in the cellular hosts in which their amplification or their expression is sought, markers or selectable markers.
The term selectable marker refers to an identifying factor, usually an antibiotic or chemical resistance gene, that is able to be selected for based upon the marker gene's effect, i.e., resistance to an antibiotic, resistance to a herbicide, colorimetric markers, enzymes, fluorescent markers, and the like, wherein the effect is used to track the inheritance of a nucleic acid of interest and/or to identify a cell or organism that has inherited the nucleic acid of interest. Examples of selectable marker genes known and used in the art include: genes providing resistance to ampicillin, streptomycin, gentamycin, kanamycin, hygromycin, bialaphos herbicide, sulfonamide, and the like; and genes that are used as phenotypic markers, i.e., anthocyanin regulatory genes, isopentanyl transferase gene, and the like.
The term reporter gene refers to a nucleic acid encoding an identifying factor that is able to be identified based upon the reporter gene's effect, wherein the effect is used to track the inheritance of a nucleic acid of interest, to identify a cell or organism that has inherited the nucleic acid of interest, and/or to measure gene expression induction or transcription. Examples of reporter genes known and used in the art include: luciferase (Luc), fluorescent proteins such as green fluorescent protein (GFP), chloramphenicol acetyltransferase (CAT), beta-galactosidase (LacZ), beta-glucuronidase (Gus), and the like. Selectable marker genes may also be considered reporter genes.
Promoter and promoter sequence are used interchangeably and refer to a DNA sequence capable of controlling the expression of a coding sequence or functional RNA. In general, a coding sequence is located 3′ to a promoter sequence. Promoters may be derived in their entirety from a native gene, or be composed of different elements derived from different promoters found in nature, or even comprise synthetic DNA segments. It is understood by those skilled in the art that different promoters may direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental or physiological conditions. Promoters that cause a gene to be expressed in most cell types at most times are commonly referred to as constitutive promoters. Promoters that cause a gene to be expressed in a specific cell type are commonly referred to as cell-specific promoters or tissue-specific promoters. Promoters that cause a gene to be expressed at a specific stage of development or cell differentiation are commonly referred to as developmentally-specific promoters or cell differentiation-specific promoters. Promoters that are induced and cause a gene to be expressed following exposure or treatment of the cell with an agent, biological molecule, chemical, ligand, light, or the like that induces the promoter are commonly referred to as inducible promoters or regulatable promoters. It is further recognized that since in most cases the exact boundaries of regulatory sequences have not been completely defined, DNA fragments of different lengths may have identical promoter activity.
The promoter sequence is typically bounded at its 3′ terminus by the transcription initiation site and extends upstream (5′ direction) to include the minimum number of bases or elements necessary to initiate transcription at levels detectable above background. Within the promoter sequence will be found a transcription initiation site (conveniently defined for example, by mapping with nuclease S1), as well as protein binding domains (consensus sequences) responsible for the binding of RNA polymerase.
The term homology refers to the percent of identity between two polynucleotide or two polypeptide moieties. The correspondence between the sequence from one moiety to another can be determined by techniques known to the art. For example, homology can be determined by a direct comparison of the sequence information between two polypeptide molecules by aligning the sequence information and using readily available computer programs. Alternatively, homology can be determined by hybridization of polynucleotides under conditions that form stable duplexes between homologous regions, followed by digestion with single-stranded-specific nuclease(s) and size determination of the digested fragments.
As used herein, the term homologous in all its grammatical forms and spelling variations refers to the relationship between proteins that possess a common evolutionary origin, including proteins from superfamilies (e.g., the immunoglobulin superfamily) and homologous proteins from different species (e.g., myosin light chain, etc.) (Reeck et al., Cell 50:667 (1987)). Such proteins (and their encoding genes) have sequence homology, as reflected by their high degree of sequence similarity. However, in common usage and in the present application, the term homologous, when modified with an adverb such as highly, may refer to sequence similarity and not a common evolutionary origin.
Accordingly, the term sequence similarity in all its grammatical forms refers to the degree of identity or correspondence between nucleic acid or amino acid sequences of proteins that may or may not share a common evolutionary origin (see Reeck et al., Cell 50:667 (1987)). In one embodiment, two DNA sequences are substantially homologous or substantially similar when at least about 50% (e.g., at least about 75%, 90%, or 95%) of the nucleotides match over the defined length of the DNA sequences. Sequences that are substantially homologous can be identified by comparing the sequences using standard software available in sequence data banks, or in a Southern hybridization experiment under, for example, stringent conditions as defined for that particular system. Defining appropriate hybridization conditions is within the skill of the art (see e.g., Sambrook et al., 1989, supra).
As used herein, substantially similar refers to nucleic acid fragments wherein changes in one or more nucleotide bases results in substitution of one or more amino acids, but do not affect the functional properties of the protein encoded by the DNA sequence. Substantially similar also refers to nucleic acid fragments wherein changes in one or more nucleotide bases do not affect the ability of the nucleic acid fragment to mediate alteration of gene expression by antisense or co-suppression technology. Substantially similar also refers to modifications of the nucleic acid fragments of the present invention such as deletion or insertion of one or more nucleotide bases that do not substantially affect the functional properties of the resulting transcript. It is therefore understood that the invention encompasses more than the specific exemplary sequences. Each of the proposed modifications is well within the routine skill in the art, as is determination of retention of biological activity of the encoded products.
Moreover, the skilled artisan recognizes that substantially similar sequences encompassed by this invention are also defined by their ability to hybridize, under stringent conditions (0.1×SSC, 0.1% SDS, 65° C. and washed with 2×SSC, 0.1% SDS followed by 0.1×SSC, 0.1% SDS), with the sequences exemplified herein. Substantially similar nucleic acid fragments of the present invention are those nucleic acid fragments whose DNA sequences are at least about 70%, 80%, 90% or 95% identical to the DNA sequence of the nucleic acid fragments reported herein.
The term corresponding to is used herein to refer to similar or homologous sequences, whether the exact position is identical or different from the molecule to which the similarity or homology is measured. A nucleic acid or amino acid sequence alignment may include spaces. Thus, the term corresponding to refers to the sequence similarity, and not the numbering of the amino acid residues or nucleotide bases.
A substantial portion of an amino acid or nucleotide sequence comprises enough of the amino acid sequence of a polypeptide or the nucleotide sequence of a gene to putatively identify that polypeptide or gene, either by manual evaluation of the sequence by one skilled in the art, or by computer-automated sequence comparison and identification using algorithms such as BLAST (Basic Local Alignment Search Tool; Altschul et al., J. Mol. Biol. 215:403 (1993)); available at ncbi.nlm.nih.gov/BLAST/). In general, a sequence of ten or more contiguous amino acids or thirty or more nucleotides is necessary in order to putatively identify a polypeptide or nucleic acid sequence as homologous to a known protein or gene. Moreover, with respect to nucleotide sequences, gene specific oligonucleotide probes comprising 20 to 30 contiguous nucleotides may be used in sequence-dependent methods of gene identification (e.g., Southern hybridization) and isolation (e.g., in situ hybridization of bacterial colonies or bacteriophage plaques). In addition, short oligonucleotides of 12 to 15 bases may be used as amplification primers in PCR in order to obtain a particular nucleic acid fragment comprising the primers. Accordingly, a substantial portion of a nucleotide sequence comprises enough of the sequence to specifically identify and/or isolate a nucleic acid fragment comprising the sequence.
One aspect of the invention is to provide a PAI-1 protein that is linked to a degron. A degron may be linked at the amino terminus of the PAI-1 protein or its carboxy terminus. Degrons, or degradation-determining signals are known in the art as short, often portable elements that induce polypeptide degradation, several examples of which are recited in Garcin, D, et al., Journal of Virology, 2004, 78(16):8799-8811 and Gardner, R G and Hampton, R Y, The EMBO Journal, 1999, 18(21):5994-6004. Examples of PAI-1 linked to a degron are shown in FIGS. 17A, 17B, 17E, 17F, 17G, and 17H.
Another aspect of the invention is to provide a PAI-1 protein that is linked to a localization signal. Non-limiting examples of cellular localization signals are signals that localize to the sarcoplamic reticulum, endoplasmic reticulum, extracellular matrix, mitochondria, golgi apparatus, peroxisomes, lysosomes, nucleus, nucleolus, endosomes, exosomes, other intracellular vesicles, plasma membrane, apical membrane, and basolateral membrane. In one embodiment, PAI-1 is delivered to the extracellular face through non-cell-specific plasma membrane localization signals such as those described in U.S. Provisional Application 60/957,328. In other embodiments, PAI-1 is delivered to the extracellular face to cell-specific localization signals such as localization signals specific for fibroblasts, endothelial cells, smooth muscle cells, adipocytes, and the sarcolemma of cardiomyocytes. In other embodiments, PAI-1 is delivered to the extracellular matrix through extracellular association domains such as collagen binding proteins, or to other extracellular components enriched in myocardial infarct regions. FIGS. 17C-17H show additional embodiments of PAI-1 linked to localization signals. The localization signals are given by way of example and without limitation.
One aspect of the invention is to provide a PAI-1 polynucleotide sequence that has been optimized for vector insertion. In one embodiment, the polynucleotides are optimized for insertion into an ULTRAVECTOR (Intrexon Corp. Blacksburg, Va., US2004/0185556) plasmid vector. In another embodiment, the polynucleotides are optimized for vector insertion through removal of the following internal restriction sites: NgoM IV, Xma I, Cla I, BamH I, BstB I, EcoR I, RcoR V, Pci I, Sac I, Stu I, ApaL I, Bgl II, Kpn I, Mfe I, Nde I, Nhe I, Nsi I, Asc I, AsiS I, BsiW I, Fse I, Mlu I, Not I, Pac I, Sal I, Sbf I, SnaB I, Swa I, Rsr II1, RsrII2, BstX I, Sap I, BsmB I, Xba I, Xho I, Hpa I, Pml I, Sph I, Aar I, Bgl I, BsmB I, BspM I, BstAP I, BstX I, Dra III, Ear I, Sap I, Bip I, and BspE I.
One aspect of the invention is to provide a PAI-1 polynucleotide sequence that has been optimized for vector insertion, that is linked to a degron polynucleotide sequence. In one embodiment, the degron sequence is linked at the 5′ end of a PAI-1 polynucleotide sequence (see FIGS. 18C and 18H for examples). In another embodiment of the invention, the degron sequence is linked at the 3′ end of a degron polynucleotide sequence (see FIGS. 18B and 18F for examples).
Another aspect of the invention is to provide a PAI-1 polynucleotide sequence that has been optimized for vector insertion, that is linked to a localization signal (see FIGS. 18D-18I for examples).
Another embodiment of the invention relates to gene constructs for selective control of expression of a vector insertion-optimized PAI-1 polynucleotide sequence in a desired cell, tissue, or physiological state. The gene constructs may include a PAI-1 gene construct optionally linked to a degron and/or a localization signal. Exemplary gene constructs are shown in FIGS. 13A-13E, 23A-23G, and 18A-18I. The promoter portion of the gene construct can be a constitutive promoter, a non-constitutive promoter, a tissue-specific promoter (constitutive or non-constitutive) or an inducible promoter. Non-limiting examples of tissue-specific promoters useful for the present invention are endothelial cell-specific promoters (White, S J, et al., Gene Ther. 2007 Nov. 8 [Epub ahead of print]), vascular smooth muscle cell-specific promoters (Ribault, S, Circ Res., 2001, 88(5):468-75; Appleby, C E, et al., Gene Ther. 2003, 10(18):1616-22), cardiomyocyte-specific promoters (Xu, L, et al., J Biol. Chem., 2006, 281(45):34430-40), coronary adipocytes-specific promoters, and cardiac fibroblast-specific promoters. Combined tissue and state specific promoters such as a cardiac and hypoxia-specific promoter (Su, H, et al., Proc Natl. Acad. Sci. U.S.A., 2004, 101(46):16280-5) are also useful for the present invention. Inducible promoters are activated by drugs or other factors. RHEOSWITCH is an inducible promoter system available from New England BioLabs (Ipswich, Mass.) that is useful for the present invention. An embodiment of the invention comprises a PAI-1 gene construct whose expression is controlled by an inducible promoter system.
Another aspect of the invention is to provide vectors containing gene constructs for expression of a mammalian cell expression and vector insertion-optimized PAI-1 polynucleotide sequence as described herein. Vectors may be viral vectors or non-viral vectors as described herein. Non-limiting examples of such vectors are shown in FIGS. 19A-19D.
FIG. 19A shows in generic form a vector containing a vector insertion-optimized PAI-1 polynucleotide sequence and optional localization signal and/or degron, wherein the gene construct is releasable from the vector as a unit useful for generating transgenic animals. For example, the gene construct, or transgene, is released from the vector backbone by restriction endonuclease digestion. The released transgene is then injected into pronuclei of fertilized mouse eggs; or the transgene is used to transform embryonic stem cells. The vector of FIG. 19A is also useful for transient transfection of the transgene, wherein the promoter and codons of the transgene are optimized for mammalian expression.
FIGS. 19B and 19C depict embodiments of gene therapy vectors for delivering and controlling PAI-1 polypeptide expression in vivo. Polynucleotide sequences linked to the gene construct in FIGS. 19B and 19C include genome integration domains to facilitate integration of the transgene into a viral genome and/or host genome.
FIG. 19D shows a vector containing a localization signal gene construct useful for generating stable cell lines.
Another aspect of the invention is to provide host cells containing vectors containing gene constructs for expression of a mammalian cell expression and vector insertion-optimized PAI-1 polynucleotide sequence as described herein. In one embodiment, the host cells are mammalian cells. Host cells include human, non-human primate, mouse, bovine, porcine, ovine, equine, rat, rabbit, dog, cat, and guinea pig. Specific types of host cells include cardiomyocytes, fibroblasts, endothelial cells, smooth muscle cells, and adipocytes.
Another aspect of the invention is to provide transgenic organisms containing a mammalian cell expression and vector insertion-optimized PAI-1 polynucleotide sequence. In one embodiment, the transgenic host is mammalian. Mammalian transgenic hosts include non-human primate, mouse, cow, pig, sheep, horse, rat, rabbit, dog, cat, and guinea pig. Transgenic organisms are generated by injecting a completed transgene into the pronuclei of fertilized oocytes or into embryonic stem cells. The completed transgene includes the mammalian cell expression and vector insertion-optimized PAI-1 polynucleotide sequence, optionally linked to degrons, localization signals, or a constitutive promoter, a non-constitutive promoter, a tissue-specific promoter (constitutive or non-constitutive) or an inducible promoter as described herein. The transgenic organisms may be used as animal models to define the role of PAI-1 in the heart.
Another aspect of the invention is a method of altering expression of PAI-1 in a host cell comprising transfecting a vector comprising a vector insertion optimized-nucleic acid molecule encoding at least one copy of PAI-1 into a host cell and culturing the transfected host cell under conditions suitable to produce at least one copy of PAI-1.
Another aspect of the invention is a method of altering expression of PAI-1 in heart tissue of a subject comprising injecting a vector comprising a vector insertion optimized-nucleic acid molecule encoding at least one copy of PAI-1 into heart tissue of a subject.
Another aspect of the invention is a method of creating a transgenic subject with altered PAI-1 expression comprising injecting a vector comprising a vector insertion optimized-nucleic acid molecule encoding at least one copy of PAI-1 into a fertilized egg or an embryonic stem cell.
An aspect of the invention is to provide novel ligand inhibitors of PAI-1 activity by modifying a natural substrate and/or regulator by truncation and/or by amino acid substitution.
Another aspect of the invention is to provide modular polyligand inhibitors of PAI-1 activity by linking together novel inhibitors and variations thereof. A further aspect of the invention is to limit the activity of a PAI-1 inhibitor, ligand, or polyligand by linkage to a degron. A further aspect of the invention is the cellular localization of a PAI-1 inhibitor, ligand, or polyligand by linkage to a localization signal.
An aspect of the invention encompasses inhibition of PAI-1 as a way to prevent fibrosis in cardiac tissue. By inhibiting PAI-1, inhibition of plasminogen activators will be relieved, resulting in activation of plasminogen to plasmin and the breakdown of fibrin. Enhancement of fibrin breakdown of a diseased heart represents a potential approach for treating or preventing cardiomyopathies due to type II diabetes, hyperglycermia, hypertension, obesity, tobacco exposure, or other causes.
Additional aspects of the invention encompass PAI-1 inhibitors useful in any tissue.
Additional embodiments of the invention encompass PAI-1 inhibitors localized to different cellular locations by linking to a localization signal targeted to a region of a cell.
The invention relates to polypeptide ligands and polyligands for PAI-1. Various embodiments of PAI-1 ligands and polyligands are represented in SEQ ID NOS:1-30 and SEQ ID NOS:37-51. More specifically, the invention relates to ligands, homopolyligands, and heteropolyligands that comprise any one or more of SEQ ID NOS:37-51. Additionally, the invention relates to ligands and polyligands comprising one or more partial sequences (truncation fragments) of SEQ ID NOS:31-36 or any portion thereof. Furthermore, the invention relates to polyligands with at least about 80%, 85%, 90%, 95%, 96%, 97%, 98% and 99% sequence identity to a polyligand comprising one or more of SEQ ID NOS:37-51 or any portion thereof. Furthermore, the invention relates to polyligands with at least about 80%, 85%, 90%, 95%, 96%, 97%, 98% and 99% sequence identity to a polyligand comprising one or more partial sequences of SEQ ID NOS:31-36.
Polyligands, which can be homopolyligands or heteropolyligands, are chimeric ligands composed of two or more monomeric polypeptide ligands. Examples of homopolyligands are shown in FIGS. 4A-4F. Examples of heteropolyligands are shown in FIGS. 6A-6J. An example of a monomeric ligand is the polypeptide represented by SEQ ID NO:40. SEQ ID NO:40 is a selected partial sequence of parental full length SEQ ID NO:32. An example of a homopolyligand is a polypeptide comprising a dimer or multimer of SEQ ID NO:37. An example of a heteropolyligand is a polypeptide comprising SEQ ID NO:37 and one or more of SEQ ID NOS:38-51. Each of SEQ ID NOS:37-51 represents an individual polypeptide ligand in monomeric form. SEQ ID NOS:37-51 are selected examples of partial sequences of SEQ ID NOS:31-36, however, other partial sequences of SEQ ID NOS:31-36 may also be utilized as monomeric ligands. Monomeric partial sequences of SEQ ID NOS:31-36 may be identical to a portion of a parent polypeptide, such as SEQ ID NO:40. Additionally, monomeric partial sequences of SEQ ID NOS:31-36 may have amino acid substitutions, such as SEQ ID NOS:41-45. Furthermore, monomeric ligands and polyligands may have at least about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to a ligand comprising an amino acid sequence in one or more of SEQ ID NOS:37-51. Furthermore, monomeric ligands and polyligands may have at least about 80%, 85%, 90%, 95%, 96%, 97%, 98% and 99% sequence identity to a partial sequence of SEQ ID NOS:31-36.
There are numerous ways to combine SEQ ID NOS:37-51 into homopolymeric or heteropolymeric ligands. Furthermore, there are numerous ways to combine additional partial sequences of SEQ ID NOS:31-36 with each other and with SEQ ID NOS:37-51 to make polymeric ligands. Non-limiting examples of homopolyligand architectures are shown in FIGS. 1A-1F. Non-limiting examples of heteropolyligand architectures are shown in FIGS. 2A-2J. The instant invention is directed to all possible combinations of homopolyligands and heteropolyligands without limitation. The ligands and polyligands of the invention are designed to modulate the endogenous effects of PAI-1.
In one embodiment of the invention, the ligand or polyligand is a PAI-1 ligand or polyligand described herein.
In another embodiment of the invention, the ligand or polyligand is at least 60%, 65%, 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98% or 99% identical to a PAI-1 ligand or polyligand described herein.
In another embodiment of the invention, the ligand or polyligand is a PAI-1 ligand or polyligand described herein that has been modified to comprise one or more amino acid deletions, substitutions, insertions, truncations, or combinations thereof.
Another embodiment of the invention is a polypeptide at least 60%, 65%, 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98% or 99% identical to a polypeptide shown in the odd SEQ ID NOS of SEQ ID NOS:1-30.
Another embodiment of the invention is a polynucleotide at least 60%, 65%, 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98% or 99% identical to a polynucleotide shown in the even SEQ ID NOS of SEQ ID NOS:1-30.
In another embodiment of the invention, the PAI-1 ligand or polyligand comprises at least one peptide at least 60%, 65%, 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98% or 99% identical to one of SEQ ID NOS:37-51.
In another embodiment of the invention, the PAI-1 ligand or polyligand possesses at least one of the following inhibition mechanisms: latent state, turn PA1 into a substrate, steric hindrance to tPA binding, steric hindrance to endogenous vitronectin, or direct competition for binding site.
Another embodiment of the invention is a polynucleotide encoding a PAI-1 ligand or polyligand described herein.
The polyligands of the invention optionally comprise spacer amino acids before, after, or between monomers (see FIGS. 1D-1F and FIGS. 2F-2J for exemplary architectures).
This invention intends to capture all combinations of homopolyligands and heteropolyligands without limitation to the examples given above or below. In this description, use of the term “ligand(s)” encompasses monomeric ligands, polymeric ligands, homopolymeric ligands and/or heteropolymeric ligands. The term ligand also encompasses the terms decoy, inhibitor, and modulator.
A monomeric ligand is a polypeptide where at least a portion of the polypeptide is capable of being recognized by PAI-1. The portion of the polypeptide capable of recognition is termed the recognition motif. In the present invention, recognition motifs can be natural or synthetic. Examples of recognition motifs are well known in the art and include, but are not limited to, naturally occurring PAI-1 substrates, pseudosubstrate motifs, and interaction domains present in PAI-1 regulatory binding proteins and modifications thereof.
In general, ligand monomers based on natural PAI-1 interaction partners are built by identifying and isolating a putative PAI-1 interaction domain recognition motif. Exemplary natural PAI-1 interaction partners are known in the art and include fibrin, tissue plasminogen activator (the protein represented by SEQ ID NO:34), urokinase plasminogen activator (the protein represented by SEQ ID NO:36), and vitronectin (the protein represented by SEQ ID NO:32). Additional monomers include the PAI-1 recognition motif as well as amino acids adjacent and contiguous on either side of the PAI-1 interaction domain recognition motif. Monomeric ligands may therefore be any length provided the monomer includes the PAI-1 recognition motif. For example, the monomer may comprise a PAI-1 recognition motif and at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or 100 or more amino acids adjacent to the recognition motif. Further design considerations are taken from three-dimensional modeling of the ligands and modeling of binding interactions with PAI-1. Modifications of the primary sequence of a ligand or polyligand may be desirable based upon such modeling.
For example, in one embodiment, the invention comprises an inhibitor of PAI-1 comprising at least one copy of a peptide selected from the group consisting of:
a) a peptide at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to a peptide comprising amino acid residues corresponding to amino acid residues 354-368 of SEQ ID NO:31;
b) a peptide at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to a peptide comprising amino acid residues corresponding to amino acid residues 300-309 of SEQ ID NO:31;
c) a peptide at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to a peptide comprising amino acid residues corresponding to amino acid residues 343-353 of SEQ ID NO:31;
d) a peptide at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to a peptide comprising amino acid residues corresponding to amino acid residues 20-63 of SEQ ID NO:32;
e) a peptide at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to a peptide comprising amino acid residues corresponding to amino acid residues 20-63 of SEQ ID NO:32, wherein the amino acid residue corresponding to amino acid residue 32 of SEQ ID NO:32 has been mutated from phenylalanine to leucine;
f) a peptide at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to a peptide comprising amino acid residues corresponding to amino acid residues 20-63 of SEQ ID NO:32, wherein the amino acid residue corresponding to amino acid residue 29 of SEQ ID NO:32 has been mutated from threonine to alanine;
g) a peptide at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to a peptide comprising amino acid residues corresponding to amino acid residues 20-63 of SEQ ID NO:32, wherein the amino acid residue corresponding to amino acid residue 42 of SEQ ID NO:32 has been mutated from glutamic acid to alanine;
h) a peptide at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to a peptide comprising amino acid residues corresponding to amino acid residues 20-63 of SEQ ID NO:32, wherein the amino acid residue corresponding to amino acid residue 43 of SEQ ID NO:32 has been mutated from leucine to alanine;
i) a peptide at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to a peptide comprising amino acid residues corresponding to amino acid residues 20-63 of SEQ ID NO:32, wherein the amino acid residue corresponding to amino acid residue 23 of SEQ ID NO:32 has been mutated from serine to phenyalanine, the amino acid residue corresponding to amino acid residue 52 of SEQ ID NO:32 has been mutated from threonine to glutamic acid, the amino acid residue corresponding to amino acid residue 53 of SEQ ID NO:32 has been mutated from aspartic acid to leucine, the amino acid residue corresponding to amino acid residue 56 of SEQ ID NO:32 has been mutated from alanine to tyrosine, and the amino acid residue corresponding to amino acid residue 57 of SEQ ID NO:32 has been mutated from glutamic acid to tyrosine
j) a peptide at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to a peptide comprising amino acid residues corresponding to amino acid residues 25-256 of SEQ ID NO:33;
k) a peptide at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to a peptide comprising amino acid residues corresponding to amino acid residues 25-44 of SEQ ID NO:33;
l) a peptide at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to a peptide comprising amino acid residues corresponding to amino acid residues 47-256 of SEQ ID NO:33;
m) a peptide at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to a peptide comprising amino acid residues corresponding to amino acid residues 301-308 of SEQ ID NO:34;
n) a peptide at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to a peptide comprising amino acid residues corresponding to amino acid residues 29-121 of SEQ ID NO:35; wherein the amino acid residue corresponding to amino acid residue 55 of SEQ ID NO:35 has been mutated from valine to alanine, the amino acid residue corresponding to amino acid residue 57 of SEQ ID NO:35 has been mutated from asparagine to tyrosine, the amino acid residue corresponding to amino acid residue 59 of SEQ ID NO:35 has been mutated from threonine to asparagine, the amino acid residue corresponding to amino acid residue 79 of SEQ ID NO:35 has been mutated from serine to lysine, the amino acid residue corresponding to amino acid residue 81 of SEQ ID NO:35 has been mutated from aspartic acid to lysine, and the amino acid residue corresponding to amino acid residue 83 of SEQ ID NO:35 has been mutated from glycine to glutamic acid; and
o) a peptide at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to a peptide comprising amino acid residues corresponding to amino acid residues 179-415 of SEQ ID NO:36; wherein the amino acid residue corresponding to amino acid residue 224 of SEQ ID NO:36 has been mutated from histidine to alanine, the amino acid residue corresponding to amino acid residue 275 of SEQ ID NO:36 has been mutated from aspartic acid to alanine, and the amino acid residue corresponding to amino acid residue 376 of SEQ ID NO:36 has been mutated from serine to alanine.
As used herein, the terms “correspond(s) to” and “corresponding to,” as they relate to sequence alignment, are intended to mean enumerated positions within a reference protein, e.g., (plasminogen activator inhibitor 1, AAA60009, SEQ ID NO:31), and those positions that align with the positions on the reference protein. Thus, when the amino acid sequence of a subject peptide is aligned with the amino acid sequence of a reference peptide, e.g., SEQ ID NO:31, the amino acids in the subject peptide sequence that “correspond to” certain enumerated positions of the reference peptide sequence are those that align with these positions of the reference peptide sequence, but are not necessarily in these exact numerical positions of the reference sequence. Methods for aligning sequences for determining corresponding amino acids between sequences are described below.
In other embodiments, a ligand may be a monoclonal antibody fragment, a phage-display product, a PAI-1 synthesis inhibitor, or a transcription factor decoy.
A monomeric ligand is a polypeptide where at least a portion of the polypeptide is capable of being recognized by PAI-1. The portion of the polypeptide capable of recognition is termed the recognition motif. In the present invention, recognition motifs can be natural or synthetic. Examples of recognition motifs are well known in the art and include, but are not limited to, naturally occurring PAI-1 substrates, pseudosubstrate motifs, and interaction domains present in PAI-1 regulatory binding proteins and modifications thereof.
A polymeric ligand (polyligand) comprises two or more monomeric ligands.
A homopolymeric ligand is a polymeric ligand where each of the monomeric ligands is identical in amino acid sequence, except that a dephosphorylatable residue, such as serine, threonine, or tyrosine, may be substituted or modified in one or more of the monomeric ligands. Modifications include, but are not limited to, substitution to a pseudophosphorylated residue (acidic amino acid) or substitution to a neutral residue.
A heteropolymeric ligand is a polymeric ligand where some of the monomeric ligands do not have an identical amino acid sequence.
The ligands of the invention are optionally linked to additional molecules or amino acids that provide an epitope tag, a reporter, and/or a cellular localization signal. The cellular localization signal targets the ligands to a region of a cell. The epitope tag and/or reporter and/or localization signal may be the same molecule. The epitope tag and/or reporter and/or localization signal may also be different molecules.
The invention also encompasses polynucleotides comprising a nucleotide sequence encoding ligands, homopolyligands, and heteropolyligands. The nucleic acids of the invention are optionally linked to additional nucleotide sequences encoding polypeptides with additional features, such as an epitope tag, a reporter, and/or a cellular localization signal. The polynucleotides are optionally flanked by nucleotide sequences comprising restriction endonuclease sites and other nucleotides needed for restriction endonuclease activity. The flanking sequences optionally provide unique cloning sites within a vector and optionally provide directionality of subsequence cloning. Further, the nucleic acids of the invention are optionally incorporated into vector polynucleotides. The ligands, polyligands, and polynucleotides of this invention have utility as research tools and/or therapeutics.
Additional embodiments of the invention include monomers (as described above) based on any putative or real interaction partner for PAI-1. Furthermore, if the substrate or binding protein has more than one recognition motif, then more than one monomer may be identified therein.
Another embodiment of the invention is a nucleic acid molecule comprising a polynucleotide sequence encoding at least one copy of a ligand peptide.
Another embodiment of the invention is a nucleic acid molecule wherein the polynucleotide sequence encodes one or more copies of one or more peptide ligands.
Another embodiment of the invention is a nucleic acid molecule wherein the polynucleotide sequence encodes at least a number of copies of the peptide selected from the group consisting of 2, 3, 4, 5, 6, 7, 8, 9 or 10.
Another embodiment of the invention is a vector comprising a nucleic acid molecule encoding at least one copy of a ligand or polyligand.
Another embodiment of the invention is a recombinant host cell comprising a vector comprising a nucleic acid molecule encoding at least one copy of a ligand or polyligand.
Another embodiment of the invention is a method of inhibiting PAI-1 in a host cell comprising transfecting a vector comprising a nucleic acid molecule encoding at least one copy of a ligand or polyligand into a host cell and culturing the transfected host cell under conditions suitable to produce at least one copy of the ligand or polyligand.
Another aspect of the invention is a method of inhibiting PAI-1 in heart tissue of a subject comprising injecting a vector comprising a nucleic acid molecule encoding at least one copy of a PAI-1 ligand or polyligand into heart tissue of a subject.
Another aspect of the invention is a method of creating a transgenic subject with reduced PAI-1 activity comprising injecting a vector comprising a nucleic acid molecule encoding at least one copy of a PAI-1 ligand or polyligand into a fertilized egg or an embryonic stem cell.
The invention also relates to modified inhibitors that are at least about 60%, 65%, 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98% or 99% identical to a reference inhibitor. A “modified inhibitor” is used to mean a peptide that can be created by addition, deletion or substitution of one or more amino acids in the primary structure (amino acid sequence) of a inhibitor protein or polypeptide. A “modified recognition motif” is a naturally occurring PAI-1 recognition motif that has been modified by addition, deletion, or substitution of one or more amino acids in the primary structure (amino acid sequence) of the motif. The terms “protein” and “polypeptide” and “peptide” are used interchangeably herein. The reference inhibitor is not necessarily a wild-type protein or a portion thereof. Thus, the reference inhibitor may be a protein or peptide whose sequence was previously modified over a wild-type protein. The reference inhibitor may or may not be the wild-type protein from a particular organism.
A polypeptide having an amino acid sequence at least, for example, about 95% “identical” to a reference an amino acid sequence is understood to mean that the amino acid sequence of the polypeptide is identical to the reference sequence except that the amino acid sequence may include up to about five modifications per each 100 amino acids of the reference amino acid sequence encoding the reference peptide. In other words, to obtain a peptide having an amino acid sequence at least about 95% identical to a reference amino acid sequence, up to about 5% of the amino acid residues of the reference sequence may be deleted or substituted with another amino acid or a number of amino acids up to about 5% of the total amino acids in the reference sequence may be inserted into the reference sequence. These modifications of the reference sequence may occur at the N-terminus or C-terminus positions of the reference amino acid sequence or anywhere between those terminal positions, interspersed either individually among amino acids in the reference sequence or in one or more contiguous groups within the reference sequence.
As used herein, “identity” is a measure of the identity of nucleotide sequences or amino acid sequences compared to a reference nucleotide or amino acid sequence. In general, the sequences are aligned so that the highest order match is obtained. “Identity” per se has an art-recognized meaning and can be calculated using published techniques. (See, e.g., Computational Molecular Biology, Lesk, A. M., ed., Oxford University Press, New York (1988); Biocomputing: Informatics And Genome Projects, Smith, D. W., ed., Academic Press, New York (1993); Computer Analysis of Sequence Data, Part I, Griffin, A. M., and Griffin, H. G., eds., Humana Press, New Jersey (1994); von Heinje, G., Sequence Analysis In Molecular Biology, Academic Press (1987); and Sequence Analysis Primer, Gribskov, M. and Devereux, J., eds., M Stockton Press, New York (1991)). While there exist several methods to measure identity between two polynucleotide or polypeptide sequences, the term “identity” is well known to skilled artisans (Carillo, H. & Lipton, D., Siam J Applied Math 48:1073 (1988)). Methods commonly employed to determine identity or similarity between two sequences include, but are not limited to, those disclosed in Guide to Huge Computers, Martin J. Bishop, ed., Academic Press, San Diego (1994) and Carillo, H. & Lipton, D., Siam Applied Math 48:1073 (1988). Computer programs may also contain methods and algorithms that calculate identity and similarity. Examples of computer program methods to determine identity and similarity between two sequences include, but are not limited to, GCG program package (Devereux, J., et al., Nucleic Acids Research 12(i):387 (1984)), BLASTP, ExPASy, BLASTN, FASTA (Atschul, S. F., et al., J Molec Biol 215:403 (1990)) and FASTDB. Examples of methods to determine identity and similarity are discussed in Michaels, G. and Garian, R., Current Protocols in Protein Science, Vol 1, John Wiley & Sons, Inc. (2000), which is incorporated by reference. In one embodiment of the present invention, the algorithm used to determine identity between two or more polypeptides is BLASTP.
In another embodiment of the present invention, the algorithm used to determine identity between two or more polypeptides is FASTDB, which is based upon the algorithm of Brutlag et al. (Comp. App. Biosci. 6:237-245 (1990), incorporated by reference). In a FASTDB sequence alignment, the query and subject sequences are amino sequences. The result of sequence alignment is in percent identity. Parameters that may be used in a FASTDB alignment of amino acid sequences to calculate percent identity include, but are not limited to: Matrix=PAM, k-tuple=2, Mismatch Penalty=1, Joining Penalty=20, Randomization Group Length=0, Cutoff Score=1, Gap Penalty=5, Gap Size Penalty 0.05, Window Size=500 or the length of the subject amino sequence, whichever is shorter.
If the subject sequence is shorter or longer than the query sequence because of N-terminus or C-terminus additions or deletions, not because of internal additions or deletions, a manual correction can be made, because the FASTDB program does not account for N-terminus and C-terminus truncations or additions of the subject sequence when calculating percent identity. For subject sequences truncated at both ends, relative to the query sequence, the percent identity is corrected by calculating the number of bases of the query sequence that are N- and C-terminus to the reference sequence that are not matched/aligned, as a percent of the total bases of the query sequence. The results of the FASTDB sequence alignment determine matching/alignment. The alignment percentage is then subtracted from the percent identity, calculated by the above FASTDB program using the specified parameters, to arrive at a final percent identity score. This corrected score can be used for the purposes of determining how alignments “correspond” to each other, as well as percentage identity. Residues of the query (subject) sequences or the reference sequence that extend past the N- or C-termini of the reference or subject sequence, respectively, may be considered for the purposes of manually adjusting the percent identity score. That is, residues that are not matched/aligned with the N- or C-termini of the comparison sequence may be counted when manually adjusting the percent identity score or alignment numbering.
For example, a 90 amino acid residue subject sequence is aligned with a 100 residue reference sequence to determine percent identity. The deletion occurs at the N-terminus of the subject sequence and therefore, the FASTDB alignment does not show a match/alignment of the first 10 residues at the N-terminus. The 10 unpaired residues represent 10% of the sequence (number of residues at the N- and C-termini not matched/total number of residues in the query sequence) so 10% is subtracted from the percent identity score calculated by the FASTDB program. If the remaining 90 residues were perfectly matched the final percent identity would be 90%. In another example, a 90 residue subject sequence is compared with a 100 reference sequence. This time the deletions are internal deletions so there are no residues at the N- or C-termini of the subject sequence which are not matched/aligned with the query. In this case the percent identity calculated by FASTDB is not manually corrected.
The polyligands of the invention optionally comprise spacer amino acids before, after, or between monomers. The length and composition of the spacer may vary. An example of a spacer is glycine, alanine, polyglycine, or polyalanine. Sometimes it is desirable to employ proline in a spacer for the purpose of interrupting secondary structure of a polypeptide. Spacer amino acids may be any amino acid and are not limited to alanine, glycine and proline. Exemplary spacers are provided in SEQ ID NOS:53-56. The instant invention is directed to all combinations of homopolyligands and heteropolyligands, with or without spacers, and without limitation to the examples given above or below.
The ligands and polyligands of the invention are optionally linked to signals that localize the ligand to a region of a cell. Non-limiting examples of cellular localization signals are signals that localize to the sarcoplamic reticulum, endoplasmic reticulum, extracellular matrix, mitochondria, golgi apparatus, peroxisomes, lysosomes, nucleus, nucleolus, endosomes, exosomes, other intracellular vesicles, plasma membrane, apical membrane, and basolateral membrane. In one embodiment, the ligands and polyligands are delivered to the extracellular face through non-cell-specific plasma membrane localization signals such as those described in U.S. Provisional Application 60/957,328. In other embodiments, the ligands and polyligands are delivered to the extracellular face to cell-specific localization signals such as localization signals specific for fibroblasts, endothelial cells, smooth muscle cells, adipocytes, and the sarcolemma of cardiomyocytes. In other embodiments, the ligands and polyligands are delivered to the extracellular matrix through extracellular association domains such as collagen binding proteins, or to other extracellular components enriched in myocardial infarct regions. FIGS. 3A-3H, 5A-5I, 11A-11I and 22A-22F show exemplary architectures of ligands and polyligands linked to localization signals. The localization signals are given by way of example and without limitation.
One embodiment of the invention is a ligand or polyligand linked to a class 1 localization tether.
Another embodiment of the invention is a ligand or polyligand linked to a class 2 localization tether.
Another embodiment of the invention a ligand or polyligand linked to a class 3 localization tether.
Another embodiment of the invention is a class 1 localization tether described herein.
Another embodiment of the invention is a class 1 localization tether at least 60%, 65%, 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98% or 99% identical to a class 1 localization tether described herein.
Another embodiment of the invention is a class 1 localization tether described herein that has been modified to comprise one or more amino acid deletions, substitutions, insertions, truncations, or combinations thereof.
Another embodiment of the invention is a class 1 localization tether at least 60%, 65%, 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98% or 99% identical to SEQ ID NOS:57-76.
Another embodiment of the invention is a class 1 localization tether comprising at least one peptide at least 60%, 65%, 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98% or 99% identical to one of SEQ ID NOS:77-95.
Another embodiment of the invention is a polynucleotide that encodes a class 1 localization tether described herein.
Another embodiment of the invention is a class 2 localization tether described herein.
Another embodiment of the invention is a polynucleotide that encodes a class 2 localization tether described herein.
Another embodiment of the invention is a class 3 localization tether described herein.
Another embodiment of the invention is a class 3 localization tether at least 60%, 65%, 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98% or 99% identical to a class 3 localization tether described herein.
Another embodiment of the invention is a class 3 localization tether described herein that has been modified to comprise one or more amino acid deletions, substitutions, insertions, truncations, or combinations thereof.
Another embodiment of the invention is a class 3 localization tether at least 60%, 65%, 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98% or 99% identical to SEQ ID NOS:100-111.
Another embodiment of the invention is a class 3 localization tether comprising at least one peptide at least 60%, 65%, 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98% or 99% identical to one of SEQ ID NOS:112-128.
Another embodiment of the invention is a polynucleotide that encodes a class 3 localization tether described herein.
The ligands and polyligands of the invention may also be linked to degrons to restrict their activity. FIGS. 21A-21H and 22A-22F show several non-limiting embodiments of ligands and polyligands linked to degrons.
Further, the ligands and polyligands of the invention are optionally linked to additional molecules or amino acids that provide an epitope tag or a reporter (see FIGS. 4A-4G). Non-limiting examples of epitope tags are FLAGTM, HA (hemagluttinin), c-Myc and His6. Non-limiting examples of reporters are alkaline phosphatase, galactosidase, peroxidase, luciferase and fluorescent proteins. The epitopes and reporters are given by way of example and without limitation. The epitope tag and/or reporter may be the same molecule. The epitope tag and/or reporter may also be different molecules.
Ligands and polyligands and optional amino acids linked thereto can be synthesized chemically or recombinantly using techniques known in the art. Chemical synthesis techniques include but are not limited to peptide synthesis which is often performed using an automated peptide synthesizer. Peptides can also be synthesized utilizing non-automated peptide synthesis methods known in the art. Recombinant techniques include insertion of ligand-encoding nucleic acids into expression vectors, wherein nucleic acid expression products are synthesized using cellular factors and processes.
Linkage of a cellular localization signal, epitope tag, reporter, or degron to a ligand or polyligand can include covalent or enzymatic linkage to the ligand. When the localization signal comprises material other than a polypeptide, such as a lipid or carbohydrate, a chemical reaction to link molecules may be utilized. Additionally, non-standard amino acids and amino acids modified with lipids, carbohydrates, phosphate or other molecules may be used as precursors to peptide synthesis. The ligands of the invention have therapeutic utility with or without localization signals. However, ligands linked to localization signals have utility as subcellular tools or therapeutics.
FIGS. 6A-6E, 13A-13E and 23A-23G show examples of PAI-1 ligand-containing gene constructs. PAI-1 ligand-containing gene constructs may be delivered via viral or nonviral vectors as described herein. FIGS. 7B and 7C depict embodiments of gene therapy vectors for delivering and controlling polypeptide expression in vivo. Polynucleotide sequences linked to the gene constructs in FIGS. 7B and 7C include genome integration domains to facilitate integration of the transgene into a viral genome and/or host genome. AttP and AttB sequences are non-limiting examples of genome integration sequences.
FIG. 7A shows a vector containing a PAI-1 ligand gene construct, wherein the ligand gene construct is releasable from the vector as a unit useful for generating transgenic animals. For example, the ligand gene construct, or transgene, is released from the vector backbone by restriction endonuclease digestion. The released transgene is then injected into pronuclei of fertilized mouse eggs; or the transgene is used to transform embryonic stem cells. The vector containing a ligand gene construct of FIG. 7A is also useful for transient transfection of the transgene, wherein the promoter and codons of the transgene are optimized for the host organism. The vector containing a ligand gene construct of FIG. 7A is also useful for recombinant expression of polypeptides in fermentable organisms adaptable for small or large scale production, wherein the promoter and codons of the transgene are optimized for the fermentation host organism.
FIG. 7D shows a vector containing a PAI-1 ligand gene construct useful for generating stable cell lines.
The invention also encompasses polynucleotides comprising nucleotide sequences encoding ligands and polyligands. The polynucleotides of the invention are optionally linked to additional nucleotide sequences encoding degrons, localization signals, epitopes, or reporters. Further, the nucleic acids of the invention are optionally incorporated into vector polynucleotides. The polynucleotides are optionally flanked by nucleotide sequences comprising restriction endonuclease sites and other nucleotides needed for restriction endonuclese activity. The flanking sequences optionally provide cloning sites within a vector. The restriction sites can include, but are not limited to, any of the commonly used sites in most commercially available cloning vectors. Sites for cleavage by other restriction enzymes, including homing endonucleases, are also used for this purpose. The polynucleotide flanking sequences also optionally provide directionality of subsequence cloning. It is preferred that 5′ and 3′ restriction endonuclease sites differ from each other so that double-stranded DNA can be directionally cloned into corresponding complementary sites of a cloning vector.
Ligands and polyligands with or without degrons, localization signals, epitopes or reporters are alternatively synthesized by recombinant techniques. Polynucleotide expression constructs are made containing desired components and inserted into an expression vector. The expression vector is then transfected into cells and the polypeptide products are expressed and isolated. Ligands made according to recombinant DNA techniques have utility as research tools and/or therapeutics.
The following is an example of how polynucleotides encoding ligands and polyligands are produced. Complimentary oligonucleotides encoding the ligands and flanking sequences are synthesized and annealed. The resulting double-stranded DNA molecule is inserted into a cloning vector using techniques known in the art. When the ligands and polyligands are placed in-frame adjacent to sequences within a transgenic gene construct that is translated into a protein product, they form part of a fusion protein when expressed in cells or transgenic animals.
Another embodiment of the invention relates to gene constructs for selective control of PAI-1 ligand or polyligand expression in a desired cell, tissue, or physiological state. Exemplary gene constructs architectures are shown in FIGS. 6A-6E. The promoter portion of the gene construct can be a constitutive promoter, a non-constitutive promoter, a tissue-specific promoter (constitutive or non-constitutive) or an inducible promoter. Non-limiting examples of tissue-specific promoters useful for the present invention are endothelial cell-specific promoters (White, S J, et al., Gene Ther. 2007 Nov. 8 [Epub ahead of print]), vascular smooth muscle cell-specific promoters (Ribault, S, Circ Res., 2001, 88(5):468-75; Appleby, C E, et al., Gene Ther. 2003, 10(18):1616-22), cardiomyocyte-specific promoters (Xu, L, et al., J Biol. Chem., 2006, 281(45):34430-40), coronary adipocytes-specific promoters, and cardiac fibroblast-specific promoters. Combined tissue and state specific promoters such as a cardiac and hypoxia-specific promoter (Su, H, et al., Proc Natl Acad Sci USA, 2004, 101(46):16280-5) are particularly useful for the present invention as they would allow expression of the ligand or polyligand in myocardial infarct regions. Inducible promoters are activated by drugs or other factors. RHEOSWITCH is an inducible promoter system available from New England BioLabs (Ipswich, Mass.) that is useful for the present invention. An embodiment of the invention comprises a ligand or polyligand gene construct whose expression is controlled by an inducible promoter system.
One embodiment of the invention is a polynucleotide encoding a ligand or polyligand linked to a tissue-specific promoter.
Another embodiment of the invention is a polynucleotide encoding a ligand or polyligand linked to an arterial smooth muscle specific-promoter.
Another embodiment of the invention is a polynucleotide encoding a ligand or polyligand linked to a vascular smooth muscle cell-specific promoter.
Another embodiment of the invention is a polynucleotide encoding a ligand or polyligand linked to an endothelial cell-specific promoter.
Another embodiment of the invention is a polynucleotide encoding a ligand or polyligand linked to a synthetic endothelial cell-specific promoter.
Another embodiment of the invention is a polynucleotide encoding a tissue-specific promoter described herein.
Another embodiment of the invention is a polynucleotide encoding a tissue-specific promoter described herein that has been modified to comprise one or more nucleotide deletions, substitutions, insertions, truncations, or combinations thereof.
Another embodiment of the invention is a polynucleotide encoding a tissue-specific promoter that is at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to a tissue-specific promoter described herein.
Another embodiment of the invention is a polynucleotide at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to a polynucleotide shown in SEQ ID NOS:132-139.
Polyligands are modular in nature. An aspect of the instant invention is the combinatorial modularity of the disclosed polyligands. Another aspect of the invention are methods of making these modular polyligands easily and conveniently. In this regard, an embodiment of the invention comprises methods of modular cloning of genetic expression components. When the ligands, homopolyligands, heteropolyligands and optional amino acid expression components are synthesized recombinantly, one can consider each clonable element as a module. For speed and convenience of cloning, it is desirable to make modular elements that are compatible at cohesive ends and are easy to insert and clone sequentially. This is accomplished by exploiting the natural properties of restriction endonuclease site recognition and cleavage. One aspect of the invention encompasses module flanking sequences that, at one end of the module, are utilized for restriction enzyme digestion once, and at the other end, utilized for restriction enzyme digestion as many times as desired. In other words, a restriction site at one end of the module is utilized and destroyed in order to effect sequential cloning of modular elements. An example of restriction sites flanking a coding region module are sequences recognized by the restriction enzymes NgoM IV and Cla I; or Xma I and Cla I. Cutting a first circular DNA with NgoM IV and Cla I to yield linear DNA with a 5′ NgoM IV overhang and a 3′ Cla I overhang; and cutting a second circular DNA with Xma I and Cla I to yield linear DNA with a 5′ Cla I overhang and a 3′ Xma I overhang generates first and second DNA fragments with compatible cohesive ends. When these first and second DNA fragments are mixed together, annealed, and ligated to form a third circular DNA fragment, the NgoM IV site that was in the first DNA and the Xma I site that was in the second DNA are destroyed in the third circular DNA. Now this vestigial region of DNA is protected from further Xma I or NgoM IV digestion, but flanking sequences remaining in the third circular DNA still contain intact 5′ NgoM IV and 3′ Cla I sites. This process can be repeated numerous times to achieve directional, sequential, modular cloning events. Restriction sites recognized by NgoM IV, Xma I, and Cla I endonucleases represent a group of sites that permit sequential cloning when used as flanking sequences.
Another way to assemble coding region modules directionally and sequentially employs linear DNA in addition to circular DNA. For example, like the sequential cloning process described above, restriction sites flanking a coding region module are sequences recognized by the restriction enzymes NgoM IV and Cla I; or Xma I and Cla I. A first circular DNA is cut with NgoM IV and Cla I to yield linear DNA with a 5′ NgoM IV overhang and a 3′ Cla I overhang. A second linear double-stranded DNA is generated by PCR amplification or by synthesizing and annealing complimentary oligonucleotides. The second linear DNA has 5′ Cla I overhang and a 3′ Xma I overhang, which are compatible cohesive ends with the first DNA linearized. When these first and second DNA fragments are mixed together, annealed, and ligated to form a third circular DNA fragment, the NgoM IV site that was in the first DNA and the Xma I site that was in the second DNA are destroyed in the third circular DNA. Flanking sequences remaining in the third circular DNA still contain intact 5′ NgoM IV and 3′ Cla I sites. This process can be repeated numerous times to achieve directional, sequential, modular cloning events. Restriction sites recognized by NgoM IV, Xma I, and Cla I endonucleases represent a group of sites that permit sequential cloning when used as flanking sequences. This process is depicted in FIG. 8.
One of ordinary skill in the art recognizes that other restriction site groups can accomplish sequential, directional cloning as described herein. Preferred criteria for restriction endonuclease selection are selecting a pair of endonucleases that generate compatible cohesive ends but whose sites are destroyed upon ligation with each other. Another criteria is to select a third endouclease site that does not generate sticky ends compatible with either of the first two. When such criteria are utilized as a system for sequential, directional cloning, ligands, polyligands and other coding regions or expression components can be combinatorially assembled as desired. The same sequential process can be utilized for epitope, reporter, degron, and/or localization signals.
Polyligands and methods of making polyligands that modulate PAI-1 activity are disclosed. Therapeutics include delivery of purified ligand or polyligand with or without a localization signal to a cell. Alternatively, ligands and polyligands with or without a localization signals are delivered via viral or retroviral constructs such as those employing adenovirus, lentivirus, adeno-associated virus, or other viral or retroviral constructs that provide for expression of protein product in a cell.
The PAI-1 ligands or polyligands, nucleic acids encoding PAI-1 ligands and polyligands, and vectors containing nucleic acids encoding PAI-1 ligands and polyligands can be used to treat a subject with a fibrotic condition or a subject at risk for developing fibrosis. The subject may be an animal with a naturally-occurring fibrotic condition or surgery-induced, chemical-induced, genetically-induced, or other experimentally-induced fibrotic condition. The fibrotic condition may result from diabetes or hyperglycemia induced by chemical exposure, dietary manipulation, genetic manipulation, obesity, or natural maturation. The fibrotic condition may also result from hypertension, ischemia, necrosis, immune-mediated injury, tobacco smoke exposure, chemical exposure, fiber exposure, viral or bacterial infection, or idiopathic causes. The PAI-1 ligands or polyligands, nucleic acids encoding PAI-1 ligands and polyligands, and vectors containing nucleic acids encoding PAI-1 ligands and polyligands can be used to treat fibrosis and other PAI-1 associated conditions in heart, blood, kidney, liver, lung, and ovary. The PAI-1 ligands or polyligands, nucleic acids encoding PAI-1 ligands and polyligands, and vectors containing nucleic acids encoding PAI-1 ligands and polyligands may also be useful for treating various cancers in which PAI-1 is expressed.
Another embodiment of the invention is a method for transferring a polynucleotide encoding a ligand or polyligand to cardiovascular tissue described herein.
Another embodiment of the invention is a method for transferring a polynucleotide encoding a ligand or polyligand to cardiovascular tissue comprising one of the following: local injection of adenovirus, ex vivo transduction of monocytes, or direct injection into aorta.
Another embodiment of the invention is a method for assessing the function of PAI-1 in the formation of unstable plaques described herein.
Another embodiment of the invention is a method for assessing the function of PAI-1 in the formation of unstable plaques comprising the step of developing an insulin resistant mouse model.
Another embodiment of the invention is a method of achieving spatial or temporal control of a ligand or polyligand described herein.
Another embodiment of the invention is a method of achieving spatial control of a ligand or polyligand comprising the step of linking the ligand or polyligand to a tissue-specific promoter.
Another embodiment of the invention is a method of achieving spatial control of a ligand or polyligand comprising the step of linking the ligand or polyligand to a localization tether.
Another embodiment of the invention is a method of achieving temporal control of a ligand or polyligand comprising the step of linking the ligand or polyligand to an inducible gene switch.
Another embodiment of the invention is a method for treating, preventing, or ameliorating a cardiovascular disease, comprising the steps of:
a) Identifying a subject with a cardiovascular disease or at risk for developing a cardiovascular disease; and
b) Administering a PAI-1 ligand or polyligand to the subject.
Another embodiment of the invention is a method for treating, preventing, or ameliorating a fibrotic condition, comprising the steps of:
a) Identifying a subject with a fibrotic condition or at risk for developing a fibrotic condition; and
b) Administering a PAI-1 ligand or polyligand to the subject.
The purified PAI-1 ligands can be formulated for oral or parenteral administration, topical administration, or in tablet, capsule, or liquid form, intranasal or inhaled aerosol, subcutaneous, intramuscular, intraperitoneal, or other injection; intravenous instillation; or any other routes of administration. Furthermore, the nucleotide sequences encoding the ligands permit incorporation into a vector designed to deliver and express a gene product in a cell. Such vectors include plasmids, cosmids, artificial chromosomes, and modified viruses. Delivery to eukaryotic cells can be accomplished in vivo or ex vivo. Ex vivo delivery methods include isolation of the intended recipient's cells or donor cells and delivery of the vector to those cells, followed by treatment of the recipient with the cells.
Another aspect of the invention is a method for treating or preventing atherosclerosis comprising:
a) Identifying a subject with vascular injury or at risk for vascular injury;
b) Isolating monocytes from said subject;
c) Introducing into said monocytes at least one polynucleotide encoding a polypeptide modulator of the fibrinolytic pathway linked to a promoter, to produce modified cells; and
d) Introducing said modified cells to said subject.
Another embodiment of the invention relates to a method of preparing modified cells for delivering a polypeptide modulator of the fibrinolytic pathway to a subject, comprising introducing into monocytes of said subject at least one polynucleotide encoding a polypeptide modulator of the fibrinolytic pathway linked to a promoter, to produce modified cells.
In one embodiment of the invention, the promoter is an inducible promoter. In another embodiment of the invention, the promoter is a macrophage-specific promoter. In another embodiment of the invention, the promoter is a foam cell-specific promoter.
The invention has several advantages over current local delivery methods for the treatment of atherosclerosis such as the use of catheter-based delivery of drug coated stents or balloon angioplasty mediated viral delivery to endothelial and/or vascular smooth muscle cells. In addition to the challenges associated with device mediated delivery approaches vascular cell types are difficult cells to transduce and exhibit poor transgene expression, making local delivery of a transgene to these cells incredibly difficult. Therefore these methods have varying degrees of effectiveness. The subject invention utilizes a circulating cell type, monocytes, that will home to areas of vascular injury, thereby eliminating the need for a device mediated local delivery of a protein-based therapeutic. Monocytes differentiate to macrophages at the site of vascular injury. The macrophages, once in the local environment of the atheroma, will further differentiate to foam cells.
Macrophages contribute to most phases of atherosclerotic development. Therefore they present as a useful cell type for delivery of a transgene, expression of a modulator of the fibrinolytic pathway, locally to atherosclerotic lesions. These lesions can occur throughout the vasculature. The fibrinolytic pathway has been shown to play key roles in atherosclerotic development and progression, however it also plays key roles in hemostasis. Therefore the invention contemplates spatiotemporal control of modulators of this pathway, in order to prevent adverse effects, such as uncontrolled bleeding, that systemic delivery could potentially cause. In one embodiment of the invention, temporal control is achieved through the use of an inducible gene switch.
For example, another aspect of the invention is a method for treating or preventing atherosclerosis comprising:
a) Identifying a subject with vascular injury or at risk for vascular injury;
b) Isolating monocytes from said subject;
c) Introducing into said monocytes (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a chemical ligand-dependent transcription factor, and (2) at least one polynucleotide encoding a polypeptide modulator of the fibrinolytic pathway linked to a promoter which is activated by said chemical ligand-dependent transcription factor, to produce modified cells;
d) Introducing said modified cells to said subject; and
e) Introducing a chemical ligand to the subject to activate the promoter.
Another embodiment of the invention relates to a method of preparing modified cells for delivering a polypeptide modulator of the fibrinolytic pathway to a subject, comprising introducing into monocytes of said subject (a) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence, wherein said at least one transcription factor sequence encodes a chemical ligand-dependent transcription factor, and (b) at least one polynucleotide encoding a polypeptide modulator of the fibrinolytic pathway linked to a promoter which is activated by said chemical ligand-dependent transcription factor, to produce modified cells.
In one embodiment, the modulator of the fibrinolytic pathway is a PAI-1 ligand or polyligand described herein. However, the methods of treating or preventing atherosclerosis are not limited to the PAI-1 ligands or polyligands described herein, but may employ any polypeptide modulator of the fibrinolytic pathway. By way of example, modulators of the fibrinolytic pathway useful in the present method may include other polypeptide PAI-1 inhibitors; natural plasminogen activators such as those disclosed in U.S. Pat. No. 5,830,849; mutant plasminogen activators such as those described in U.S. Pat. No. 5,866,413; or plasminogen activator fragments such as those disclosed in U.S. Pat. No. 5,039,791.
The instant invention also contemplates the use of ma crophage-specific regulatory elements to control an inducible gene switch to restrict transgene expression to macrophages. In this way, both spatial and temporal control of transgene expression can be achieved, so that expression is restricted to macrophages and/or macrophage derived cells within the atheroma. The macrophage-specific regulatory elements are utilized in an inducible gene switch system that can regulate expression of the modulator of the fibrinolytic pathway, within the specified cell type, with the addition of a chemical. The gene expression program is transduced into a macrophage precursor cell, such as a monocyte, ex vivo, and reintroduced into the body for treatment of atherosclerosis. An example of a macrophage-specific regulatory element useful for the present invention are regulatory elements from the macrophage-restricted CD68 gene described in Gough, P. J. and E. W. Raines, Blood 101(2): 485-91 (2003).
For example, another aspect of the invention is a method for treating or preventing atherosclerosis comprising:
a) Identifying a subject with vascular injury or at risk for vascular injury;
b) Isolating monocytes from said subject;
c) Introducing into said monocytes (1) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence linked to a macrophage-specific regulatory element, wherein said at least one transcription factor sequence encodes a chemical ligand-dependent transcription factor, and (2) at least one polynucleotide encoding a polypeptide modulator of the fibrinolytic pathway linked to a promoter which is activated by said chemical ligand-dependent transcription factor, to produce modified cells;
d) Introducing said modified cells to said subject; and
e) Introducing a chemical ligand to the subject to activate the promoter.
Further, another embodiment of the invention relates to a method of preparing modified cells for delivering a polypeptide ligand or polyligand to a subject, comprising introducing into monocytes of said subject (a) a polynucleotide encoding a gene switch, said gene switch comprising at least one transcription factor sequence linked to a macrophage-specific regulatory element, wherein said at least one transcription factor sequence encodes a chemical ligand-dependent transcription factor, and (b) at least one polynucleotide encoding a polypeptide modulator of the fibrinolytic pathway linked to a promoter which is activated by said chemical ligand-dependent transcription factor, to produce modified cells.
In other embodiments, additional polynucleotides encoding other therapeutic proteins such an apolipoprotein are introduced into the monocytes.
The present invention contemplates the treatment of other conditions involving fibrosis in other tissues through targeting other macrophage populations. For example, other fixed macrophages, such as alveolar macrophages, can be targeted through specific promoters or other means to direct expression of fibrinolytic modulators for a potential treatment of pulmonary fibrosis. Other fixed macrophages and their location within tissues that fall within the scope of the invention include histiocytes in connective tissue, kupffer cells in the liver, microglial cells within neural tissue, epithelioid cells within granulomas, osteoclasts within bone, sinusoidal lining cells within the spleen and mesangial cells within the kidney. The present invention contemplates treatment of any fibrotic condition involving these and other macrophage sub-types through targeted expression of a polypeptide modulator of the fibrinolytic pathway.
Another aspect of the invention is a method for treating, preventing, or ameliorating a fibrotic condition involving a fixed macrophage population comprising
a) Identifying a subject with a fibrotic condition;
b) Isolating monocytes from said subject;
c) Introducing into said monocytes at least one polynucleotide encoding a polypeptide modulator of the fibrinolytic pathway linked to a regulatory element specific for a fixed macrophage population, to produce modified cells; and
d) Introducing said modified cells to said subject.
The present invention also contemplates in vivo approaches for targeted expression of a polypeptide modulator of the fibrinolytic pathway to cells of monocytic origin through the use of a monocyte-specific vector such as that described in U.S. Pat. No. 6,875,612.
Methods
Outcome:
The collective data, obtained from both in vitro and in vivo experimentation, demonstrating successful modulation of fibrinolytic activity in cardiovascular tissues will demonstrate therapeutic efficacy of localized PAI-1 inhibition in diseased cardiovascular tissues. The clinical significance for the development of PAI-1 decoys will be, in patients with type II diabetes, to decrease the formation of unstable atherosclerotic plaques.
Objective:
The targeted goal is to develop an adenoviral gene therapeutic with inducible, tissue-specific expression of a PAI-1 decoy that is targeted to the extracellular face membrane and/or extracellular milieu of diseased vessels. The individual components that make up this therapeutic are described below.
Individual Components—PAI-1 Decoys:
Plasminogen activator inhibitor-1 (PAI1) is a serine protease inhibitor (serpin) involved in regulating fibrinolysis. Among its targets are tissue plasminogen activator (tPA) and urokinase plamsinogen activator (uPA). PAI1 binds its targets in a suicide inhibitor reaction, covalently binding in an intermediate state that only very slowly cleaves (not before normal clearance of the complex). PAI1 alone possesses a short half-life in solution—less than 2 hrs. It spontaneously undergoes a conformational shift into a latent form that is non-functional. Association of PAI1 with vitronectin can greatly increase the viable lifetime of the molecule, as well as target it to particular locations in the extracellular matrix (ECM), as vitronectin possesses binding domains for other ECM proteins. The decoys designed combine multiple strategies to inhibit PAI-1 and include sequestration of the molecule, down-regulation via peptides that cause a conformational shift, and proteolysis of the molecule.
Spatial and Temporal Control of PAI-1 Decoys:
Proper spatial localization of PAI-1 decoys, both at the tissue and cellular level, is necessary in order to maximize the effectiveness and minimize the toxicity of PAI-1 decoys. At the level of the tissue, this will be achieved through the use of tissue specific promoters controlling PAI-1 decoy expression. While at the level of the cell, this will be achieved by utilization of localization tethers fused to the PAI-1 decoys.
Tissue Specific Promoters:
In order to limit expression of PAI-1 decoys to a target organ(s), tissue specific promoters have been designed to direct expression of a transgene to specific vascular cell types, to include; vascular smooth muscle cells and endothelial cells. Temporal control will be engineered using RheoSwitch technology for inducible expression using the validated tissue specific promoters.
Localization Tethers:
For the purpose of spatial control at the cellular level, localization tethers have been designed that, when fused to a PAI-1 decoy, will transport it to the proper locale for therapeutic benefit. Some in vivo optimization of therapeutic decoy delivery may be required in order to achieve an outcome that is most beneficial for atherosclerotic plaques. For example, cells targeted by the gene therapy might yield the best effects if the concentration gradient of therapeutic decoy were shallow and broad—perhaps diffusing far and wide to even yield some subtle endocrine effects (Class 2). On the other hand, it may also be desirable to limit the concentration gradient of decoy such that it is primarily present on the surfaces of transfected cells; this approach would limit the zone of therapy to a much smaller region (Class 1). Class 3, the subject of this summary, attempts to “steer a middle course,” and enable paracrine diffusion of the decoy under conditions (i.e., a proteolytic milieu) where injury healing is underway.
Scope:
Development of validated decoy, loc and promoter components in addition to successful integration of these individual components for the development of a gene therapeutic for use in preclinical studies. Successful completion of these experiments will demonstrate that modulation of fibrinolysis by localized inhibition of PAI-1 will, in a metabolic disease model, reduce the formation of unstable atherosclerotic plaque formation in the vasculature.
Preclinical Model:
A preclinical mouse model of insulin resistance with atherosclerotic development will be used to assess the function of PAI-1 in the formation of unstable plaques. Gene transfer techniques in mice will be evaluated for use in gene delivery to target tissues.
Insulin Resistant Mouse Model—Overall Plan for Development of the Mouse Model):
Exp. 1) induction of atherosclerosis and myocardial infarction in insulin resistant mice (IRS 1+/− ApoE−/− and IRS2+/− ApoE−/−) with insulin resistance verified by assay of FFA, triglycerides, and insulin and control (C57BL6) non-insulin resistant mice, and insulin resistant PAI-1 deficient mice (IRS1+/− ApoE−/− PAI-1+/− and IRS2+/− ApoE−/− PAI-1+/−) of 10 weeks of age; performance of high resolution ultrasonic cardiac interrogation when the animals are 12 weeks and 16 weeks of age for assessment of systolic and diastolic function; and assessment of infarct size, the extent of fibrosis, and the amount and localization of PAI-1 in left ventricles of the hearts of mice of 16 weeks of age subjected to coronary occlusion at 10 weeks of age; 2) delineation of the relationship between the extent of fibrosis and concomitant impairment of left ventricular function normalized for infarct size in the diverse strains of mice; 3) elimination of the potential role of PAI-1 in the generation of cardiac fibrosis following coronary occlusion and induction of infarction by crossbreeding PAI-1 deficient animals with insulin resistant animals that otherwise overexpress PAI-1 and performing the same studies as those described in 1 and 2 above; and, 4) characterization of aortic atherosclerotic plaques with cell imaging techniques.
Gene Transfer of Cardiovascular Tissues:
While multiple studies in gene transduction of vascular tissues have been attempted, both the ideal vector and route of administration have not been defined for clinical gene therapeutics. Systemic delivery will result in rapid clearance of adenovirus and attachment/infection in the liver. Local transduction of cardiovascular tissues has been reported. While cardiomyocytes are easily transduced by adenovirus, endothelial cells (ECs) and vascular smooth muscle cells (VSMCs) are not. VSMCs are largely refractory to gene transfer mediated by adenoviruses of serotypes 2 and 5. This is due to poor viral entry and inefficient transcription of the transgene itself from traditional ubiquitous promoters. Reduced viral entry is explained largely by the limited expression of the coxsackie adenovirus receptor (CAR) on the surface of SMC, which results in transduction levels that are markedly lower than those achieved in epithelial cells infected at the same dose [(Beck, Uramoto et al. 2004) see attached article].
Local Injection of Adenovirus:
One recommendation is to perform intraventricular injections into the lumen of the left ventrical through the apex of the heart. This procedure has been shown to result in transgene expression in the aortic endothelium (Juan, Lee et al. 2001). Although no VSMC expression was seen using this method, this may be due to inefficient transcription of the transgene. CMV mediated transgene expression is inefficient in VSMCs, therefore inclusion of VSMC specific promoters has been shown to result in increased expression in vivo (Akyurek, Yang et al. 2000; Akyurek, Nallamshetty et al. 2001; Appleby, Kingston et al. 2003). Therefore use of a strong VSMC promoter in combination with a high titer of virus could result in VSMC expression using this technique. Additionally by clamping the outgoing vessels during the injection it would be possible to increase exposure of the virus to the target cells. This will also result in perfusion of the heart through the coronaries (Roth, Lai et al. 2004)
Summary—Local Injection of Adenovirus:
This strategy is appropriate for in vivo gene transfer of cardiomyocytes and endothelial cells. However, based on reported findings in the literature it is unlikely that robust expression in VSMCs would be possible, due to the EC barrier and low transduction efficiency.
Ex Vivo Transduction of Monocytes:
The other recommendation is to use an ex vivo approach. Macrophages function in all phases of atherosclerotic development, within the vascular wall. Monocytes are recruited and adhere to sites of vascular injury and differentiate into macrophages. Additionally, they also have a high biosynthetic capacity (Beck, Uramoto et al. 2004). Bone marrow cells can be easily isolated, transduced and placed back into the animal for an ex vivo gene delivery approach.
This approach has been used previously to deliver a therapeutic gene to an atherosclerotic region. In most instances of this approach, expression of ApoE was used to promote reverse cholesterol transport (Hasty, Linton et al. 1999; Van Eck, Herijgers et al. 2000; Ishiguro, Yoshida et al. 2001; Juan, Lee et al. 2001; Yoshida, Hasty et al. 2001; Gough and Raines 2003). Additionally, monocyte-derived macrophages contribute to the inflammatory response to MI. Therefore this approach could also be used in the MI model to decrease PAI-1 activity in the infarct.
Summary—Ex Vivo Transduction of Monocytes:
The major drawback with this approach is that monocytes are resistant to the Ad5 serotype (Burke, Sumner et al. 2002; Burke 2003). Ad11p and Ad35 serotypes as well as lentiviral and retroviral vectors readily infect hematopoetic cell types, including myeloid cell types such as monocytes (Segerman, Lindman et al. 2006).
Direct Injection into the Aorta:
Another approach is to perform direct intra-arterial injections into the ascending aorta, in the area of the plaque. This is a common approach used for gene transfer to the myocardium, however, I am unsure of the feasibility of this approach for gene transfer to the aorta.
Overall Summary—Gene Transfer of Cardiovascular Tissues:
Based on assessment of the various gene transfer strategies that have been reported, either transduced monocytes or intracoronary delivery, via injection into the lumen of the left ventricle, while cross-clamping the pulmonary artery and the aorta would provide a feasible gene transfer approach for multiple cardiovascular cell types.
Experimental Framework
Decoys—Project 1
1. In vitro validation using HepG2 cells for PAI-1 elaboration
a. Antigen
b. Activity
2. In vitro validation using VSMC for PAI-1 elaboration
a. Antigen
b. Activity
3. In vitro validation using VSMC migration assay
a. Human VSMC
b. Mouse VSMC
Localization Tethers—Project 2
1. In vitro validation using VSMC
a. Antigen in media vs. cell (membrane) lysate
b. Localization by fluorescent microscopy
2. In vitro validation using EC
a. Antigen in media vs. cell (membrane) lysate
b. Localization by fluorescent microscopy
3. In vitro validation monocyte/macrophage cell
a. Antigen in media vs. cell (membrane) lysate
b. Localization by fluorescent microscopy
Promoters—Project 3
4. In vitro validation using VSMC
a. Reporter activity in VSMC and non-VSMC
b. Inducible reporter activity in VSMC and non-VSMC
5. In vitro validation using EC
a. Reporter activity in EC and non-EC
b. Inducible reporter activity in EC and non-EC
6. In vitro validation monocyte/macrophage cell
a. Reporter activity in monocyte/macrophage cell and non-monocyte/macrophage cell type
b. Inducible reporter activity in monocyte/macrophage cell and non-monocyte/macrophage cell type
Localized Decoys—Project 4
1. In vitro validation of transduced VSMC (assay expression and localization)
2. In vitro validation of transduced EC (assay expression and localization)
3. In vitro validation using transduced VSMC migration assay
a. Human VSMC
b. Mouse VSMC
4. In vitro validation of transduced monocyte/macrophage cell (assay expression and localization)
Virus with Inducible/Tissue Specific Expression of a Reporter—Project 5
1. In vitro validation VSMC
2. In vitro validation EC
3. In vitro validation monocyte/macrophage cell
Viral Gene Therapeutic—Project 6
1. In vitro validation using VSMC (assay expression and localization)
2. In vitro validation of transduced EC (assay expression and localization)
3. In vitro validation using transduced VSMC migration assay
a. Human VSMC
b. Mouse VSMC
4. In vitro validation of transduced monocyte/macrophage cell (assay expression localization)
Compiled Report of In Vitro Data—Project 7
1. Compiled data from projects 1-6
Preclinical Model—Project 8
1. Induction of atherosclerosis in insulin resistant (IR) mice with or without PAI-1 deficiency.
2. Characterization of aortic atherosclerotic plaques in PAI-1 null, insulin resistant (IR) mice.
3. Validation of gene transfer model
a. Ex vivo transduced monocytes
b. Intramyocardial injection with or without blockage of outgoing vessels
c. Direct injection into the aorta
EXAMPLES
Examples
PAI-1 Decoys and Inhibition Strategies
Exemplary inhibition mechanisms for PAI-1 decoys are depicted in FIG. 16.
In most every case, the following exemplary decoy designs cover multiple inhibition mechanisms. A schematic representation of each exemplary decoy design and its inhibition mechanisms is depicted in FIG. 9. The decoy designs depicted in FIG. 9 and described in the foregoing examples are intended to serve as illustrative embodiments of the invention. It will be understood by those of ordinary skill in the art that the invention is not limited to the particular embodiments described herein, and that a wide range of equivalent designs and inhibition strategies fall within the scope of the invention.
See ‘Description of the Polypeptide and Polynucleotide Sequences’ for corresponding SEQ ID NOS of the following exemplary PAI-1 decoys.
PAI-1 Decoys 1-3:
Native PAI1 possesses a short half-life in solution—less than 2 hrs. It spontaneously undergoes a conformational shift into a latent form that is non-inhibitory. The reactive center loop (RCL) peptide, which is immediately adjacent to the protease cleavage site (R346-M347), undergoes insertion into an existing b-sheet on the PAI1 structure upon shift into latent form. Peptides based on this RCL sequences can block PAI1 protease inhibitory activity.
Based on this PAI-1 decoys 1-3 will exploit the RCL sequence to inhibit the molecule. Recombinant peptides based on this sequence have been shown to be inhibitory to PAI1 action, operating much the same as the native RCL but on a shorter time scale. Individual sequences, multiple sequences, and multiple sequences separated by spacers (to potentially multimerize with PAI1 molecules) will be evaluated. The sequences will mimic the natural RCL peptide action. These DCYs will almost definitely inhibit—the goal is to identify which type of construct will inhibit most effectively and potentially combine it with other designs below.
PAI1-DCY-94-1:
Four tandem repeats of the RCL peptide will be used to inhibit the normal PAI1 suicide reaction. This DCY can be compared to PAI1-DCY-94-2 and to PAI1-DCY-94-3 for relative efficiency.
PAI1-DCY-94-2:
A single RCL will be used to inhibit the normal PAI1 suicide reaction. This DCY can be compared to PAI1-DCY-94-1 and to PAI1-DCY-94-3 for relative efficiency.
PAI1-DCY-94-3:
Four tandem repeats of the RCL peptide, separated by spacers to enhance interactions with multiple PAI1 molecules, will be used to inhibit the normal PAI1 suicide reaction. This DCY can be compared to PAI1-DCY-94-1 and to PAI1-DCY-94-2 for relative efficiency.
PAI-1 Decoys 4 and 5:
Upon binding to any of several serine proteases (for example tPA, uPA, thrombin), PAI1 undergoes a dramatic conformational shift during cleavage that results in a suicide inhibitory reaction. Experimental evidence shows that this rearrangement in structure is an important part of the inhibition mechanism. Delaying this conformational shift so the cleavage reaction can proceed to completion would turn PAI1 into no more than a normal substrate. The reactive center loop (RCL) peptide, which is disordered in structures of active PAI1 inserts into a beta sheet.
PAI-1 decoys 4 and 5 attempt to interact with the RCL of active pAI1 with either of two potential goals in mind-1) to slow the insertion of RCL into the PAI1 structure and allow PAI1 to be naturally cleaved by serine protease targets, or 2) through steric interference to prevent binding to protease targets altogether. The RCL peptide interacts with a beta-sheet in PAI1. Sequences from this sheet are adopted to engage the native RCL.
PAI1-DCY-94-4:
The goal of this DCY is to stabilize the RCL while it is still independent of the sheet and allow the cleavage reaction to proceed. Beta strands that make up part of the sheet into which the RCL inserts will be used to provide an alternative binding surface for the RCL peptide. Two antiparallel beta strands from PAI1 will be used to create part of the native beta sheet to which the RCL insets and binds. The two strands making up this DCY are non-contiguous in sequence, so four residues that form a beta turn will be used to attach them and allow for proper secondary structure.
PAI1-DCY-94-5:
The goal of this DCY is to stabilize the RCL while it is still independent of the sheet and allow the cleavage reaction to proceed. The actual insertion of the RCL peptide occurs in between two beta strands that run parallel in the PAI1 structure. These two strands are not contiguous in sequence in the native structure, although they are sequential members of this beta sheet in PAI1.
Leucine rich repeats (LRR) are motifs found in several proteins, including the extracellular matrix proteins decorin and biglycan, and the Toll-like receptors. The motif consists of a slightly concave surface consisting of beta strands and a convex surface of helical or semi-helical structure. The repeated stacking of these motifs produces a solenoid structure with a series of parallel beta strands forming a concave sheet. Leucines occur in critical parts of the sequence and provide internal packing that allows for great variability on the outward-facing residues. The motif is stable, especially when repeated consecutively. Several LRRs from the Toll like receptor 3 ectodomain will be used as a scaffold to recreate a portion of the native sheet structure into which the RCL inserts. The LRR, because of its stacking of parallel strands, makes it ideal for mimicking a portion of the PAI1 beta sheet structure. Due to the size of the sheets in PAI1, they will be recreated in two sections on the LRR scaffold.
PAI-1 Decoys 6 and 7:
Kallikrein 2 (hK2) is a serine protease normally expressed in prostate and useful as a marker for prostate cancer. It exhibits strong specificity for Arg in the P1 cleavage site. It can cleave and subsequently inactivate PAI1 with high efficiency compared to other proteases. The expression profile for this protein combined with its specificity make it good candidate for a DCY that will actually cleave and inactivate PAI1. If targeted to a region where PAI1 is present, it should be able to cleave and thereby inactivate PAI1 efficiently.
PAI-1 Decoys 6 and 7 use an active protease, kallikrein 2 (hK2), to digest PAI1. hK2 is a serine protease normally found in prostate. It is specific in its expression profile and has use as a marker for prostate cancer. It is specific in its substrates and has been shown to digest PAI1 specifically as opposed to being inhibited by it. One of these construct possesses a charged loop that mimics a native tPA sequence shown to be important in PAI1 binding.
PAI1-DCY-94-6:
Potential mutations to kallikrein 2 could be made to enhance binding specificity. A loop present in tPA contains several charged residues that are important in tPA-PAI1 binding. The corresponding loop in hK2 could be mutated to match this sequence and potentially enhance binding specificity for PAI1.
PAI1-DCY-94-7:
Kallikrein 2 (hK2) is a serine protease normally expressed in prostate and useful as a marker for prostate cancer. It exhibits strong specificity for Arg in the P1 cleavage site. It can cleave and subsequently inactivate PAI1 with high efficiency compared to other proteases. The expression profile for this protein combined with its sequence specificity make it good candidate for a DCY that will actually cleave and inactivate PAI1.
A positively charged loop on the surface of tissue plasminogen activator (tPA) has been shown to be important in PAI1 binding. It is believed to interact with a series of acidic residues near the RCL peptide of PAI1. This region is harvested replaces the shorter loop present in hK2. The addition of this sequence could result in higher affinity binding and more efficient cleavage.
PAI-1 Decoys 8-12:
Plasminogen activator inhibitor-1 (PAI1) is a serine protease inhibitor involved in regulating fibrinolysis. Among its targets are tissue plasminogen activator (tPA) and urokinase plamsinogen activator (uPA). PAI1 binds its targets in a suicide inhibitor reaction, covalently binding in an acyl enzyme intermediate state that only very slowly cleaves (and not before clearance of the complex). PAI1 possesses a short half-life in solution—less than 2 hrs. It spontaneously undergoes a conformational shift into a latent form that is non-functional. The reactive center loop (RCL) peptide, which is immediately adjacent to the cleavage site, undergoes insertion into an existing b-sheet on the PAI1 structure. Peptides based on this RCL sequences can block PAI1 protease inhibitory activity.
Vitronectin is an extracellular matrix (ECM) molecule that binds to multiple ECM partners. It binds PAI1 with high affinity and dramatically increases its half-life, allowing it to interact with and inhibit tPA, uPA, and other serine proteases. The interaction with PAI1 occurs through vitronectin's somatomedin B (SMB) domain. The binding is specific and high affinity (Kd ̃1 nM).
PAI-1 Decoys 8-12 make use of the vitronectin interaction with PAI1 and combine it with the RCL inhibitory peptide. Vitronectin's somatomedin B (SMB) domain binds with high affinity to PAI1 and can greatly extend its effective half-life. Several papers have shown that mutations of tyrosines on this binding surface can abrogate binding completely. Our goal here, though, is not to abolish binding but to minimize the stabilization effect of SMB binding while retaining at least some of the binding affinity. A series of conservative mutations are made to probe the binding surface. The SMB mutations are combined with RCL peptides which will bestow considerable inhibitory properties on the DCYs. A construct that maximizes binding while minimizing stability will be found, whether it is the native SMB domain or one of the mutant structures. The high affinity binding of SMB will in effect tether the RCL peptides to PAI1 and should promote more ready interaction.
PAI1-DCY-94-8:
The DCY will use the SMB domain of vitronectin to target PAI1 binding with high affinity and specificity. The SMB domain will be attached to multiple repeats of an inhibitory peptide based on the RCL of PAI1. The initial SMB binding will bring the peptide into close proximity, and insertion into the b-sheet can occur, resulting in inhibition, and possible disengagement of the SMB domain. The RCL peptide could potentially act either in cis or in trans, affecting nearby PAI1 molecules with these multiple binding and inhibiting domains.
PAI1-DCY-94-9:
The decoy will use the somatomedin B domain of vitronectin to target PAI1 binding with high affinity and specificity. The SMB domain will be attached to multiple repeats of an inhibitory peptide based on the RCL of PAI1. The initial SMB binding will bring the peptide into close proximity, and insertion into the b-sheet can occur, resulting in inhibition, and possible disengagement of the SMB domain. The RCL peptide could potentially act either in cis or in trans, affecting nearby PAI1 molecules with these multiple binding and inhibiting domains. The SMB domain will be mutated. The mutation will potentially reduce the stabilizing effect of vitronectin for PAI1 but will maintain sufficient affinity to target the RCL peptide effectively.
PAI1-DCY-94-10:
The decoy will use the somatomedin B domain of vitronectin to target PAI1 binding with high affinity and specificity. The SMB domain will be attached to multiple repeats of an inhibitory peptide based on the RCL of PAI1. The initial SMB binding will bring the peptide into close proximity, and insertion into the b-sheet can occur, resulting in inhibition, and possible disengagement of the SMB domain. The RCL peptide could potentially act either in cis or in trans, affecting nearby PAI1 molecules with these multiple binding and inhibiting domains. The SMB domain will be mutated. The mutation will potentially reduce the stabilizing effect of vitronectin for PAI1 but will maintain sufficient affinity to target the RCL peptide effectively. Several research articles have demonstrated mutations that abolish binding, specifically T→A mutations at the binding interface. The goal here is not to eliminate binding but to eliminate as much as possible the secondary stabilization effect of vitronectin binding to PAI1.
PAI1-DCY-94-11:
The decoy will use the somatomedin B domain of vitronectin to target PAI1 binding with high affinity and specificity. The SMB domain will be attached to multiple repeats of an inhibitory peptide based on the RCL of PAI1. The initial SMB binding will bring the peptide into close proximity, and insertion into the b-sheet can occur, resulting in inhibition, and possible disengagement of the SMB domain. The RCL peptide could potentially act either in cis or in trans, affecting nearby PAI1 molecules with these multiple binding and inhibiting domains. The SMB domain will be mutated. The mutation will potentially reduce the stabilizing effect of vitronectin for PAI1 but will maintain sufficient affinity to target the RCL peptide effectively.
PAI1-DCY-94-12:
The decoy will use the somatomedin B domain of vitronectin to target PAI1 binding with high affinity and specificity. The SMB domain will be attached to multiple repeats of an inhibitory peptide based on the RCL of PAI1. The initial SMB binding will bring the peptide into close proximity, and insertion into the b-sheet can occur, resulting in inhibition, and possible disengagement of the SMB domain. The RCL peptide could potentially act either in cis or in trans, affecting nearby PAI1 molecules with these multiple binding and inhibiting domains. The SMB domain will be mutated. The mutation will potentially reduce the stabilizing effect of vitronectin for PAI1 but will maintain sufficient affinity to target the RCL peptide effectively.
PAI-1 Decoys 13 and 14:
Vitronectin is an extracellular matrix (ECM) molecule that binds to multiple ECM partners. It binds PAI1 with high affinity and dramatically increases its half-life, allowing it to interact with and inhibit tPA, uPA, and other serine proteases. The interaction with PAI1 occurs through vitronectin's somatomedin B (SMB) domain. The binding is specific and high affinity (Kd ̃1 nM).
Kallikrein 2 (hk2) is a serine protease normally expressed in prostate and useful as a marker for prostate cancer. It exhibits strong specificity for Arg in the P1 cleavage site. It can cleave and subsequently inactivate PAI1 with high efficiency compared to other proteases. The expression profile for this protein combined with its sequence specificity make it good candidate for a DCY that will actually cleave and inactivate PAI1.
PAI-1 decoys 13-14 also use the SMB domain to increase binding affinity to PAI1, in this case combined with either an inactive protease that can bind and sequester PAI1, or with kallikrein 2, which can digest it.
PAI1-DCY-94-13:
Urokinase-type plasminogen activator (uPA) is a serine protease involved in activation of fibrinolytic pathways as well as in signaling responses through its receptor. uPA is a target of PAI1. The enzyme will be truncated to contain only the catalytic domain, and the catalytic residues will be mutated to eliminate activity. This inactive enzyme will be attached to the SMB domain of vitronectin to provide a binding platform for PAI1. PAI1 will be sequestered from interacting with and inhibiting other serine proteases. In contrast to PAI1-DCY-94-7 and PAI1-DCY-94-14, this DCY will not introduce any new enzymatic activity into the target region.
PAI1-DCY-94-14:
The decoy will use the somatomedin B domain of vitronectin to target PAI1 binding with high affinity and specificity. The SMB domain will be attached to the active kallikrein 2 molecule to target PAI1 with high affinity and specificity and cleave it, thereby inactivating it.
PAI-1 Decoy 15:
Vitronectin is an extracellular matrix (ECM) molecule that binds to multiple ECM partners. It binds PAI1 with high affinity and dramatically increases its half-life, allowing it to interact with and inhibit tPA, uPA, and other serine proteases. The interaction with PAI1 occurs through vitronectin's somatomedin B (SMB) domain. The binding is specific and high affinity (Kd ̃1 nM).
PAI-1 decoy 15 is a further set of mutations on the SMB domain. The structure of SMB is almost symmetrical in terms of its backbone. It has a helix and lop that are oriented almost identically on both the PAI1 binding face and on the face opposite the binding site. Five mutations can in many respects recreate a second PAI1 binding site on the SMB molecule. While the spacing between a helix and loop on the rear face is slightly smaller than on the native binding site, the helical region may provide sufficient interaction to bind with some affinity a second PAI1 molecule. RCL peptides are attached so as to potentially interact with both bound PAI1 molecules if two do indeed bind.
The face opposite the native binding site possesses a similar backbone to the binding site. Mutations in this face could partially reproduce a PAI1 binding site. Introduction of several mutations were made to recapitulate most of the PAI1 binding face of SMB. The alpha carbons of the residues to be mutated superimpose with 0.99 Angstroms RMS, and the helical domain superimposes with an RMS of 0.49 Angstroms on alpha carbons.
This could potentially lead to a dimerization of PAI1 molecules in a face-to-face manner. At least two possibilities exist—the RCL peptides from the molecules could interfere with each other, there could be substantial steric hindrance that affects PAI1 inhibitory properties. To augment inhibition of PAI1, exogenous RCL peptide, which binds to and inhibits PAI1 will be attached as a tetrameric repeat to the mutated SMB domain.
Examples
Tissue-Specific Promoters
See ‘Description of the Polypeptide and Polynucleotide Sequences’ for corresponding SEQ ID NOS of the following exemplary tissue-specific promoters.
MOD 5306—Arterial Smooth Muscle-Specific Promoter (Depicted Schematically in FIG. 10)—Rationale:
The desmin gene encodes an intermediate filament protein that is present in skeletal, cardiac, and smooth muscle cells. The promoter region used here contains CArG/octamer overlapping element that can bind the serum response factor and an Oct-like factor; It also contains a minimal promoter (determined by promoter prediction tools); This region is active in arterial smooth muscle cells but not in venous smooth muscle cells or in the heart in vivo.
MOD Rationale for Synthetic Promoters:
Analysis of the promoter regions of collection of genes that are expressed in vascular smooth muscle cells (VSMC) provided a list of several regulatory elements associated with VSMC-specific expression. A combination of one set of such regulatory elements was used in this synthetic promoter construct: the smooth muscle contractile protein SM22 alpha gene fragment fused to nephroblastoma overexpressed (Nov) minimal promoter region. SM22 alpha is an established VSMC differentiation marker. Its minimal promoter has been shown to direct arterial smooth muscle-specific expression of different transgenes. Recently, very high Nov expression in adult rat aorta also has been reported.
Exemplary synthetic vascular smooth muscle promoters of the invention include MOD 5309—Synthetic VSMC-specific promoter 1 (depicted schematically in FIG. 11A), MOD 5312—Synthetic VSMC-specific promoter 2 (depicted schematically in FIG. 11B), and MOD 5315—Synthetic VSMC-specific promoter 3 (depicted schematically in FIG. 11C)
MOD Rationale:
Analysis of the promoter regions of collection of genes that are expressed in vascular smooth muscle cells (VSMC) provided a list of several regulatory elements associated with VSMC-specific expression. A combination of one set of such regulatory elements was used in this synthetic promoter construct: the smooth muscle contractile protein SM22 alpha gene fragment fused to HUMAN myosin, heavy chain 11, smooth muscle promoter region. SM22 alpha is an established VSMC differentiation marker. The rat minimal promoter has been shown to direct arterial smooth muscle-specific expression of different transgenes. Similarly, MYH11 also is specific to smooth muscles.
MOD 4012—ESM1, Endothelial Cell-Specific Promoter (Depicted Schematically in FIG. 12A)—Mod Rationale:
This gene encodes a secreted protein which is mainly expressed in the endothelial cells. The promoter of this gene could be used for gene therapy approaches where endothelial cell-specific expression of therapeutic/decoy molecule is needed.
MOD 4399—FLT1, Endothelial Cell-Specific Promoter (Depicted Schematically in FIG. 12B)—MOD Rationale:
The human transmembrane fms-like receptor tyrosine kinase Flt-1 is one of the receptors for vascular endothelial growth factor, a growth factor which induces endothelial proliferation and vascular permeability. Flt-1 is expressed specifically in endothelium. The flt-1 promoter will be useful as a tool in targeting the expression of exogenously introduced genes to the endothelium.
MOD 4790—Synthetic Endothelial Cell-Specific Promoter 1 (Depicted Schematically in FIG. 13A) and MOD 4791—Synthetic Endothelial Cell-Specific Promoter 2 (Depicted Schematically in FIG. 13B)—MOD Rationale:
A major goal of gene therapy is the introduction of genes of interest into desired cell types. Endothelial cells line essentially all major blood vessels and thus have direct access to the circulatory system. Potential gene products to be delivered via endothelial cells include hormones, protein factors found in plasma such as insulin, growth hormone, factor VIII, as well as angiogenic or angiostatic molecules for the treatment of ischemic or neovascular conditions, respectively. Inspection of promoter regions of endothelial cell-specific genes reveals that most have binding sites for both specific and non-specific transcription factors. The goal of this design was to construct a small synthetic endothelial cell-specific promoter. Sequences of known transcription factor binding sites that are located 5′ of many endothelial cell-specific mRNA transcripts were linked to the human ICAM2 minimal promoter to generate a synthetic, endothelial cell-specific promoters 1 and 2.
Examples
Localization Tethers
See ‘Description of the Polypeptide and Polynucleotide Sequences’ for corresponding SEQ ID NOS of the following exemplary localization tethers.
Localization Tethers, Class 1—Lipid-Modified, Integral to Plasma Membrane, Extracellular (Depicted Schematically in FIGS. 14A-14B):
Localization Tethers, Class 1 are designed to anchor the cargo at the extra-cellular surface of the plasma membrane. They were designed with cardiac, skeletal or fibroblast tissue in mind. The majority of the constructs utilize a glycosylphosphatidylinositol (GPI) lipid modification to anchor to the membrane. GPI biosynthesis occurs post translation in the ER. A hydrophobic motif is recognized in the C-terminal region of the protein and subsequently cleaved. After cleavage, the complete GPI moiety is added to the protein. GPI anchors are diverse in structure and composition and may be protein or tissue specific. Once at the cell surface, GPI anchors are subject to cleavage by phospholipases. The kinetics of GPI cleavage are determined by lipid length, membrane surface charge, and physiochemical properties of the membrane bilayer itself. As such, different GPI anchors were used in the designs to provide an array of surface retention times.
Designs 91-1 through 91-4 contain the hemojuvelin (HJV) GPI-anchor cleavage/addition domain. HJV was chosen because it is expressed in skeletal muscle and if addition of the correct GPI anchor is tissue specific, provides a domain ideal for use in muscle tissue. 91-1 is the basic signal peptide/cargo/GPI motif blueprint. 91-2 provides the addition of a linker between the cargo and the lipid anchor to increase the field of cargo movement. 91-3 contains a longer c-terminal region of HJV containing a mutation that prevents the binding of HJV to neurogenin but has been demonstrated to traffic to the membrane properly. 91-4 is the same as 91-2 but adds in the MAGP1 fibrillin-binding domain. When the GPI anchor is cleaved, this construct is designed to bind surrounding matrix microfibrils. This would keep the cargo in close proximity to matrix modifying proteins.
Designs 91-5 and 91-6 utilize the Thy-1 GPI cleavage/addition site. Thy-1 was chosen because the retention time has been studied and determined to be greater than other GPI anchored proteins. The structure of the Thy-1 anchor may cause a steric hindrance with the phospholipase and decrease the rate of cleavage. 91-7 builds on 91-6 with the addition of a tenascin-X (TNX) matrix-binding domain. This domain should target the cleaved GPI-anchored protein to collagen type I microfibrils. 91-8 also contains a matrix binding domain, but rather than targeting the matrix framework this ApoB domain binds glycosaminoglycans (9637699).
Designs 91-9 through 91-11 follow the same design rationale, but utilize the glypican-1 GPI motif. Glypican-1 is a GPI-anchored proteoglycan localizing to rafts and caveolae. It is widely expressed in different tissues and provides potentially different retention time to the other GPI's in this MDR. 91-12 through 91-16 follow similar rationale but contain the MT-MMP6 GPI cleavage/addition site and different combinations of linkers and matrix binding domains.
Designs 91-17 and 91-18 attempt to create a simple transmembrane LOC which will traffic properly and present the cargo at the extra-cellular face. MT1-MMP C-terminal tail and transmembrane region have no known function other than putative trafficking information. 91-18 adds a glycosylated ectodomain to aid in trafficking if 91-17 is not presented at the membrane. 91-19 and 91-20 achieve cargo placement at the c-terminus. Matriptase is a type II serine protease. The protease domain is in the C-terminal region, which is removed in these constructs. The remaining portion is potentially glycosylated to mediate plasma membrane delivery.
As a whole, designs 91-1 through 91-16 attempt to achieve varying membrane retention times to obtain the ideal cargo presentation tailored to the decoy added. Some designs contain matrix-binding domains to increase the activity of the cargo within the matrix at the site of delivery. Designs 91-17 through 91-20 attempt to achieve the simplest designs possible that possess no intrinsic activity. A potential pitfall for all the designs will be a defect in plasma membrane trafficking.
Localization Tethers, Class 2—Secreted and-or Extracellular, Soluble:
These localization modules are intended to carry a cargo through the cell by way of either the regulated secretory pathway or the constitutive pathway for release at the cell membrane into the extracellular space. Once outside the cell, binding sequences would allow for attachment of the peptide to the outer leaflet of the plasma membrane of the cell in which it was synthesized, or to proteins forming the extra cellular matrix.
For secretion, three strategies were utilized. In the first, the regulated secretory pathway of the cell is taken advantage of through the use of aggregation and/or binding to the lipids or proteins at the inner face of the granule. In the second, the constitutive secretory pathway is taken advantage of through the use of common signals for entrance into these vesicles. In the third, both pathways are taken advantage of. This was done due to the potential that one or the other pathways becomes “overloaded” under the conditions of the disease state, and the use of two functionally distinct signals should not act as a deterrent for exit of activity of the peptide as a whole. When association with the inner face of the secretory granule was utilized, binding that is sensitive to changes in pH or calcium levels to aid in release of the peptide at the cell surface was chosen.
Once released from the vesicle at the surface, the peptide is then expected to bind either proteins bound at the surface of the outer leaflet of the cell (i.e., uPAR or annexin), or to proteins that comprise the extra cellular matrix (i.e., fibrin). In some of the constructs, protease sites for those enzymes known to be over-expressed within the region of the infarct to cause “exposure” of a “hidden” ECM binding motif were used. In this way, prevention of cargo from being held and active towards proteins within regions of healthy tissue is attempted. In others, the site is placed in a way that the cargo is released from the main body of the localization peptide for release of only itself into the extra cellular matrix. Binding to the ECM is expected to confer “staying power” of the cargo, whereas maintained binding to proteins on the membrane would allow for turnover of our peptide.
Localization Tethers, Class 3—Conditionally Soluble Extracellular (Depicted Schematically in FIG. 15):
The basic modular elements of this design are as follows: a transmembrane protein (or pre-protein) that is predicted to behave relatively inertly, a well-known signal peptide, lipid membrane attachment motifs (GPI and palmitoyl), and a conditionally cleavable proteolytic site (for TACE/ADAM17, MT1-MMP, uPA/tTPA, or a multiple protease cut). These components are varied through the eleven designs and one potential positive control. The design set as a whole attempts to strike a balance between different risk considerations, both experimental and practical.
LOC-93-1 is in a class by itself. It is based on pre-pro-TGF-alpha, but in this design, the secreted and processed growth factor is deleted, and in its stead lies the therapeutic decoy, tag, or fluorescent protein. For this design to “work,” the decoy must be processed in much the same way as mature TGF-alpha. Pre-pro-TGF-alpha is largely cleaved and activated by Tumor necrosis factor Alpha Converting Enzyme (TACE/ADAM17), which also is involved in the “shedding” of numerous pro-inflammatory cytokines such as TNF-alpha. TACE is induced by a pro-inflammatory milieu, and can be artificially induced by phorbol ester treatment. TACE is abundant in zones of cardiac injury, tissue remodeling, and tumor microenvironment, and can be active at either the cell surface or even prior to secretion, in secretory vesicles. Other designs in this set that employ TACE (or predicted TACE consensus) cut sites are LOC-93-2, -3, -4, and -9. However, these consensus sites are expected to localize to the surface via different means.
LOC-93-2, -3, -4, -5, -6, -7 and -12 (control) employ a somewhat obscure polypeptide known as TM10, the human homologue of Opalin, a brain-specific protein of unknown function. This protein was identified via searches for small (i.e., <200 amino acids) transmembrane proteins in the EMBL-GFP (Heidelburg, Germany) localization database project. It has no obvious signal peptide, ligand receptor, or kinase domain, and BLAST searches of its 141 amino acid sequence reveal no close homologues. Although the LOCATE database reports TM10 to be a type II membrane protein, multiple analyses of the sequence reveal that it is, in fact, a Type I without exception or ambiguity (including the analysis sites that are linked to via LOCATE). Most recently, after the completion of these designs, TM10 (TMEM10) was characterized by Kippert et al (Apr. 25, 2008; 18439243), and demonstrated experimentally to be a Type I with robust plasma membrane localization and possible actin binding. The rationale for using a small, compact transmembraneLOCsig nearly speaks for itself, since many of such examples are larger in size and may be more likely to engage in pleiotypic signaling—a potential hazard in a therapeutic. The rationale for employing an oligodendrocyte-specific polypeptide for a cardiac-based therapy is that brain-specific proteins would be less likely to interfere with cardiac-specific processes.
LOC-93-2, -3, and -4 are theme together in a group for the sake of experimental comparison. A chimeric, synthetic TACE substrate (based on TGF-alpha TACE site plus two substitutions from TNF-alpha, flanked by short spacer residues) is fused with TM10 N-terminus, forming the junction between the TAG/DCY and the LOC. LOC-93-3 converts 93-2 into an “internal cargo” via inclusion of an n-terminal signal peptide from EGFR; this tests whether delivery to the surface is enhanced by a signal peptide. LOC-93-4 adds a c-terminal palmitoyl attachment site to LOC-93-3; this addition, in turn tests whether localization and/or retention on the cell surface is enhanced via c-terminal lipidation.
LOC-93-3, -5, -6, -7 may also be themed together in another set to compare different proteolytic sites. The proteolytic cut site may be for TACE/ADAM17, uPA/tPA, MT1-MMP, or a site that is more labile and the target of numerous proteases (i.e., alpha-2 macroglobulin).
LOC-93-8, -9, -10, and -11 are designed as follows. The configuration is a signal peptide (from pre-Glypican) followed by the internal cargo, and ending at the c-terminus with a putative GPI anchorage site (from MMP 25). Like LOC-93-3, -5, -6 and -7, these test four variables of protease cut sites. However, here the context of membrane attachment is different, which is not via transmembrane, but via a single mode of lipidation.
LOC-93-12 is a potential positive control for plasma membrane localization, and has been characterized by the GFP-LOC project out of EMBL-Heidelberg—and more recently, a paper via Kippert et al (Apr. 25, 2008; 18439243).
The present invention also provides the following non-limiting embodiments.
E1. An isolated polypeptide ligand, wherein the ligand modulates PAI-1 activity.
E2. An isolated polypeptide heteropolyligand, wherein the heteropolyligand modulates PAI-1 activity.
E3. An isolated polypeptide homopolyligand, wherein the homopolyligand modulates PAI-1 activity.
E4. An isolated fusion protein, wherein the fusion protein comprises one or more fragments of a parent protein that has at least one putative PAI-1 interaction domain recognition motif.
E5. The isolated fusion protein of E4, wherein the parent protein is fibrin, tissue plasminogen activator, urokinase plasminogen activator, or vitronectin.
E6. The polypeptide of E1-E5, further comprising one or more of a degron, a localization signal, an epitope, or a reporter.
E7. An isolated polynucleotide comprising a nucleotide sequence encoding the polypeptide of each of E1-E7.
E8. A vector comprising a polynucleotide of E7.
E9. A host cell comprising a polynucleotide E7.
E10. A non-human organism comprising a polynucleotide of E7.
E11. The polynucleotide of E7 operably linked to a promoter.
E12. The polynucleotide operably linked to a promoter of E11, wherein the promoter is a constitutive promoter, a non-specific promoter, an inducible promoter, or a tissue-specific promoter.
E13. The polynucleotide operably linked to a promoter of E12, wherein the tissue-specific promoter is an endothelial cell-specific promoter, a vascular smooth muscle cell-specific promoter, a cardiomyocyte-specific promoter, a coronary adipocytes-specific promoter, or a cardiac fibroblast-specific promoter.
E14. The host cell of E9, wherein the host cell is a mammalian cell.
E15. The host cell of E14, wherein the host cell is an endothelial cell, a vascular smooth muscle cell, a cardiomyocyte, a coronary adipocyte, or a cardiac fibroblast.
E16. The non-human organism of E10, wherein the organism is a non-human primate, mouse, cow, pig, sheep, horse, rat, rabbit, dog, cat, or guinea pig.
E17. A method of inhibiting PAI-1 in a cell comprising transfecting a vector of E8 into a host cell and culturing the transfected host cell under conditions suitable to produce at least one copy of the polypeptide.
E18. A method of inhibiting PAI-1 in heart tissue of a subject comprising injecting a vector of E 8 into heart tissue of a subject.
E19. A method of creating a transgenic subject with reduced PAI-1 activity comprising injecting a vector of E8 into a fertilized egg.
E20. An isolated fusion protein, wherein the fusion protein comprises PAI-1 linked to a degron.
E21. An isolated fusion protein, wherein the fusion protein comprises PAI-1 linked to a localization signal.
E22. An isolated fusion protein, wherein the fusion protein comprises PAI-1 linked to a degron and a localization signal.
E23. An isolated polynucleotide comprising a nucleotide sequence encoding the polypeptide of each of E20-E22.
E24. An isolated polynucleotide comprising a nucleotide sequence encoding PAI-1 that has been optimized for vector insertion.
E25. The isolated polynucleotide of E24, wherein the vector is ULTRAVECTOR.
E26. A vector comprising a polynucleotide of E23-E25.
E27. A host cell comprising a polynucleotide of E23-E25
E28. A non-human organism comprising a polynucleotide of E23-E25.
E29. The polynucleotide of E23-E25 operably linked to a promoter.
E30. The polynucleotide operably linked to a promoter of E29, wherein the promoter is a constitutive promoter, a non-specific promoter, an inducible promoter, or a tissue-specific promoter.
E31. The polynucleotide operably linked to a promoter of E29, wherein the tissue-specific promoter is an endothelial cell-specific promoter, a vascular smooth muscle cell-specific promoter, a cardiomyocyte-specific promoter, a coronary adipocytes-specific promoter, or a cardiac fibroblast-specific promoter.
E32. The host cell of E27, wherein the host cell is a mammalian cell.
E33. The host cell of E32, wherein the host cell is an endothelial cell, a vascular smooth muscle cell, a cardiomyocyte, a coronary adipocyte, or a cardiac fibroblast.
E34. The non-human organism of E28, wherein the organism is a non-human primate, mouse, cow, pig, sheep, horse, rat, rabbit, dog, cat, or guinea pig.
E35. A method of altering expression of PAI-1 in a host cell comprising transfecting a vector of E26 into a host cell and culturing the transfected host cell under conditions suitable to produce at least one copy of PAI-1.
E36. A method of altering expression of PAI-1 in heart tissue of a subject comprising injecting a vector of E26 into heart tissue of a subject.
E37. A method of creating a transgenic subject with altered PAI-1 expression comprising injecting a vector of E26 into a fertilized egg.
The previous examples and embodiments are intended to serve as illustrative embodiments. It will be understood by those of ordinary skill in the art that the invention is not limited to the particular embodiments described herein, and that a wide range of equivalent designs fall within the scope of the invention.
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## Claims

1. An isolated polynucleotide encoding a polypeptide comprising an amino acid sequence that is at least 95% identical to SEQ ID NO: 25, wherein said amino acid sequence, that is at least 95% identical to SEQ ID NO: 25 binds to plasminogen activator inhibitor 1 (PAI-1) thereby inhibiting the activity of PAI-1 to inhibit plasminogen activator.

2. The isolated polynucleotide of claim 1, wherein said amino acid sequence that is at least 95% identical to SEQ ID NO: 25 is at least 96% identical to SEQ ID NO: 25.

3. The isolated polynucleotide of claim 1, wherein said amino acid sequence that is at least 95% identical to SEQ ID NO: 25 is at least 97% identical to SEQ ID NO: 25.

4. The isolated polynucleotide of claim 1, wherein said amino acid sequence that is at least 95% identical to SEQ ID NO: 25 is at least 98% identical to SEQ ID NO: 25.

5. The isolated polynucleotide of claim 1, wherein said amino acid sequence that is at least 95% identical to SEQ ID NO: 25 is at least 99% identical to SEQ ID NO: 25.

6. The isolated polynucleotide of claim 1, wherein said amino acid sequence that is at least 95% identical to SEQ ID NO: 25 is SEQ ID NO: 25.

7. The isolated polynucleotide of claim 1, wherein said polynucleotide is linked to a tissue-specific promoter.

8. The isolated polynucleotide of claim 7, wherein the tissue-specific promoter is an arterial smooth muscle cell-specific promoter, a vascular smooth muscle cell-specific promoter, an endothelial cell-specific promoter, or a synthetic endothelial cell-specific promoter.

9. A vector comprising the isolated polynucleotide of claim 1.

10. The vector of claim 9, wherein the vector is a monocyte-specific vector.

11. An isolated host cell comprising the isolated polynucleotide of claim 1.

12. The isolated host cell of claim 11, wherein the host cell is a mammalian cell.

13. The isolated host cell of claim 12, wherein the host cell is a monocyte, a macrophage, a foam cell, an arterial smooth muscle cell, a vascular smooth muscle cell, an endothelial cell, a cardiomyocyte, a coronary adipocyte, or a cardiac fibroblast.