Anti-HIV group I introns and uses thereof in treating HIV infections

Abstract

Described is a unique class of antiviral molecule that can be applied to control and eliminate HIV infection in patients using myeloablation therapies and replenishment with transformed bone marrow stem cells programmed to express the antiviral molecule. These anti-viral molecules target the HIV genome in a highly conserved domain, and when expressed in cells prior to infection will cause the cell to die upon infection with HIV. Cell death insures no proliferation of new virus. Reconstituting the immune system with cells expressing these antivirals prevents re-establishment of HIV infection from reservoirs in the re-established lymphocyte and macrophage populations. Over time, reservoirs will be depleted entirely, effectively eliminating the virus. In effect, this new type of antiviral can be used to cure HIV infections.

Claims

1. An antiviral molecule comprising an anti-HIV-Group 1 (HIV-Grp1) trans-splicing intron targeting one or more uracils within the HIV Primer Signal (HIVPAS) or the HIV primer binding site (HIVPBS) of any HIV target RNA, wherein said antiviral molecule comprises the following nucleic acid sequences in a 5 to 3 order: (a) an External Guide Sequence (EGS) complementary to a segment of the target RNA downstream in a 3 direction from the target uracil; (b) an Internal Guide Sequence (IGS) at least 9 nucleotides in length that is partially complementary to and capable of forming a P1 helix with a sequence comprising one or more uracils of the HIVPAS or HIVPBS target sequence; wherein said P1 Helix comprises a G residue at position 4 of the IGS paired to a U residue of the target sequence, and each nucleotide residue of the IGS in the P1 helix flanking the GU pair is complementary to a corresponding nucleotide residue in the target sequence; (c) a nucleic acid sequence comprising a catalytic domain of a Group 1 trans-splicing intron; and (d) a nucleic acid sequence comprising an exon encoding a polypeptide capable of inducing apoptosis in a cell; wherein said nucleic acid sequence (c) comprising a catalytic domain of a Group 1 trans-splicing intron is linked to said nucleic acid sequence (d) comprising an exon encoding a polypeptide capable of inducing apoptosis in a cell by the RNA equivalent of a nucleotide sequence selected from the group consisting of: (i) 5-TGCATTCTGC-3 (corresponding to residues 14 to 23 of SEQ ID NO: 8); (ii) 5-GGTTGGAACTC-3 (corresponding to residues 16 to 26 of SEQ ID NO: 9); (iii) 5-GCTTGGCATTGC-3 (corresponding to residues 16 to 27 of SEQ ID NO: 11); (iv) 5-GCTTGCCATTC-3 (corresponding to residues 16 to 26 of SEQ ID NO: 12); and (v) 5-GTCGTGACCAC-3 (corresponding to residues 15 to 25 of SEQ ID NO: 10).

2. The antiviral molecule of claim 1, wherein the intron targets a uracil selected from the following positions: (a) uracil position U 126 within the HIV Primer Activation Signal (HIVPAS), corresponding to nucleotide 4 within the sequence 5-GACUCUGG-3 (SEQ ID NO: 13), wherein said IGS has the sequence 5-CAGGGUCAC-3 (SEQ ID NO: 15), which is complementary to the HIVPAS at 6 of 8 positions; (b) uracil position U 128 within the HIV Primer Activation Signal (HIVPAS), corresponding to nucleotide 6 within the sequence 5-GACUCUGG-3 (SEQ ID NO: 13), wherein said IGS has the sequence 5-ACCGGAGUC-3 (SEQ ID NO: 16), which is complementary to the HIVPAS at 7 of 8 positions; and (c) uracil position U 182 within the HIV primer binding site (HIVPBS), corresponding to nucleotide 1 within the sequence 5-UGGCGCCCGAACAGGGAC-3 (SEQ ID NO: 14), wherein said IGS has the sequence 5-GCCGCUGCU-3 (SEQ ID NO: 17), which is complementary to the HIVPBS at 3 of 4 positions.

3. A vector comprising a promoter operably-linked to a nucleotide sequence encoding the antiviral molecule of claim 1, wherein said vector is capable of transforming a population of cells to produce transformed cells that constitutively express said HIV-Grp1 trans-splicing intron under the control of said operably-linked promoter.

4. The vector of claim 3, wherein said vector is a retroviral vector comprising a 5 retroviral Long Terminal Repeat (LTR), a retroviral -packaging signal, a nucleotide sequence encoding a selectable marker operably-linked to a promoter, and a 3 retroviral LTR, wherein said 5 LTR and 3 LTR flank the retroviral packaging signal, wherein each of said operably-linked promoters are active in said transformed cells.

5. The retroviral vector of claim 4, wherein said promoter operably-linked to the nucleotide sequence encoding the antiviral molecule, is a CMV promoter.

6. A nucleic acid molecule encoding the antiviral molecule of claim 1.

7. The nucleic acid of claim 6, wherein said HIV-Grp1 intron is selected from the group consisting of (a) an intron, designated a PAS126 intron, targeting nucleotide 4 within the HIVPAS sequence 5-GACUCUGG-3 (SEQ ID NO: 13); (b) an intron, designated a PAS128 intron, targeting nucleotide 6 within the HIVPAS sequence 5-GACUCUGG-3 (SEQ ID NO: 13); and (c) an intron, designated a PBS182 intron, targeting nucleotide 1 within the (HIVPBS) sequence 5-UGGCGCCCGAACAGGGAC-3 (SEQ ID NO: 14).

8. A nucleic acid encoding an anti-HIV-Group 1 (HIV-Grp1) trans-splicing intron targeting one or more uracils within the HIV Primer Signal (HIVPAS) or the HIV primer binding site (HIVPBS) of any HIV target RNA, comprising the following nucleic acid sequences in a 5 to 3 order: (a) an External Guide Sequence (EGS) complementary to a segment of the target RNA downstream in a 3 direction from the target uracil; (b) an Internal Guide Sequence (IGS) at least 9 nucleotides in length that is partially complementary to and capable of forming a P1 helix with a sequence comprising one or more uracils of the HIVPAS or HIVPBS target sequence; wherein said P1 Helix comprises a G residue at position 4 of the IGS paired to a U residue of the target sequence, and each nucleotide residue of the IGS in the P1 helix flanking the GU pair is complementary to a corresponding nucleotide residue in the target sequence; (c) a nucleic acid sequence comprising a catalytic domain of a Group 1 trans-splicing intron; and (d) a nucleic acid sequence comprising an exon encoding a polypeptide capable of inducing apoptosis in a cell; wherein said nucleic acid sequence (c) comprising a catalytic domain of a Group 1 trans-splicing intron is linked to said nucleic acid sequence (d) comprising an exon encoding a polypeptide capable of inducing apoptosis in a cell by a nucleotide sequence selected from the group consisting of: (i) 5-TGCATTCTGC-3 (corresponding to residues 14 to 23 of SEQ ID NO: 8); (ii) 5-GGTTGGAACTC-3 (corresponding to residues 16 to 26 of SEQ ID NO: 9); (iii) 5-GCTTGGCATTGC-3 (corresponding to residues 16 to 27 of SEQ ID NO: 11); (iv) 5-GCTTGCCATTC-3 (corresponding to residues 16 to 26 of SEQ ID NO: 12); and (v) 5-GTCGTGACCAC-3 (corresponding to residues 15 to 25 of SEQ ID NO: 10); wherein said HIV-Grp1 intron is selected from the group consisting of (i) an intron, designated a LOOP126 intron, targeting nucleotide 4 within the HIVPAS sequence 5-GACUCUGG-3 (SEQ ID NO: 13), and said EGS is complementary to the HIV Primer Binding Site (HIVPBS); and (ii) an intron, designated a LOOP 128 intron, targeting nucleotide 6 within the HIVPAS sequence 5-GACUCUGG-3 (SEQ ID NO: 13), and said EGS is complementary to the HIV Primer Binding Site (HIVPBS).

9. The nucleic acid of claim 6, wherein said polypeptide capable of inducing apoptosis in a cell is a cysteine-dependent aspartate-specific protease.

10. The nucleic acid of claim 9, wherein said cysteine-dependent aspartate-specific protease is a caspase.

11. The nucleic acid of claim 6, wherein said polypeptide capable of inducing apoptosis in a cell is the proapoptotic pore-forming protein Bax, or derivatives thereof.

12. A vector comprising the nucleic acid encoding an HIV-Grp1 intron of claim 6.

13. The vector of claim 12, further comprising a promoter that is functional in a mammalian cell, operably-linked to said intron.

14. The vector of claim 13, wherein said nucleic acid comprising said intron and said operably-linked promoter is capable of being stably-integrated into the genome of a mammalian cell.

15. A vector comprising the nucleic acid encoding an HIV-Grp1 intron of claim 7.

16. The vector comprising the nucleic acid encoding an HIV-Grp1 intron of claim 15, further comprising a promoter that is functional in a mammalian cell, operably-linked to said intron.

17. The vector of claim 16, wherein said nucleic acid comprising said intron and said operably-linked promoter is capable of being stably-integrated into the genome of a mammalian cell.

18. A vector comprising the nucleic acid encoding an HIV-Grp1 intron of claim 8.

19. The vector of claim 18, further comprising a promoter that is functional in a mammalian cell, operably-linked to said intron.

20. The vector of claim 19, wherein said nucleic acid comprising said intron and said operably-linked promoter is capable of being stably-integrated into the genome of a mammalian cell.

21. The nucleic acid of claim 8, wherein said polypeptide capable of inducing apoptosis in a cell is a cysteine-dependent aspartate-specific protease.

22. The nucleic acid of claim 21, wherein said cysteine-dependent aspartate-specific protease is a caspase.

23. The nucleic acid of claim 8, wherein said polypeptide capable of inducing apoptosis in a cell is the proapoptotic pore-forming protein Bax, or derivatives thereof.

24. An antiviral molecule of claim 1, wherein said HIV-Grp1 trans-splicing intron targets one or more uracils within the HIV Primer Signal (HIVPAS) of any HIV target RNA.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

(1) FIG. 1a-1b: FIG. 1aGroup I intron structure and activity. Left: Structural features of Trans-splicing Group I introns showing alignment with the target sequence (top strand, left (5) to right (3), SEQ ID NO: 1), the relative positions of the antisense IGS and EGS (bottom strand, right (5) to left (3) SEQ ID NO: 2), as well as the P10 helix (embedded as UCCUCG, left (5) to right (3) within SEQ ID NO: 3), and intron catalytic core (Intron) (sequence not shown). FIG. 1b: Trans-splicing reaction catalyzed by the group I intron. First step: Intron finds its target RNA sequence through complimentary base pairing with the guide sequences. The 3 GNP OH attacks the phosphodiester backbone directly downstream of the reactive uracil on the 5 exon. Second step: The 3 exon is brought into proximity with the newly freed 3-OH on the cleavage uracil, guided by the P10 helix. The 3-OH attacks the phosphodiester backbone just upstream of the 3 exon in another transesterification reaction, resulting in the 5 exon and the 3 exon being joined covalently. The end result is a new RNA molecule.

(2) FIG. 2: The 5 region of the HIV genome was amplified from a lentivirus vector, pLVX-Puro (Clontech), inserted into the pBSK+downstream of the T7 promoter for in vitro expression as RNA.

(3) FIG. 3: Provirus sequence and transcription map showing the inclusion of the PBS at the 5 end of all transcripts produced from an integrated HIV provirus (Lamothe and Joshi (2000)).

(4) FIG. 4: tRNA.sup.lys3 binds HIV-2 to prime reverse transcription. Binding interaction is highly conserved between HIV-1 and -2. In HIV-I PAS is GACUCUGG rather than HIV-2's GACCCUGG pictured. Initial bases added are those immediately upstream of the PBS. Figure adapted from Freund et al. (2001).

(5) FIG. 5: Schematic depicting the binding of the Loop126 anti-HIV group I introns to the conserved PBS (SEQ ID NO: 6) and its complement (SEQ ID NO: 7) and PAS sequences. The intron binds in a similar way as the tRNA.sup.lys3 binds to these sequences, allowing a large loop bulge which forms a natural stem loop structure. Such a large loop bulge region has previously never been designed into a trans-splicing Group I intron, and is one of the innovative aspects of the design of these introns. The fact that incorporation of such a large loop bulge does not significantly detract from the trans-splicing activity permits applications of these introns where conserved regions are separated by more than a few non-conserved sequences.

(6) FIG. 6: Sequencing results of RTPCR recovered splice products from in vitro trans-splicing reactions with PBS-PAS targeting Group I introns. Sequence alignments are shown for different introns with the splice junctions located between the indicated nucleotides (noted between V characters above the coordinate positions) and differences between experimental and expected results noted by a * below the appropriate nucleotides in the bottom row of expected results. The ATG start codon of the 3 exon encoding a polypeptide capable of inducing apoptosis in a cell, exemplified by ATG GTC ATA G. (corresponding to nucleotides 24-32 of SEQ ID NO: 8), is underlined in the bottom row of expected results for the PAS126 Sequence Alignment, and corresponding codon sequences in the PAS128, PBS182, and LOOP128 Sequence Alignments.

(7) FIG. 7: Trans-splicing activity of HIV-Grp1 introns in transiently co-transfected 293 cells. A. Lentivirus expression plasmids were constructed to express the HIV-Grp1 introns from the CMV promoter. B. The target transcript for firefly luciferase was expressed from the native HIV-1 LTR promoter to generate transcripts having the 5 terminal sequences of native HIV, including the PBS and PAS targets. C. Target transcript, HIV-Grp1 introns, and splice products were detected in cells 96 hours post transfection using RT-PCR with sequence specific primers. The introns PAS 128 and PAS 128L (L stands for long external guide sequence) yielded the best results in this assay.

(8) FIG. 8: Cells were infected with the HIV-iGFP chimeric fluorescent virus, incubated for 48 hours, and then transfected with pLXRN CMV expression vectors expressing HIV-Grp1 intron 128L either with (128L tBax) or without (128L) an attached 3 tBax exon. Controls were HIV-iGFP infection alone (HIV) and post infection transfection with a DsRed expression plasmid (DsRed). Virus amounts are recorded as relative fluorescence in virus supernatants, and are relative to the HIV infection control.

DETAILED DESCRIPTION OF THE EMBODIMENTS

(9) Presented are HIV-Grp1 intron constructs that are useful in the control and inhibition of HIV infection. Methods employing these constructs are also provided that present a method for treating and/or curing HIV and the progression thereof the AIDS. Several assays for trans-splicing activity are provided that employ both artificial sequences and infectious targets. These designs involve the addition of an extended external guide sequences (EGS) that functions to improve recognition, alteration of a p10 helix to provide an even more favorable splicing context, and lesser conserved targets within the same region of the HIV genome. A quantitative RT-PCR protocol is developed to make more quantitative comparisons of the data.

Example 1Construction of Retroviral Vectors

(10) The present example demonstrates the construction and use of retroviral vectors containing HIV-Grp1 introns having a 3 apoptosis-inducing gene to establish transformed cells that constitutively express these selected Group I introns, and that may be used in the treatment and cure of a human immunodeficiency virus in an animal. These transformed cells are challenged with active HIV virus to demonstrate the efficacy of the introns in suppressing lentivirus infections in the transformed cell cultures. Retrovirus vectors will be constructed for transduction of these expressed introns in HEK293 cells.

(11) Following selection and cell sorting, the effectiveness of these introns in suppressing HIV infection of these transformed cell cultures will be assessed.

Example 2Apoptosis-Inducing Gene Products for Suppression of HIV Infection

(12) The present example demonstrates the effectiveness of alternative apoptosis-inducing gene products for suppression of HIV infection in the present HIV-Grp1 intron strategy. Initial examinations into apoptosis inducing gene products focused on the tBax inducer. While the tBax protein has proven to be an effective inducer of apoptosis in both the mosquito cell and human cell applications, it does not have enzymatic activity, and may therefore be inferior to other inducers of apoptosis such as Caspases. The present invention will employ certain caspases as an alternative 3 exon for apoptotic induction following trans-splicing.

Example 3Hematopoietic Stem Cell Replacement

(13) The present example presents a transgenic HIV-Grp1 intron hematopoietic stem cell replacement strategy in a mouse system. A chimeric HIV virus will be used that has an the envelope coding domain from an ecotropic MLV that restricts replication of the chimeric virus to rodents (Potash et al., 2005). This will be used to establish infections in young adult mice. These mice will serve as models for the present transduced hematopoietic stem cell therapies using the HIV-Grp1 introns.

(14) While this proposal is designed to validate this approach using a less costly and more rapid mouse system, the data provided will serve to provide support for the successful expectation of the use of this approach in simian models.

(15) This invention provides a means of eradicating HIV virus from an infected individual. This strategy will be effective either alone or in conjunction with other strategies currently being used and/or proposed for use for transduced hematopoietic stem cell therapies.

Example 4Studies Targeting Conserved Sequences of the HIV Genome

(16) Two sequences that are highly conserved within the HIV genome are the -packaging signal (Amarasinghe et al., 2000) near the 5 end of the gag gene and the adjacent upstream tRNA.sup.lys3 primer binding site (PBS). The accessibility of these conserved sequences to Group I intron attack was examined by constructing a 540 nt long target sequence encompassing the 5 terminus of the HIV genome and including the tRNA PBS and -packaging signal (FIG. 5).

(17) Group I introns targeting the -packaging signal were unsuccessful because the targeted sequence for cleavage occurred in a complex of stem loop structure that was not accessible to the intron under normal physiological conditions.

(18) The tRNA.sup.lys primer binding sequence was then examined. The tRNA.sup.lys primer binds the host genome at three sites: the PBS (Primer Binding Site), the PAS (Primer Activation Signal), and anticodon recognition sequence (Dobard et al., 2007). Abbink et al., (2004) recognized that the PBS is almost completely conserved across HIV as it is encoded by the tRNA primer.sup.19. The PBS-tRNA interaction is stronger than the other two sites because of the greater number of base pairs. A point mutation in the PBS has been seen to occur if a virus uses tRNA.sup.lys5 to prime reverse transcription instead, but frequently this mutation will revert by binding tRNA.sup.lys3 imperfectly in the next generation's reverse transcription. The PAS motif also appears to be necessary to initiate reverse transcription and thus should also be well conserved.

(19) A Quick Align search using the Los Alamos National Laboratory HIV sequence database reveals the PAS is fairly well conserved, though a few point mutations exist within several viral clades. The PBS is nearly perfectly conserved across the major clades B, C, and D. Clades B is the most prominent clade in the US and Western Europe, and displays a highly conserved PBS and PAS, while Clade D, prevalent in Eastern Europe and Sub-Saharan Africa, display 100% conserved PBS and PAS. In nearly all sequences the PBS's upstream flanking sequence is perfectly conserved as well. Unfortunately, the first several hundred nucleotides of the viral genome (including the presently described sequence of interest) are not well represented in Los Alamos' sequence database, and the smaller number of sequences observed could misrepresent the true conservation of the PAS and PBS. By both the conservation and accessibility, it was determined that the PAS and PBS would be good candidates for intron targeting.

Example 5Design and Testing of HIV-Grp1 Introns

(20) Targetable uracils were identified, two within the PAS (U126 and U 128) and one within the PBS (U182). Four introns were then designed. Three standard introns targeted each uracil (PAS 126, PAS 128, PBS 182), and a fourth (LOOP 126) targets U 126 from the PAS and base pairs with the PBS via EGS. This latter intron is quite different from the previously designated introns, and novel among all published introns, as the region of non-homology termed the loop bulge in the target HIV RNA is a rather large stem loop that forms between the PAS and PBS sequences (FIG. 5, and SEQ ID NOS: 6 and 7). The intron models tRNA.sup.lys3 in binding both PAS and PBS. Successful splicing was observed in our in vitro reaction system for each of the Group I introns targeting the PBS and PAS sequences (FIG. 6).

(21) Splicing assays were also performed against target plasmids containing the 5 LTR sequence of HIV-1 in transiently transfected 293 cells. Each HIV-Grp1 intron was expressed from the CMV promoter of a lentiviral vector construct (FIG. 7b) in the presence of a co-transfected plasmid that expressed a firefly luciferase gene transcript from the HIV-1 LTR (see FIG. 7b). The resulting RT-PCR analysis (FIG. 7c) revealed the presence of spliced product, and subsequent analyses confirmed proper splicing of the 3 exon by the HIV-Grp1 introns.

Example 6Confirmation of HIV-Grp1 Intron Activity Against HIV

(22) While activity assays against the plasmid-encoded LTR-linked sequences demonstrated the splicing activity of the HIV-Grp1 introns, the present study was conducted to confirm that this activity would translate into an effective suppression of HIV in a productively infected cell.

(23) A preliminary study was conducted using the HIV-Grp1 intron 128L. A previously developed GFP labeled HIV virus clone, HIV iGFP (Hubner et al., 2007), was employed. This clone that allows fluorescent quantification of virus production in 293 cells. Virus produced with this clone was used to establish infection in 293 cells for 48 hours, at which time the infected cells were transfected with pLXRN CMV vectors (see FIG. 7A) expressing HIV-Grp1 introns having either nonsense sequence or tBax as the 3 exon. After a further 96 hours, virus was collected from the supernatants and the EGFP fluorescence was quantified using a Spectramax M5e.

(24) The results (FIG. 8) clearly show a significant reduction in the production of labeled virus in the presence of the HIV-Grp1 intron, whether or not tBax was used as the 3 exon. In the absence of tBax, reduction levels reflect the inhibition of new virus as a result of the activity of the ribozyme alone. In contrast, when tBax is substituted as the 3 exon, virus reduction is even greater.

(25) Because these assays were done using transfected expression plasmids and established HIV infections in the cells, they may not accurately reflect the levels of reduction expected if cells are first transformed to express the HIV-Grp1 intron and then challenged with HIV. In fact, priming the cells with expressed HIV-Grp1 intron prior to infection with virus should lead to significantly better protection of the cultures and significantly greater reductions of produced virus.

Example 7HIV Treatment and Validation

(26) The present example validates an HIV-Grp1-apoptosis effector molecule for suppression of HIV in transgenic hematopoietic stem cell replacement therapies. The method is designed to ultimately test the efficacy of this approach in an animal model system. The model system of choice for these first analyses is the mouse. This strategy as validated in this less expensive, more easily analyzed model system will provide a solid foundation to propose later primate studies.

(27) The present example presents the construction and evaluation of additional HIV-Grp1 introns utilizing the several previously established assays for trans-splicing activity employing both artificial sequences and infectious virus targets.

(28) While the present initial results with constructing and testing HIV-Grp1 introns have been relatively productive in that one intron has been identified that seems to have optimal activity, improvements in the activity of the other introns designed can be made with further design changes. These design changes involve the addition of extended external guide sequences (EGS), alterations of the p10 helix to provide a more favorable splicing context, and examination of less conserved targets within the same region of the genome. The present intron constructs also include an Internal Guide Sequence (IGS), whose sequence/structure may also be optimized for the present intron constructs.

(29) Bell et al. (2004) suggest several ways to optimize the activity of Group I introns. For example, shortening the P10 helix and lengthening the P9.0 domain to eight base pairs can increase the efficiency of the second step reaction of trans-splicing.

(30) Study Design:

(31) An in vitro, transiently transfected cell system will be used, and HIV-iGFP assays will be utilized for determining the activity of each HIV-Grp1 intron. All assays will employ RT-PCR as a first analysis to confirm splicing activity. A quantitative RT-PCR protocol will be developed to make more quantitative comparisons of the data. Up until this point the data have been qualitative only with respect to the RT-PCR analyses, and even though there may appear to be differences in activities in the in vitro and transient transfection assays, these differences may reflect subtle differences in assay conditions or variability in concentrations of substrate and intron rather than true differences in activity of the introns.

(32) Activities of all new constructs will be evaluated against the 128L standard as a control. While consistently good results were obtained with the 128L intron in the present assays, other introns may also be similarly effective if the assays are repeated and optimized. In addition, while this standard may represent the most effective intron under conditions of the assays, further examination of the introns may be pursued that appear to yield somewhat less effective results in the context of these particular assays in the event that acceptable results would still be obtained when applied in the context of the transformed cell assays as described in above.

(33) Retroviral vectors containing HIV-Grp1 introns having 3 apoptosis-inducing genes will be constructed and used to establish transformed cells that constitutively express these selected Groups I introns. These transformed cells will be challenged with active HIV virus to test the efficacy of the present introns in suppressing lentivirus infections in transformed cell cultures.

(34) Thus far none of the assays employed to test the activity of the present HIV-Grp1 introns are reflective of the actual conditions under which the introns are expected to be employed in an HIV infection suppression scenario. For this reason, transformed cell cultures will be developed that constitutively express the HIV-Grp1 intron, and will then be exposed to low levels of infectious HIV virus.

(35) Transformed 293 cells will be prepared that express the present HIV-Grp1 introns. Cultures of these transformed cells will then be used to determine the effectiveness of these introns in suppressing HIV infection. To do this, the retrovirus vectors will first be altered for transduction of the expressed introns in a way that permits optimized selection of the resulting transformed cells.

(36) (a). Modification of the pLXRN-Based Vector to Express the mCherry Fluorescent Marker Gene:

(37) The pLXRN-CMV base vector will be altered to incorporate an ECMV IRES directed mCherry downstream of the 3 exon of the HIV-Grp1 introns. The effectiveness of incorporating an IRES expressed downstream introns has already been demonstrated (Carter et al., 2010). The advantage of employing this intimately linked marker gene is two-fold. First, this will establish that if cells are expressing the mCherry, they are also expressing the HIV-Grp1 intron, since both are part of the same di-cistronic transcript. Second, the mCherry fluorescence provides a handle useful to sort the transformed cells for enrichment following hygromycin selection.

(38) In previous analyses with the DENV-Grp1 introns, a level of background DEN virus infection was observed in hygromycin selected cultures. This level may be due to the presence of hygromycin resistant untransformed cells in the cultures because these levels are influenced by the stringency of selection and the freshness of the hygromycin. To insure optimal results, inclusion of a marker that can provide a handle for cell sorting may be used.

(39) Finally, by validating this IRES-coupled gene expression approach with respect to the HIV-Grp1 introns, the introduction of a coupled selectable gene that may be useful in subsequent development of in vivo applications is supported. Specifically, this will establish that it is possible to provide an IRES-expressed, intimately linked gene that under given conditions (e.g., drug exposure), would permit selective amplification of transformed hematopoietic stem cells in a patient without the need for the more extreme measure of first ablating the immune system.

(40) (b.) Transformation of 293 Cells with Lentivirus Vectors Expressing the HIV-Grp1 Introns and Testing for HIV Infection.

(41) 293 cells will be infected with each lentivirus vectors at an MOI of 10 to insure relatively complete infection of the cell culture. Following a 72 hour recovery period, the cells will be subject to staged selection with hygromycin over a three week period, monitoring mCherry fluorescence to insure enrichment for those cells expressing the HIV-Grp1 intron. The expression of each intron will also be confirmed using qRT-PCR. Following the three week selection period we will sort the cell populations using a BD Biosciences FACSAria III cell sorter to enrich for optimal expression of the mCherry marker, which should also insure optimal expression of the HIV-Grp1 intron.

(42) The negative control for trans-splicing activity will be produced by removing of domains P4 through P6 of the trans-splicing domain (Cech, 1990). Domains P4 to P6 must be removed instead of only the Pabc5 domain, as previously described (Ayre et al. 1999), since in our previous analyses DENV-Grp1 Pabc5 retained residual activity. Domains P4, P6 and Pabc5 form an extensive interface with each other to form the basis of the catalytic core (Murphy and Cech 1993; Murphy and Cech 1994; Cate et al. 1996).

(43) (c.) Challenge of HIV-Grp1 Intron Expressing Cells with HIV:

(44) The HIV-iGFP virus (Hubner et al., 2007) will be used as well as wild type NL4-3 in assays for the effectiveness of HIV suppression in our transformed cell cultures. While the HIV-iGFP mutant virus has the advantages of ease of assaying, there are some problems with relative infectivity compared with the wild type virus (Muller et al., 2004). In addition, the fluorescent counts alone cannot be considered reliable predictors of actual infectious virus production. Therefore, the standardized p24 assays will be used as well as qRT-PCR assays to determine the relative effectiveness of our HIV-Grp1 introns in suppression of virus infection of the transformed cells. Finally, the effectiveness of the apoptotic response will be assessed using Annexin V staining to confirm that apoptotic cell death is occurring in HIV-challenged cultures.

(45) iii.) Examining the Relative Effectiveness of Alternative Apoptosis-Inducing Gene Products for Suppression of HIV Infection in our HIV-Grp1 Intron Strategy.

(46) While the tBax protein has proven to be an effective inducer of apoptosis in both the mosquito cell and human cell applications, it does not have enzymatic activity that could effectively enhance its performance. The buildup of sufficient tBax is relied upon as a result of the splicing and translation reaction, and as a result this may not be the a somewhat less effective means of inducing apoptosis than generating a protein with enzymatic properties.

(47) It may be more advantageous to use caspases as a 3 exon since it takes multiple tBax molecules to form a single pore, while the enzymatic activity of the caspase amplified its effect within the cell. Listed below are several caspases that may be of interest.

(48) Caspase 3:

(49) Activated in the apoptotic cell both by extrinsic (death ligand) and intrinsic (mitochondrial) pathways making this the most logical candidate as the expression of the active form of this caspase would activate both pathways simultaneously (Salvesen 2002; Ghavami et al., 2009), leading to activation of other caspases that will cleave of cellular substrates and resulting in apoptosis.

(50) Caspase-6:

(51) Plays a central role in the execution phase of apoptosis activating targets following activation by initiator caspases (Cowling and Downward, 2002). Activation of caspase 6 in the absence of initiator caspases in cells would lead to the initiation of apoptosis without down regulation of this event by inhibitors of apoptosis (IAP) that act upon initiator caspases.

(52) Caspase 8:

(53) An initiator caspase. According to the induced-proximity model (Salvensen and Dixit, 1999) procaspase-8 undergoes autoproteolytic cleavage, following recruitment to the death-inducing signaling complex (DISC) forming active caspase-8, which in turn can activate other procaspases, leading to cleavage of cellular substrates, and apoptosis.

(54) Caspase-9:

(55) Activated Caspase-9 is able to cleave Caspase-3 (Li et al., 1997) leading to initiation of the extrinsic and intrinsic apoptotic pathways.

(56) Each of these caspases exists in an inactive and an active form. In some cases modification of the sequence can lead to a constitutively active enzyme that, when expressed, will irreversibly induce apoptosis (Srinivasula et al., 1998). These sequences may be designed to serve as 3 exons similarly to the way we designed the tBax 3 exon.

(57) Sequences encoding the active forms of each caspase will be placed in the 3 exon position of the 128L HIV-Grp1 intron for comparative analysis of their effectiveness in inducing apoptotic cell death in transformed 293 cells challenged with HIV. The standard assays for splicing and apoptosis induction will be performed as above.

(58) iv.) Modeling a Transgenic HIV-Grp1 Intron Hematopoietic Stem Cell Replacement Strategy in a Mouse System.

(59) Mouse models for HIV infection are limited in their relevance, particularly when considering immunological responses. Even humanized mouse models fall short of predictive validity in this respect. However, the approach here examined does not rely on immune function for its effectiveness. In fact, immune function is irrelevant to the characterization of the effectiveness of the present HIV-Grp1 intron as a suppressive tool. Therefore, an appropriate mouse model could provide a cost effective and rapid means for obtaining valuable information justifying this transgenic hematopoietic stem cell replacement strategy.

(60) Instead of relying on the more complex humanized mouse models, a chimeric HIV virus, Eco-HIV will be utilized that is built upon the clade B NL4-3 backbone. This virus has a replacement of the HIV gp120 sequence with the envelope coding domain from an ecotropic MLV that restricts replication of the chimeric virus to rodents (Potash et al., 2005). Infection of mice with this virus produces the repertoire of infected cell types typical of an HIV infection. Any mouse strain of choice may be inoculated with this chimeric virus and results in infection of all major target cell types of HIV-1. Virus burdens in the spleen are comparable to HIV-1 burdens in resting lymphocytes in human (Potash et al., 2005). Therefore, this chimeric virus in the mouse system seems to be good choice for the present studies.

(61) The chimeric virus will be used to establish infections in young adult (8-10 weeks) mice for a six week period. To insure complete infection we will sample hematopoietic tissues, particularly lymphocyte and macrophage populations, for the Eco-HIV virus. Assays will include circulating virus assays as well as PCR assays of provirus. Once infection has been established mice will be irradiated and/or subjected to chemical myeloablation followed by transfusion through tail vein with HIV-Grp1 intron transformed syngeneic hematopoietic stem cells. The HIV infection will be held in check with drug therapies to allow reconstitution of the immune system within the mice in the absence of significant virus load. Lymphocyte and macrophage cell populations will be monitored to insure full reconstitution. This strategy models clinical protocols for hematopoietic stem cell therapies (e.g. Cartier et al., 2009). Following the reconstitution of the immune system the antiviral therapy will be removed and the levels of lymphocyte and macrophage cell populations will be monitored to determine the impact of the active infection on these transformed cells. It is expected that there will be a reduction in the cell counts for HIV susceptible cell populations as a result of the impact of the DUI activity. The virus and provirus load will also be monitored to establish maintenance of a low viremia.

(62) A unique and revolutionary strategy for combating and curing HIV infections is provided with the present anti-HIV Group 1 intron strategies. By providing reconstituted susceptible cells with a targeted trans-splicing molecule that generates apoptotic cell death in the presence of the HIV mRNA substrate following infection, the ability of the virus to re-establish infection in the transduced reconstituted immune cells is eliminated. This has the dual effect of stabilizing the viral load at sub-clinical levels, as well as acting as a sponge for virus shed from long term reservoirs. The key to this approach is successful attack of invariant sequence within the HIV genome, which have been identified and confirmed are subject to trans-splicing. Another advantage of this approach is the ability to couple the trans-splicing intron to an IRES-expressed gene product with allows for engineering of a selective genes that insures maintenance of the transgene in reconstituted tissues, and may also allow repopulation of the immune system without myeloablation therapies.

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(64) TABLE-US-00001 TABLE 1 List of Sequences SEQ Length ID Short Name Organism Description Support Type (aa/nt) NO Dengue Virus 2 Dengue misc_feature (1)..(9) FIG. 1a, RNA 41 1 Target RNA virus Target sequence in a Dengue Virus 2 RNA first line type 2 complementary to Internal Guide Sequence (IGS) in an exemplary trans-splicing intron. misc_feature (10)..(13) Loop Bulge sequence in Dengue Virus 2 RNA located between a target sequence and a sequence complementary to an External Guide Sequence (EGS) in an exemplary trans-splicing intron. misc_feature (14)..(41) A sequence in Dengue Virus 2 RNA complementary to an External Guide Sequence (EGS) in an exemplary trans-splicing intron targeting a uracil residue in the target sequence. acgccuuuca auaugcugaa acgcgagaga aaccgcgugu c EGS and IGS of Artificial Synthetic oligonucleotide comprising EGS and FIG 1a, RNA 47 2 exemplary trans- IGS of an exemplary trans-splicing intron second line splicing intron targeting a Dengue Virus 2 RNA. misc_feature (1)..(28) External Guide Sequence (EGS), which can be of variable length, in a trans-splicing intron targeting a viral RNA, exemplified by a Dengue virus 2 sequence, wherein the EGS is capable of forming a transient helix downstream from the target sequence. misc_feature (32)..(41) Internal Guide Sequence (IGS), at least 9 nt in length, targeting a viral RNA, exemplified by a Dengue virus 2 sequence, wherein the IGS is capable of forming a P1 helix with target sequence comprising one or more uracil residues. gacacgcggu uucugagcgc uuucagcacu ugagcgagga agggcgu P10 Helix 3 exon Artificial Synthetic oligonucleotide comprising P10 Helix FIG 1a, RNA 18 3 region of an and AUG codon of a 3 exon of an exemplary third line exemplary trans- trans-splicing intron targeting a Dengue Virus 2 splicing intron RNA. misc_feature (5)..(10) Region in an exemplary trans-splicing intron targeting a Dengue Virus 2 RNA is complementary to a portion of the Internal Guide Sequence (IGS) of the intron capable of forming a P10 helix. misc_feature (16)..(18) AUG start codon in an exemplary trans-splicing intron targeting a Dengue Virus 2 RNA. ucgauccucg agaccaug HIV HIV misc_feature (1)..(166) FIG. 4 RNA 166 4 Residues of an HIV RNA illustrated in FIG. 4, corresponding to residues 206 to 371. ccgccugguc auucgguguu caccugagua acaagacccu ggccuguuag gacccuucuu 60 gcuuugggaa accgaggcag gaaaaucccu agcagguugg cgcccgaaca gggacuugaa 120 gaagacugag aagucuugga acacggcuga gugaaggcag uaaggg 166 tRNA-Lys3 Human tRNA (1)..(76) FIG. 4 tRNA 76 5 tRNA- Sequence corresponding to tRNA-Lys3 Lys3 complementary to a portion of the 5 end of an HIV RNA, including an HIV Primer Activating Sequence (HIVPAS) and an HIV Primer Binding Sequence (HIVPBS). gcccggauag cucagdcggd agagcaucag acuuuurauc ugagggdcca ggguucaagu 60 cccuguucgg gcgcca 76 HIV Primer HIV 2 misc_feature (1)..(18) FIG. 4 RNA 18 6 Binding Site Region corresponding to nucleotides 303-320 (HIVPBS) in FIG. 4 of an HIV RNA comprising an HIV Primer Binding Sequence (HIVPBS). uggcgcccga acagggac Anti-HIVPBS in Synthetic misc_feature (1)..(18) FIG. 4 RNA 18 7 tRNA-Lys3 Region in a tRNA-Lys3 complementary to the HIV Primer Binding Sequence (HIVPBS). gucccuguuc gggcgcca PAS126 Splice Synthetic misc_feature (1)..(33) FIG. 6 DNA 33 8 Junction Experimental and Expected Splice Junctions for (Expected and trans-splicing intron targeting U126 in HIV RNA Observed) comprising HIV sequences, intergenic region, and ATG start codon of 3 exon, illustrated in FIG. 6. ctgttgtgtg acttgcattc tgcatggtca tag PAS128 Splice Synthetic misc_feature (1)..(34) FIG. 6 DNA 34 9 Junction Experimental and Expected Splice Junctions for (Expected and trans-splicing intron targeting U128 in HIV RNA Observed) comprising HIV sequences, intergenic region, and ATG start codon of 3 exon, illustrated in FIG. 6. ctgttgtgtg actctggttg gaactcatgg tcat PBS182W Splice Synthetic misc_feature (1)..(33) FIG. 6 DNA 34 10 Junction Experimental and Expected Splice Junctions for (Expected and trans-splicing intron targeting U182 in HIV RNA Observed) comprising HIV sequences, intergenic region, and ATG start codon of 3 exon, illustrated in FIG. 6. aaatctctag cagtgtcgtg accacatggt cat LOOP128 Splice Synthetic misc_feature (1)..(34) FIG. 6 DNA 34 11 Junction Expected Splice Junction for trans-splicing (Expected) intron targeting U128 with an EGS targeting the HIVPBS in HIV RNA comprising HIV sequences, intergenic region, and ATG start codon of 3 exon, illustrated in FIG. 6. ctgttgtgtg actctgcttg gcattgcatg gtca Loop Splice Synthetic misc_feature (1)..(33) FIG. 6 DNA 33 12 Junction Experimental Splice Junction for trans-splicing (Observed) intron targeting U128 with an EGS targeting the HIVPBS in HIV RNA comprising HIV sequences, intergenic region, and ATG start codon of 3 exon, illustrated in FIG. 6. ctgttgtgtg actctgcttg ccattcatgg tca HIVPAS HIV misc_feature (1)..(9) FIGS. 4 &5 RNA 8 13 9 nt target region designated HIVPAS (corresponding to nt 577 to 584 of prototype strain HIV HBX2, or nt 123 to 130 of Beerens and Berkhout) which has affinity to IGS region of trans-splicing intron gacucugg HIVPBS HIV misc_feature (1)..(18) FIGS. 4 &5 RNA 18 14 HIV Primer Binding Site (HIVPBS) uggcgcccga acagggac IGS126 Artificial Synthetic Internal Guide Sequence (IGS), part FIGS. 1, 7, RNA 9 15 Sequence of a trans-splicing intron partially paras complementary to and targeting uracil position [0008, U126 corresponding to nucleotide 4 in the 0029, 0030, HIVPAS sequence 5-GACUCUGG-3 in HIV 0057] RNAs. misc_feature (1)..(9) Synthetic Internal Guide Sequence (IGS), part of a trans-splicing intron partially complementary to and targeting uracil position U126 corresponding to nucleotide 4 in the HIVPAS sequence 5-GACUCUGG-3 in HIV RNAs. cagggucac IGS128 Artificial Synthetic Internal Guide Sequence (IGS), part FIGS. 1, 7, RNA 9 16 Sequence of a trans-splicing intron partially paras complementary to and targeting uracil position [0008, U128 corresponding to nucleotide 6 in the 0029, 0030, HIVPAS sequence 5-GACUCUGG-3 in HIV 0057] RNAs. misc_feature (1)..(9) Synthetic Internal Guide Sequence (IGS), part of a trans-splicing intron partially complementary to and targeting uracil position U128 corresponding to nucleotide 6 in the HIVPAS sequence 5-GACUCUGG-3 in HIV RNAs. accggaguc IGS182 Artificial Synthetic Internal Guide Sequence (IGS), part FIGS. 1, 7, RNA 9 17 Sequence of a trans-splicing intron partially paras complementary to and targeting uracil position [0008, U182 corresponding to nucleotide 1 in the 0029, 0030, HIVPBS sequence 5-GACUCUGG-3 in HIV 0057] RNAs. gccgcugcu