CA2066684A1

CA2066684A1 - Therapeutic ribozyme compositions and expression vectors

Info

Publication number: CA2066684A1
Application number: CA002066684A
Authority: CA
Inventors: Allan R. Goldberg; Shaji T. George; Hugh D. Robertson
Original assignee: Individual
Current assignee: Sirna Therapeutics Inc
Priority date: 1989-09-25
Filing date: 1990-09-25
Publication date: 1991-03-26
Also published as: AU7893194A; EP0494244A1; KR920703119A; US5763268A; US5773260A; KR960012066B1; WO1991004319A1; AU6505990A; AU674104B2; US5225347A; JPH05502999A

Abstract

Hepatitis delta is used as a vector for inhibition of viral infection and to express proteins in vivo in a cell-specific manner. The scope of delta's use as a vector is broadened in the present invention in several important ways. For example, a delta RNA
genome capable of self-replication is enlarged to carry additional information, either coding for messenger RNA for a protein, or for a targeted ribozyme, which can be delivered to liver cells using delta's normally infectious properties, or to other cell types using chimeric delta viral agents carrying altered surface proteins. In another embodiment, the delta vector is made self-limiting, so that its role in delivering targeted information is separated from its viral property of unlimited infectious replication.
Targeting is achieved through the use of sequences flanking the delta sequences that have affinity for sites on RNA to be cleaved.

Description

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THERAPEllIlC RIBOZYl\IE COMPOSITIONS
AND EXPRESSION VECTORS

Background of the Invention This invention is in the general area of genetic engineering of nucleic acid sequences, especially RNA sequences having protein encoding or ribozyme activity derived from hepatitis delta virus.
This is a continuation-in-part of U.S. Serial No. 07/411,713 entitled "Ribo~yme Compositions and Methods for Use" filed September 25, 1989 by Hugh D. Robertson and Allan 1?. Goldberg.
Constructing vectors for delivery of therapeutic ribozymes and/or mRNA sequences to target cells is a difEicult challenge. In U.S. Serial No.07/411,713, vectors created from retroviruses were described as a means for delivering therapeutic ribo2ymes capable of 15 cleaving viral mRNAs to limit viral infections. In one embodiment, the ribo~yme from the RNA of the hepatitis delta virus in combination with appropriate T-cell specific re~oviruses was described as a means of targeting and cleaving RNAs in cells infected with `~ human immunodeficiency virus (HIV). U.S. Serial No.07/411,713 also 20 outlined a method to use the delta viral RNA genome as a vector, '3' carrying information from one cell to another.
;.................... Historical Background. Discoveries in the basic realm of molecular biology over the past five years have led to the realization that RNA has a series of distinct capabilities and biological activities 25 previously unsuspected. l'he most important of these novel RNA-- level discoveries has been the finding that RNA can be an enzyme as ,~, ~ well as an information carrier.
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Since 1982, several unexpected diseases caused by RNA-based pathogenic agents have emerged. These include the lethal 30 Acquired Immune Deficiency Syndrome (AIDS) and delta hepatitis, a particularly virulent form of fulminant hepatitis caused by a viroid-, J lL~ce RNA agent. These blood-borne diseases are spread at the RNA
tl level, manifest themselves in cells of patients, and are by now present ~ vithin the bloodstream of rnillions of individu ls. Conventional '~' ^, .

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biotechnology, with its reliance on recombinant DNA methods and DNA-level intervention schemes, has been slow to provide valid approaches to combat these diseases.
Hepatitis B Virus (H~V!
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S HBV, a member of a group of small DNA-containing viruses that cause persistent noncytopathic infections of the liver, is an infectious agent of humans that is found worldwide and which is perpetuated among humans in a large resenoir of chronic carriers. It is estimated that about 6-7% of the earth's population is infected (300 - 10 million carriers). The prevalence of the infection is not uniform throughout the world. There is a geographic gradient in distribution of HBV. It is lowest in North America and Western Europe, where the virus can be detected in 0.1 to 0.5% of the populatior, and highest in Southeast Asia and sub-Saharan Africa, where the frequency of infection may vary from 5 to 20% of the population. This skewed distribution parallels that of hepatocellular carcinoma and provides strong epiderniologic evidence for an association between chronic HBV infection and this type of malignancy.
Hepatitis B is of great medical importance because it is probably the most common cause of chronic liver disease, including hepatocellular carcinoma in humans. Infected hepatocytes continually ~; secrete viral particles that accumulate to high levels in the blood.
These particles are of two types: (i) noninfectious particles consisting of excess viral coat protein (HBsAg) and cont~ining no nucleic acid (in concentrations of 10'3 particles/ml blood), and (ii) infectious, DNA-containing particles ~Dane particles) consisting of a 27 nm nucleocapsid core (HBcAg) around which is assembled an envelope `~ containing the major viral coat protein, carbohydrate, and lipid, present in lower concentrations (10' particles/ml blood). The DNA
genome is about 3000 nucleotides in length, circular and partially `` single-stranded, sontaining an incomplete plus strand. The incompleteplus strand is complexed with a DNA polymerase in the virion which, .

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,.,,, - ~ ,' ' ' ' . ' . " ', :' ' ., -, : ' WO gl/04319 2~ PCr/US90/05450 under appropriate in l~itro conditions, can elongate the plus strand using the complete minus strand as the template. These morphological and structural features distinguish hepatitis B viruses from all known classes of DNA-containing viruses.
S The replication cycle of hepatitis B viruses is also strikingly different from other DNA-containing viruses and suggests a close relationship with the RNA-contair~ing retroviruses. The principal unusual feature is the use of an RNA copy of the genome as an intermediate in the replication of the I)NA genome. Infecting DNA
genomes are converted to a double-stranded form(s) which serve(s) as a template for transcription of RNA. Multiple RNA transcripts are synthesized from each infecting genome, which either have messenger function or DNA replicative function. The latter, termed "pre-genomes," are precursors of the progeny DNA genomes because they are assembled into nucleocapsid cores and reverse-transcribed into `-~ DNA before coating and export from the cell. Thus each mature virion contains a DNA copy of the RNA pre-genome and a DNA
polymerase.
The first DNA to be synthesized is of ~unus strand polarity ;; 20 and is initiated at a unique site on the viral genetic map. Very small ; nascent DNA mtnus strands (less than 30 nucleotides) are covalently linked to a protein, and are likely to act as primer for minus strand - DNA synthesis. Growth of ~be minus strand DNA is accompanied bya coordinate degradation of the pre-genome so that the product is a full-length single-stranded DNA, rather than an RNA:DNA hybrid.
Plus strand DNA synthesis has been observed only after completion of `; the minus strand, and initiates at a unique site close to the 5' end of ` - the minus strand. Complete elongation of the plus strand is not a requirement for coating and export of the nucleocapsid cores, thus most extracellular virions contain incomplete plus strands and a large single-stranded gap in their genomes.

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The Causative Agent of Delta Hepatitis: Hepatitis Delta Virus fHDV
The first evidence for the existence of hepatitis delta agent was the discovery by Dr. Mario Rizzetto in 1977 in Italy of the delta hepatitis antigen as a novel nuclear antigen in liver biopsies from 5 patients with chronic hepatitis B virus. Carriers expressing this antigen exhibited a greater incidence of severe chronic active hepatitis and cirrhosis; the antigen was also implicated in a substantial number of cases of fulrninant hepatitis. Chimpanzee transrnission studies showed that a defective viral agent was associated with delta hepatitis, 10 and that, to replicate, this agent required HBV or another hepadna virus. It was later shown that HDV replicates efficiently and suppresses helper replication, and can thereby lead to substantially higher titers of HDV relative to the hepadna virus.
HDV is now known to be endernic among the HBV carrier 15 population in all parts of the world, where it occurs either as the result of super-infection of the HBV carrier individuals or as an acute co-infection. The consequences of the infection seem to depend upon the prior status of the patient with respect to HBV. Co-infection with both HBV and HDV of an HBV-naive individual is apparently less 20 dangerous than the superinfection of an individual who already has a chronic active HBV infection. In the latter case, the apparent extent , - of liver damage is greatly enhanced with a major risk of death from fulminant hepatitis. Examples of the latter are epidemics of HDV in parts of South America and Central Africa. The virus is found in 25 southern Europe, the Middle East, and parts of Africa, South America, and the South Pacific. Interestingly, HDV infection is somewhat rare in the Orient even though the prevalence of HBV is high in that part of the world. The spread of HDV is by mechanisms sirnilar to that of HBV, by parenteral and transmucosal routes, so the 30 population at risk in non-endemic areas is similar. These include, in order of frequency, intravenous drug addicts, recipients of blood products, and male homosexuals.

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WO 9l/04319 Pcr/US90/05450 In infectious sera, HDV particles of about 35-37 nm in diameter have been distinguished from the 42 nm Dane particles and 22 nrn surface antigen moieties derived from HBV. The HDV virions have an envelope in which the hepatitis B surface antigen (HBsAg) is 5 embedded. This complex encapsidates the hepatitis delta antigen (HDAg) and the single-stranded RNA genome of 1.7 kilobases (kb) (Fig.1).
Molecular studies of the HDV RNA genome have shown that it has a circular conformation, unlike any other known animal 10 virus, and has the ability to fold on itself by intramolecular base pairing to forrn an unbranched rod structure. The generation of recombinant probes to HDV has made it possible to study the intracellular replication of the genome. HDV replication is unlike that of the helper hepadnavirus in that it does not involve reverse 15 transcription. HDV genome replication actually involves the copying of the genomic RNA into a complementary RNA, called the antigenornic RNA, which in turn acts as the template for the synthesis of more genomic RNA. In infected cells the genomic RNA is present ~- in approximately 5- to 20-fold excess relative to the antigenom~c RNA.
20 HDV genomic RNA can accumulate in the infected liver to a level of 1% of all liver RNAt which corresponds to an average of 300,000 copies per liver cell.
In surnmary, several aspects of HDV genome replication serve to differentiate this virus from other anirnal viruses: the HDV
25 virion genome is a single-stranded RNA of about 1,700 nucleotides; at least 96% of the genomic RNA is in a circular conforrnation; the genomic RNA has the ability to fold on itself by base pairing to create ;~
- an unbranched structure; intracellularly, there is not only genomic RNA but also, in a relatively lower amount, a complementary RNA
30 called the antigenomic RNA; most of the intracellular genomic and antigenornic RNA species are monomeric, of unit genome length;
most of those monomers have a circular conformation; multimeric ., .

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lengths of genomic and antigenom~c RNAs are present intracellularly at low levels relative to monomeric RN~
Current evidence indicates that the rolling-circle model of replication ~or plant viroids is applicable to HDV, as reported by S Chen, et al., Proc. Natl Acad. Sci. Il~A 83: 8774-8778 (1986). This mode of replication requires RNA cleavage and ligation to produce progeny monomer circles, reactions which can occur in vitro with HDV
RNA in the absence of proteins. Several laboratories have demonstrated that ribozyme activities, sequence-specific RNA
catalysts, are embodied within the genomic and anti-genornic sense strands of HDV. Self-cleavage has been shown to occur at unique sites on each strand and the junction fragments, as in virusoid self-cleavage, contain a cyclic 2'3'-monophosphate and 5'-hydroxyl terrnini.
In addition, it has been shown that subfragments, of 110 nucleotides or less around the cleavage site, of delta RNA can undergo autocatalytic cleavage at a faster rate and relatively low Mg ~ concentrations, in comparison with other ribozymes.
; Back~round on ribozvmes:
There are five classes of ribozymes now known which are involved in the cleavage and/or ligation of RNA chains. A ribozyme is defined as an enzyme which is made of RNA, most of whish work on RNA substrates. Ribozyrnes have been known since 1982, when Cech and colleagues (Cell, 31: 147-157) showed that a ribosomal RNA
precursor in tetrahymena, a unicellular eukaryote, undergoes cleavage catalyzed by elements in the RNA sequence to be removed during the conversion of the rRNA precursor into mature rRNA. This sequence .~ to be removed (called an intervening sequence or intron) is one of what are now known to be numerous examples of "Class I" intron ribozyme activities. A similar "Class II" intron nbozyme mechanism ` 30 was discovered more recently, involving the cleavage and subsequent ligation of a number of yeast mitochondrial RNAs (Nature, 324: 429-433). Cech and colleagues described certain in ~itro applications of .

WO 9l/04319 ;~r~ Q~ ~ PCr/US90/05450 "class I" ribozymes in PCI/US887/03161 by University Patents, Inc., (published as WO 88/04300 16 June 1988). Their potential for therapeutic applications in cells and in patients remains unclear.
A third class of ribozyme, discovered in 1983, was the first 5 to be shown to work in trans (i.e., to work under conditions where the ribozyrne is built into one RNA chain while the substrate to be cleaved is a second, separate RNA chain). This ribozyme, called M1 RNA, was characterized in 1983 by Altman and colleagues as responsible for the cleavage which forms mature 5' ends of all transfer 10 RNAs (tRNAs) in E. coli. Analogous RNA ribo~nes concerned with tRNA synthesis have since been found in all cells in which they have been sought, including a number of human cell lines.
The two remaining ribozyme classes are related to the replication cycle of a group of self-replicating RNAs called "viroid-15 like pathogens", or VLPs. Plant viroids, RNA satellites of plantviruses, and the delta agent are all members of the VLP group. In - 1984, Branch and Robertson (Science, 233: 45W55) published the replication cycle strategies for thee pathogens, subsequently verified by experiments conducted in several laboratories. A key element of 20 this "rolling-circle" replication strategy is that the VLP undergoing ` replication makes greater-than-unit-length copies of its information, which are then cleaved to monomeric size by ribozyrne activities built into the RNA of the VLP itself. One class of VLP ribozyrnes is defined by a small structural domain~ consisting of only about 30 25 nucleotides, called a "hammerhead". Uhlenbeck (Nature ~, 596-600, 1987) and Forster and Symons (Cell 50, 9-16, 1987), defined the ; requirements for cleavage by this riboz~ne class. Various embodiments and potential applications have also been described by .~ Haseloff, Gerlach and Jemungs in PCI`/A U88/00478 by 30 Cormmonwealth Scientific and Industrial Research Organization ; ~' (published as WO 90/05852 29 June 1989).
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WO 91/04319 ~ C~ PCr/US90/05450 The delta agent RNA also replicates by a rolling circle mechanism, and ribozymes are key in cleaving multimeric genomic and anti-genomic RNAs to monomers. Sharmeen at. al., J. Virol., 62, 2674-2679 (1988); Branch, et. al., Science, 243, 649-652 (1989); and Wu and Lai, Science 243, 652-655 (1989), defined the ribozyme cleavage points of both delta strands and the domains containing them. In U.S. Serial No. 07/411,713, the properties of these ribozyme elements were summarized and their use in anti-viral therapy delineated.
It is an object of the present invention to provide methods and compositions for delivering therapeutic entities incorporating targeted ribozymes to cells to bring about a specific therapeutic effect therein.
It is another object of the present invention to provide methods and compositions for delivering genes encoding specific proteins to cells, such as hepatocytes, for expression therein.
It is a further object of the invention to provide methods and compositions based on hepatitis delta virus, or other viruses, whose replication cycle is or can be engineered to be self-limiting.
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Summar~ of the Invention ~` The scope of delta's use as a vector is broadened in the ' present invention in several important ways. In one embodiment, a ~~ delta RNA genome capable of self-replication is enlarged to carry additional information, either coding for messenger RNA for a ~ 25 protein, or for a targeted ribo~yme~ which can be delivered specifically -~ to liver cells using delta's nonnally infectious properties, or to othercell types using chimeric delta viral agents car~ying altered surface proteins. In another embodiment, the delta vector is made self-limiting, so that its role in delivering targeted information is separated from its viral property of unlirnited infectious replication. Targeting of RNA is achieved through the use of sequences in the vicir~ity of the ., . .
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delta sequences which interact specifically with sequences at or near the site to be cleaved.
These embGdiments are particularly useful in the treatment of viral diseases such as hepatitis B and human immunodeficiency 5 virus (HIV) infections.

Brief Description of the Drawings Figure 1 is a schematic of the structure of HDV. The envelope (shaded) composed of HBsAg is derived from hepadna viruses (hepatitis B). The interior contains a self-annealing circular 10 RNA and the delta antigen (HDAg).
Figure 2 is a schematic of infection and replication by HBV and coinfection and replication by HDV.
Figure 3 is the proposed secondary structure of the 110 (662-771) nucleotide subfragment of the genomic sequence of hepatitis - 15 delta which possesses autocleavage activity~ Arrow indicates the site of cleavage. The top half of the stem (nucleotides 662-707) depicts the putative substrate half of the self-cleaving RNA while the bottom half of the stem (nucleotides 708-771) depicts the putative enzyme half of the molecule. This exarnple of a proposed secondary structure was derived using Tinoco energy rules and the dynarnic programming rules of Zuker.
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Detailed Description of ~he Invention While ribozymes are an important part of the delta viral RNA life cycle, and represent one of the several therapeutic 25 approaches using delta RNA vectors described herein, the major underlying theme of the methods and vectors disclosed here is that delta RNA can be used as a self-lirniting vector to carry therapeutic information (in the forrn of ribo~yme RNAs or proteins) into liver and other cells; and that delta vectors can do all of this at the RNA level .
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without involving or altering the chromosomal DNA in the cells of the treated patient.
Delta viral RNA vectors have been constructed carrying the ribozymes needed for their own amplification as well as those targeted for specific RNA sequences in pathogenic agents. The principal emphasis here is on the role of delta virus as a vector to deliver mRNA sequences and ribozymes to appropriate targets, and to use the self-replica~ing capability of delta to amplify the needed information for the most effective therapy. Information can be added to the basic genome comprising at least 1100 bases above the canonical 1679-base length, so that targeted ribozymes or templates for mRNA can be carried into target cells, where their RNA will be arnplified, and/or work in trans on specific target RNA sequences. In the latter case, targeting sequences are added to the delta genome and the composite RNAs packaged into particles and introduced into liver or other cells as appropriate. An enlarged delta genornic RNA is constructed embodying one or more additional ribozymes, over and above the two ribozymes required for the normal delta replication cycle described in the background of this invention. The additional s 20 ribozyme(s) is positioned at a point in the genome which does not ~ interrupt any critical RNA structures, and will cleave in trans only - ~ when the targeted sequence of the virus being treated is detected.
~ The applications described in detail in the examples below - can be surnmarized as follows~ Delivery to the liver of delta viral RNA embodying ribozyme activi~ies targeted to HBV mRNAs; (2) Delivery to the liver of delta viral RNA carrying mRNA for specific . liver or other non-liver proteins; (3) Construction of packaging celllines for production of delta viral particles for delivery to the liver or other tissues; ~4) Implementation of a built-in "self-limiting" approach - 30 to the delta-based RNA vectors to be used, allowing amplification oftheir information as RNA but limiting their spread as infectious agents; (5) Construction of "chimeric" delta vectors carrying altered '~, / ~
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surface proteins allowing them to target to non-liver cells, e.g. T-cells;
and (6) Construction of defective, non-replication competent retroviral vectors, as an alternative to delta vectors, rnissing part of the envelope (env) gene and/or other gene segrnents, for use as self-limiting alternative carriers of riboz3 mes.
These new vectors provide a therapeutic means to treat a varie~ of diseases, especially those of viral origin, as well as diseases resulting from a deficiency or defect in specific protein expression.
For example, the pattern of growth and replication of hepatitis B, the helper virus providing surface protein for the delta viral particles, in liver cells capable of infection by delta vectors makes it particularly susceptible as a target for anti-viral therapy using the modified delta hepatitis vectors. Another virus particularly well suited for use as a target is the human imrnunodeficiency virus (HIV), using the modified delta vector to cleave and thereby inactivate critical RNA encoding HIV proteins and the HIV genome itself. A variety of disorders can be treated using the delta vectors to specifically infect and deliver RNA encoding the desired proteins to liver. For example, the genes encoding liver proteins such as coagulation factors or non-liver - 20 proteins such as insulin, can be directed to liver cells using the modified delta vectors.
There is a variety of available HDV sequences isolated from different geographic locations which show a spectrum of - ` pathogenicity ranging from severe to ve~y mild. For example, there is a strain isolated from the Mediterranean area (Naples) which presents with nearly 50~o of patients having fulminant hepatitis (Sherlock, S.
and Thomas, H.C. J.Hepatology, 3: 419423 (1986)) in contrast with strains from the Pacific area (Melbourne) which showed no fulminant hepatitis in lQ0% of the cases (Jacobson, I.M., et al., J.Hepatology, 5:
~, 30 188-191 (1985)). Use of the mild strains ensures virus vectors that are minirnally toxic to the host.
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The present invention will be further understood by reference to the following non-limiting examples.
Example 1: Delivery to the liver of delta viral RNAs car~ing ribozyme activities targeted to HBV mRNAs.
5Hepatitis B virus (HBV) infection is common throughout the world, often causing severe disease symptoms and sometimes even death. As shown in Figure 1, the envelopes of HDV virions have the hepatitis B surface antigen (HBsAg) on their exterior, which targets the viral particle to hepatic cells. The interior contains a self-annealing circular RNA and the delta antigen (HDAg). Figure 2 is a schematic of infection and replication by HBV and coinfection and replication by HDV. The specific targeting ability of delta virus can therefore be used for the delivery of riboyme activity directed against HBsAg mRNA, or against mRNA encoding other HBV proteins, to hepatic cells infected with HBV.
As described in U.S. Serial No.07/411,713, HDV RNA
possesses an autocleaving riboz3/1ne activity at position 685/686 on the genornic strand and at position 900/901 on the antigenornic strand, ~' both of which are necessary for HDV replication. A 110 base fragment of the genornic RNA is capable of autocleavage. Analysis of the probable structure of this sequence, verifiable by ultraviolet cross-linking studies, reveals a closed structure with a spatial arrangement containing both a substrate and an en~ne portion, as shown in . Figure 3, and a cleavage site between nucleotides 685 and 686. Partsof this structure can be deleted without any effect on the riboz~ne ^~ activity. Separation of the two halves confers one half (662-707) with ~rp substrate-like properties and the other half (708-771) with eDzyme-like properties.
In one form of the construct having nbozyme activit~
directed against specific HBV RNA sequences, the stem portion of the enzyme half is replaced, for example, with a 15 nucleotide-long guide sequence complementary to the HBV RN.~ The site is so : ~ .

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Other forms of the construct having ribozyme activity would target cleavage sites by local tertiary RNA:RNA interactions or by common protein recogIution of features on the enzyme and subs~rate RNAs.
Such constructs are then capable of cleaving the HBV RNA at a site that is specified by the appropriate structural interactions.
Additional engineered ribozyme sequences can be built into HDV RNA at more than one site provided that they do not interfere with HDV replication. The cloning procedures are carried out on the cDNA sequence corresponding to the entire HDV genome, using standard polymerase chain reaction techniques to clone the anti-HBV
ribozyme fragment into the HDV cDNA at the specified site. In one approach to constructing appropriate delta vectors, a sequential lS trimer of HDV cDNA is constructed and cloned into a eukaryotic SV40 expression vector plasmid downstream of a SV40 early gene promoter. The plasmid is then transfected into a hepatic cell line.
The resulting RNA transcript is a trimeric RNA of the delta which is processed into self-replicating monomeric delta RNA. The SV40 ; 20 promoter is necessary to produce the initial round of the trimeric - RNA transcripts, which then becomes self-replicating. In a second approack to constructing appropriate delta vectors, appropriately engineered DNA inserts carrying delta sequences under the control of T7 or SP6 promoters can be transcribed in vitro with bacteriophage T7 or SP6 RNA polymerases and the resulting RNAs can be introduced into cell lines by lipofection or similar means.
This delta RNA is packaged in virions possessing HBsAg using special cell lines expressing HBsAg. Upon introduction of the engineered delta virus into the bloodstrearn of a patient infected with HBV, the delta virus specifically infects the hepatic cells. Once inside such cells, the delta virus replicates to produce high copy levels of the . genorne which can then cleave the HBsAg rnRNA, other HBV

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Hepatitis delta virus possesses considerable internal complementarity in the sequence of its genome. E',y virtue of this property, the ribozyme region of the anti-genornic strand of delta is very sirnilar in sequence to the ribozy~ne region of the genomic strand;
however, the cleavage on the anti-genomic strand occurs between nucleotides 900 and 901 instead of 685 and 686. Secondary structure predictions of the antigenomic strand around the ribozyme cleavage site reveal a very similar structure to that of the genomic strand shown in Figure 3 with corresponding stems and loops. This structure can be engineered to produce both enzyme and substrate halves, as is the case for the genomic strand, that can function as a trans-acting ribozymie. Delta vectors also can be engineered to use this anti-genornic ribozyme activity to cleave HBV or other RNA molecules, as well as the ribozyme activity embodied within the genomic s~rand.
Example 2: Example of using delta agent as an RNA-level vector for the specific delivery of protein-coding sequences.
As described above, delta virus has a specific tropism for - 20 liver because of the presence of HBsAg as the sole component of the virus coat, presumably by interaction with a specific and unique receptor on the liver cells for that antigen. Accordingly, a gene encoding a protein (to be preferentially expressed in hepatic cells) can be inserted with an appropriate start and stop codon for intracellular expression of that protein. The antigenomic strand of the delta has several open reading frames (ORFs) but only ORF5, which codes for the delta antigen, is translated in infected liver cells. Accordingly, the sequence coding for the protein of interest will be inserted under the control of ~hese translational signals for construction of an expression vector targeting hepatic cells.
~: The isolation of a delta variant whose genome contains2,942 nucleotides, in contrast with 1,679 nucleotides found in the ., ~

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-lS-canonical delta virus, demonstrates the feasibility of inserting extra protein coding sequences into the delta viral RN~
In preferred applications in vivo, patients having deficiencies in liver proteins such as alcohol dehydrogenase or blood 5 clotting proteins, such as anti-hemophilic factor, are infected with an appropriate delta viral RNA vector to enhance or replace the deficient or rn~ssing protein. Delta vectors carrying se~uences for non-liver proteins, such as insulin, can also be infected into liver cells for systernic release.
10 Example 3: Development of packa~ng cell lines for growth of delta nral particles fcr targeting of the liver or other tissues as appropriate.
Engineered delta viral RNAs, whether possessing ribozyme activities directed against viral or cellular mRNA, as described in 15 Example 1 and modifications thereof, or possessing translatable RNA
sequences for production of proteins, as described in Exarnple 2, must be packaged into virions before they can be used as drug delivery vehicles for targeting informaeion to specific tissues. In order to package delta RNA into virions coated with HBsAg, a trimer of the 20 engineered delta cDNA under the control of a SV40 promoter is -~ constructed and transfected into hepatic or other cell lines expressing large amounts of HBsAg. Such cell lines can be of mamrnalian (for example, HepG2) or yeast origin and can be easily constructed by transfection of the HBsAg gene under the control of an SV40 25 promoter, vaccinia virus promoter, or other appropriate promoter.
Shuttle vector plasmids carrying the SV40 prornoter are commercially available from Pharmacia.
` Clones expressing large amounts of HBsAg are selected and grown in culture. When the engineered trimeric delta cDNA, or 30 an appropriate RNA copy, is transfected or lipofected into these cell lines, the replicating delta packages itself in virions, to yield an RNA:delta-antigen complex enveloped by HBsAg protein. These .

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virions bud from the membrane of infected cells and can be collected from the cell culture supernatant and used for subsequent infections.
When the engineered ribozyme activity of the delta is directed against the HBsAg mRNA, a cell line that produces HBsAg RNA in excess of S the capacity of the ribozyme to destroy it is used for production of the modified virus.
For the production of chimeric delta vectors, described in example 5, cell lines producing the specific surface antigen of the new delta virus vector must be used. For example, to package chimeric 10 delta virus RNA in.o pseudo-HIV virions, the altered delta viral cDNA is transfected into a cell line expressing the HIV envelope glycoproteins. The resulting chimeric delta virions are surrounded by the HIV coat proteins and are able to speci~lcally target CD4- cells in the same manner as wild-type HIV-1.
15 Example 4: Development of "self-limiting" delta-based RNA
ectors for amplification of their infonnation 8S
RNA but limited with respect to their spread as infectious agents.
The success of an anti-viral drug is measured by its ability 20 both to destroy the pathogenic virus and to be minimally toxic to the host. To that end, virus vectors whose propagation is self-limiting have been created. This achievement is made possible in the case of delta - virus because its replication is helper virus dependent (Fig.2).
Although delta virus RNA can replicate in any cell type, it cannot 25 form infectious particles without the help of the HBV-supplied surface - antigen, which is why infectious delta virus particles can only be produced in HBV-infected patients. Engineered delta virus vectors carrying a ribozyme directed against HBV surface antigen and/or core antigen mRNA or the HBV pregenome RNA, as detailed in Example 30 2, can be used to infect the liver of a HBV-infected patient, and ~` thereby destroy the HBV by virtue of its anti-HBV ribozyme activity.
By this process, the HDV deprives itself of the HBsAg necessary for ,:

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-WO 91/04319 ~,~C~i$~ PCI/US90/054S0 further production of infectious delta particles. Eventually, when all the HBV RNA has been destroyed, the delta virus will no longer be able to produce infectious particles and its spread will thereby be limited. This self~ uting replication scheme also limits the toxic 5 effects normally associated with viremia.
Example 5: De~elopment of chimeric delta vectors car~ing altered surface proteins which allow them to be delivered to non-liver cells.
Although delta virus is an excellent vector for the specific 10 delively of ribozymes and mRNA sequences to liver cells by virtue of - HBsAg on the surface of the virion, it cannot be used in unmodified form for the delivery of therapeutics to any other cell types. To circumvent this limitation, delta vectors vith altered specificity for cell types other than hepatic cells are constructed.
Delta virus RNA encodes the delta antigen ~HDAg), a 27 kd protein, on its anti-genomic strand. Genomic delta RNA is surrounded by this antigen before being enveloped by the HBsAg to form infectious HDV particles (Fig.1). The arnino terminal domain of the delta antigen binds strongly to the delta RNA. It is the C-20 terminal domain of the antigen that binds to HBsAg envelope protein provided by helper HBV.
Like delta virus, retroviral RNAs, such as HIV, are surrounded by a protein before they are directed into the budding envelope. The gag protein is the retroviral equivalent of the delta ; 25 antigen. VVhen delta RNA corresponding to the C-terminus of the delta antigen is replaced with RNA sequences encoding the gag protein of HIV, the product is a chimeric delta antigen-gag protein, which can bind to delta RNA by virtue of the delta antigen N-terrninal sequences. When this delta RNA is replicated, as in 30 example 3, in a cell line expressing the HIV envelope proteins, the RNA surrounded by the chimeric protein will package itself into virions whose envelope is composed of HIV proteins. These chimenc .

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delta viral particles, by virtue of the HIV glycoprotein envelope, will have specificity for CD4' cells. If the genome of this delta virus is also carrying a ribozyme against the env o~ gag rnRNA of HIV, as described in Example 1, and is used to superinfect T-cells previously S infected with HIV, the chimeric delta virus will recogruze the CD4 molecules on the T-cells and will infect those cells. The delta RNA
will replicate and its HIV-specific ribozyme will destroy the HIV
sequences. The delta vector will form new infectious particles as long as sufficient HIV env protein remains available to allow assembly and spread. Similarly, the chimeric vector can infect stem cell in vitro, which can then be used in an autologous bone marrow transplant in a partially cytoablated patient to create a population of T-cells that are resistant to HIV because of the presence of a ribozyme directed against HIV sequence(s).
The same technique can be used to create a variety of chimeric delta antigens possessing the N-terminus of the delta antigen , and the surface antigen of another virus of choice to produce pseudo-virions with altered cell specificity.
Example 6: Development of defective retro~iral ~ectors for targeting ribozymes.
Retroviral vectors also caII be used to target anti-viral ribozymes to various cell types. Unfortunately, only very limited numbers of human retroviruses are known which show speci~lcity for `- limited number of cell types. In this example, defective viruses are used as a vector for ribozymes. The specific example uses a defective HIV vector carrying a ribozyrne targeted to HIV mRN~ The vector can target itself to CD4+ cells but cannot produce infectious virions.
In one embodiment, a retroviral vector capable of targeting HIV infected cells is created by deleting 10~200 nucleotides from the env gene and replacing it with a ribozyme targeted against the same region of the HIV RNA or to other regions of the HIV RNA (for , example gag). The engineered HIV RNA is packaged in cell lines , : . .
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expressing the surface glycoproteins of HIV. The resulting virus particles are isolated from the culture supernatant and used to infect patients infected with HIV. The defective HIV virus particles carrying the ribozyme are able to target to the CD4~ cells, where they are S endocytosed and uncoated. These particles can then replicate and express the anti-HIV ribozymes and inactivate the HIV RNA particles.
These altered HIV particles can form infectious particles only if they are provided with the envelope glycoproteins necessary for the formation of whole virions.
This general method can be applied to other retroviruses and possibly other non-retroviruses to produce defective and "self-lirniting" viruses to carry ribo~ymes to destroy the native virus.
Modifications and variations of the methods and resulting targeted vectors having ribozyme activity will be obvious to those skilled in the 15 art from the foregoing detailed description. Such modifications and variations are intended to come vithin the scope of the appended claims.

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Claims

We claim:

1. A vector for delivering a ribozyme to a cell to specifically cleave RNA in the cell comprising hepatitis delta virus RNA having ribozyme activity in combination with nucleotide sequences specifically binding targeted nucleotide sequences in the cell, wherein the sequences are positioned at a point in the delta virus RNA which does not interrupt any critical RNA structures, and the hepatitis delta virus RNA contains sufficient sequence and is of appropriate secondary structure to replicate in the cell.

2. The vector of claim 1 wherein the hepatitis delta virus RNA comprises nucleotides between delta genomic nucleotides 708-771 having enzymatic activity.

3. The vector of claim 1 wherein the hepatitis delta virus RNA comprises delta virus anti-genomic nucleotides including residue 900 and flanking nucleotides having enzymatic activity.

4. The vector of claim 2 wherein the stem portion of the enzymatically active delta virus RNA includes sequences for specific targeting to defined RNA substrates.

5. The vector of claim 1 wherein the hepatitis delta virus RNA comprises nucleotides from a hammerhead ribozyme of the class derived from plant viroid-like pathogens having enzymatic activity.

6. The vector of claim 1 in a cell line with DNA encoding HBsAg under the control of an appropriate promoter.

7. The vector of claim 6 wherein the cells are hepatic cells.

8. The vector of claim 1 in a CD4+ cell line with DNA
encoding HIV envelope glycoproteins.

9. The vector of claim 1 wherein the ribozymes are targeted to sequences such that cleavage of the sequences by the ribozyme result in inactivation of RNA selected from the group consisting of oncogenes, tumor suppressor genes, viral genes, and cellular mRNAs which encode proteins selected from the group consisting of enzymes, hormones, cofactors, antibodies, and growth factors.

10. The vector of claim 1 comprising a chimeric sequence encoding a targeted viral protein in combination with a hepatitis delta viral protein.

11. A method for constructing a vector for delivering a ribozyme to a cell to specifically cleave RNA in the cell comprising:
providing cDNA transcribed as hepatitis delta virus RNA
having ribozyme activity in combination with nucleotide sequences specifically binding targeted nucleotide sequences in the cell, wherein the hepatitis delta virus RNA contains sufficient sequence and is of appropriate secondary structure to replicate in the cell, and the targeted sequences position the ribozyme activity at a site to be cleaved.

12. The method of claim 11 wherein the hepatitis delta virus RNA comprises nucleotides between delta 708-771, further comprising altering the nucleotide sequence to maximize enzymatic activity.

13. The method of claim 12 wherein the stem portion of the enzymatically active delta virus RNA is substituted with binding sequences.

14. The method of claim 11 wherein the targeting sequences are synthesized based on a sequence of the viral genome to be cleaved.

15. The method of claim 14 wherein the viral genome is hepatitis B virus.

16. The method of claim 14 wherein a hepatitis delta virus-complementary viral sequence is cloned by the polymerase chain reaction.

17. The method of claim 11 wherein a sequential trimer of the hepatitis delta sequence is constructed.

18. The method of claim 17 wherein the trimer is cloned into a eukaryotic viral expression vector downstream of a viral early gene promoter.

19. The method of claim 18 wherein the vector and promoter virus is SV40.

20. The method of claim 11 wherein a greater than unit length DNA insert encoding the hepatitis delta sequence is constructed.

21. The method of claim 20 further comprising packaging the hepatitis delta virus construct into a cell line expressing a specific surface antigen recognized by selected cells.

22. The method of claim 21 wherein the construct is transfected into the cells.

23. The method of claim 21 wherein the greater than unit length delta RNA synthesized in vitro is lipofected into a cell line expressing a specific surface antigen recognized by selected cells.

24. The method of claim 21 wherein the specific surface antigen is HBsAg and the selected cells are hepatic cells.

25. The method of claim 21 wherein the specific surface antigens are HIV envelope glycoproteins and the selected cells express CD4 antigen on their surface.

26. The method of claim 21 further comprising collecting the packaged delta viral RNA complex budded from the membrane of the infected cells.

27. The method of claim 16 wherein a greater than unit length delta sequence is cloned into a prokaryotic expression vector downstream from a bacteriophage RNA polymerase promoter.

28. The method of claim 27 wherein the vector is derived from a bacterial plasmid and the promoter is derived from bacteriophage selected from the group consisting of 1-7 and SP6.

29. The method of claim 28 wherein the vector is selected from the group consisting of PBR322 and PUC.

30. The method of claim 11 further comprising providing at least one additional ribozyme to those needed for normal delta replication, positioned at a point in the genome which does not interrupt any critical RNA structures, which will cleave in trans only when the targeted sequence is bound.

31. A vector for expression of a protein in a cell comprising hepatitis delta translational control sequences located 5' to the initiation codon of hepatitis delta virus open reading frame 5 in combination with a sequence encoding a protein to be expressed in the cell.

32. The vector of claim 31 packaged with specific surface antigen recognized by selected cells.

33. The vector of claim 32 wherein the selected cells are hepatic cells.

34. The vector of claim 33 wherein the protein encoding sequence encodes a protein expressed by an organ selected from the group consisting of liver, pancreas, spleen, stomach, intestine, and brain.

35. The vector of claim 34 wherein the protein encoding sequence encodes a protein selected from the group consisting of blood clotting proteins, enzymes, hormones, cofactors, antibodies, growth factors, oncogenes, and tumor suppressor genes.

36. A cell line for packaging a hepatitis delta viral vector, wherein the cell line expresses a specific coat protein allowing the packaged viral vector to interact with specific cell surface receptors during infection.

37. The cell line of claim 35 wherein the vector includes a viral promoter, translation start and stop signals, and sequences encoding the specific viral coat protein.

38. The cell line of claim 36 wherein the promoter is selected from the group consisting of SV40 promoters, vaccinia virus promoters, hepatitis B promoters, and delta promoters.

39. The cell line of claim 35 wherein the specific viral coat protein antigen is HBsAg.

40. The cell line of claim 35 wherein the specific viral coat protein antigens are HIV envelope glycoproteins.

41. A method for treating a viral infection comprising providing a vector comprising hepatitis delta virus RNA
having ribozyme activity in combination with nucleotide sequences binding to targeted viral nucleotide sequences in the cell, wherein the hepatitis delta virus RNA contains sufficient sequence and is of appropriate secondary structure to replicate in the cell.

42. The method of claim 40 wherein the virus is hepatitis B virus and the targeting sequences bind mRNA sequences encoding a protein selected from the group consisting of hepatitis B surface antigen and hepatitis B core antigen or the HBV pregenome RNA42.
The method of claim 41 wherein the target mRNA sequence is the HBsAg mRNA and the replication of the delta vector is rendered self-limiting by the inhibition of HBsAg protein synthesis.

43. The method of claim 40 wherein the C-terminus of the hepatitis delta virus RNA encoding the hepatitis delta antigen is replaced with sequence encoding an internal protein from another virus to form a new sequence encoding a chimeric hepatitis delta antigen-viral protein.

44. The method of claim 43 wherein the chimeric hepatitis delta antigen-viral protein encoding sequence can bind to delta RNA.

45. The method of claim 44 further comprising replicating the chimeric sequence in a cell line expressing additional proteins encoded by the virus being treated.

46. The method of claim 45 wherein the additional protein encoded by the virus is the env protein and the chimeric sequence packages itself into virions whose envelope is composed of non-hepatitis delta viral proteins.

47. The method of claim 45 wherein the hepatitis delta viral sequences having ribozyme activity are targeted to and cleave viral messenger RNA and/or genomic RNAs of the virus being treated.

48. The method of claim 45 wherein the protein sequences are the human immunodeficiency virus gag or env proteins.

49. The method of claim 48 used to treat a patient whose CD4+ cells are infected with HIV.

50. The method of claim 49 further comprising using autologous bone marrow transplantation in combination with the appropriate RNA vector to make a patient's T cells resistant to infection with human immunodeficiency virus.

51. The method of claim 45 wherein the target mRNA
sequence is the env protein, wherein the growth of the chimeric vector is rendered self-limiting by the inhibition of env protein synthesis.

52. A method for making defective retroviral vectors for targeting ribozyme delivery to specific cell types comprising a retroviral vector having ribozyme activity and sequences targeted to RNA sequences encoding proteins essential for replication of a virus.

53. The method of claim 52 wherein the specific cell type is liver and the essential proteins are hepatitis B proteins.

54. The method of claim 52 wherein the specific cell type is CD4+ cells and the essential proteins are human immunodeficiency virus proteins.

55. The method of claim 52 wherein the target RNA
encodes env protein of HIV and the replication of the defective retroviral vector is rendered self-limiting by the inhibition of env protein synthesis.

56. A defective retroviral vector comprising a retroviral vector having ribozyme activity and sequences targeted to RNA
sequences encoding proteins essential for replication of a virus.

57. The vector of claim 56 wherein the essential proteins are hepatitis B proteins.

58. The vector of claim 56 wherein the essential proteins are human immunodeficiency virus proteins.

59. The vector of claim 56 wherein the target RNA
encodes env protein of HIV and the replication of the defective retroviral vector is rendered self-limiting by the inhibition of env protein synthesis.