Patent Application
20190032088
The invention pertains to therapies that require gene editing, and more specifically to non-viral methods for in vivo delivery of endonuclease reagents to specific tissues or cells. According to the invention, the endonuclease reagents are encapsulated into micelle structures of 50 to 150 nm diameter for intravenous injection. The invention thus provides therapeutic composition including such micelles structures, by which endonuclease reagents can be released into cell under RNA form for their use in the treatment of gene related diseases.
The potential of gene editing in various therapies has long been envisioned by the applicant (WO2004067753), especially to repair or modulate the expression of deficient genes causing genetic disease, or to knock-out deleterious genetic sequences, either sexually inherited or introduced into the cells by infectious agents.
Since the emergence of the first programmable meganuclease reagents by the turn of the century (Smith et al. (2006) A combinatorial approach to create artificial homing endonucleases cleaving chosen sequences. Nucleic Acids Res. 34(22):e149), endonucleases reagents have rapidly evolved, offering improved specificity, safety and reliability. In particular, TALE-nucleases, which are fusions of a TALE binding domain with a cleavage catalytic domain (WO2011072246) have proven to be highly specific for therapeutic purposes (Leukaemia success heralds wave of gene-editing therapies (2015) Nature 527:146-147). TALE-nucleases are particularly specific when they are used by pairs under obligatory heterodimeric form, by using the dimeric cleavage domain of Fok-1. Left and right heterodimer members each recognizes a different nucleic sequences of about 14 to 20 bp, together spanning target sequences of 30 to 50 bp overall specificity.
More recently, further endonucleases reagents have been developed based on the components of the type II prokaryotic CRISPR (Clustered Regularly Interspaced Short palindromic Repeats) adaptive immune system of the bacteria S. pyogenes. This multi-component system referred to as RNA-guided nuclease system (Gasiunas, Barrangou et al. 2012; Jinek, Chylinski et al. 2012), involves members of Cas9 or Cpf1 endonuclease families coupled with a guide RNA molecules that have the ability to drive said nuclease to some specific genome sequences (Zetsche et al. (2015). Cpf1 is a single RNA-guided endonuclease that provides immunity in bacteria and can be adapted for genome editing in mammalian cells. Cell 163:759-771). Such programmable RNA-guided endonucleases are easy to produce because the cleavage specificity is conferred by the sequence of the guide RNA, which can be cheaply adapted. Their specificity although stands on shorter sequences than TAL-nucleases of about 10 pb, which must be located near a particular motif (PAM) in the targeted genetic sequence.
Various proofs of concept of the efficiency and safety of the above specific endonuclease reagents have been reported in human cells in-vitro or ex-vivo, but the delivery of the same reagents into the body has still to be very carefully considered due to the risk of off-site mutations inherent to such reagents. This risk increases when the reagents, which are mainly proteins, are being degraded in-vivo, altering their specificity and cleavage properties.
The primary challenge for gene therapy is thus to develop a method that delivers a therapeutic gene (e.g. transgene) or sequence specific reagent (e.g. nuclease) to selected cells where proper gene expression can be achieved. An ideal gene delivery method needs to meet 3 major criteria: (1) it should protect the transgene or reagent against degradation by nucleases in intercellular matrices, (2) it should bring the transgene or reagent across the plasma membrane and into the nucleus of target cells, and (3) it should have no detrimental effects (Gao, X. et al. (2007) Non-viral Gene Delivery: What we know and What is next. APPS Journal. 9(1) Article 9:92-104).
Viral vectors are able to mediate gene transfer with high efficiency and the possibility of long-term gene expression, may satisfy 2 out of 3 criteria. However, the acute immune response, immunogenicity, and insertion mutagenesis uncovered in gene therapy clinical trials have raised serious safety concerns about some commonly used viral vectors.
The inventors have explored safer means for in-vivo delivery and more particularly of endonucleases reagents, which could be used to target specific tissues into the human body especially delivery of sequence specific TAL-nucleases and Cas9/CRISPR into liver cells. They have determined that encapsulating nuclease reagent under RNA form in micelle structures of 50 to 100 nm was particularly appropriate to deliver the reagents into the nucleus of the cells by intravenous injection, in efficient amount and with limited off-site effects. This was primarily demonstrated by targeting cccDNA of HBV into liver cells, but this strategy has since been proven to be expandable to various type of cells by anchoring specific cell surface protein receptors or ligand into the micelle structures, as further detailed herein.
The present invention is drawn to a method for encapsulating an endonuclease reagent, wherein said endonuclease reagent is prepared under RNA form and complexed with at least one biodegradable matrix comprising at least a core hydrophobic domain and a proximal polar domain to form particles of 50 to 100 nm diameter range, suitable for in-vivo injection.
The endonuclease reagent is generally a RNA molecule coding for a sequence-specific endonuclease reagent, such as a homing endonuclease, a zing finger nuclease, or a TALE-Nuclease, or a RNA guide optionally co-delivered with a RNA-guided endonuclease, such as cas9 or Cpf1.
Various types of biodegradable delivery capsules comprising RNA endonuclease reagents can be manufactured, depending on the structure of the biodegradable matrices involved and the monomers forming said core hydrophobic domain and polar domains.
Such biodegradable delivery capsules according to the invention are useful to deliver endonuclease reagent into the cells under RNA form, especially when co-delivery of different endonuclease reagents is sought, like for instance, messenger RNAs encoding right and left heterodimer TALE-nucleases.
Delivery specificity can be improved by linking a targeting domain to the proximal polar domain of said biodegradable matrix, such that the delivery capsules of the invention can bind surface antigens of different cell types. The delivery capsules are particularly suited for intravenous injection to target endogenous genetic sequences into cells.
The present application more particularly claims pharmaceutical compositions comprising the biodegradable delivery capsules of the invention into treatments involving endonuclease reagents. Such treatments may be part of a gene therapy, where specific genetic sequences have to be knocked-out or repaired, of an anti-infection therapy, by targeting the genome of infectious agents, or cancer therapy. The biodegradable delivery capsules of the present invention have proven to be particularly adapted to treat infectious agents that present a DNA intermediate in the liver cells, such as the cccDNA (covalently closed circular DNA) of Hepadnavirus, in particular HBV (Hepatitis B Virus), which are resistant forms of these viruses lodged into hepatocytes.
A and B: Structures comprising a distal hydrophilic domain conjugated to a hydrophobic domain, itself conjugated to a proximal hydrophilic domain complexed with the endonuclease reagents under RNA form. In A, said proximal hydrophilic domain is optionally linked to an external binding protein, such as N-acetylgalactosamine. These structures self-assemble under micelles that harbor a central hydrophilic pocket.
C and D: Simpler structures consisting of a hydrophobic domain conjugated to the proximal hydrophilic domain, which is complexed with the endonuclease reagents under RNA form. In A, said proximal hydrophilic domain is optionally linked to an external binding protein, such as N-acetylgalactosamine.
Table 1: Exemplary list of target genes that can be modified by the gene editing method according to the invention and their associated diseases.
Table 2:: Engineered TAL-nucleases used in the in-vivo gene editing method to target HBV (cccDNA) and the genes encoding respectively APOC3, TTR, SMN2, IDOL, ANGPTL3, IDOL and PCSK9 (detailed target and polypeptide sequences are provided in Table 7).
Table 3 (
Table 4 (
Table 5: Quantitation of the PCR bands with Biorad Lab Image program obtained upon cleavage with the HBV TALENs of the present invention.
Table 6: Summary of the mice treatment schedule to target factor VII gene in the liver.
Table 7: TALE-nucleases engineered to target the HBV genome, APOC3, TTR, SMN2, IDOL, ANGPTL3 and PCSK9 genes, along with their polypeptide sequences et target polynucleotide sequences.
Unless specifically defined herein, all technical and scientific terms used have the same meaning as commonly understood by a skilled artisan in the fields of gene therapy, biochemistry, genetics, and molecular biology.
All methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, with suitable methods and materials being described herein. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will prevail. Further, the materials, methods, and examples are illustrative only and are not intended to be limiting, unless otherwise specified.
The practice of the present invention will employ, unless otherwise indicated, conventional techniques of cell biology, cell culture, molecular biology, transgenic biology, microbiology, recombinant DNA, and immunology, which are within the skill of the art. Such techniques are explained fully in the literature. See, for example, Current Protocols in Molecular Biology (Frederick M. AUSUBEL, 2000, Wiley and son Inc, Library of Congress, USA); Molecular Cloning: A Laboratory Manual, Third Edition, (Sambrook et al, 2001, Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press); Oligonucleotide Synthesis (M. J. Gait ed., 1984); Mullis et al. U.S. Pat. No. 4,683,195; Nucleic Acid Hybridization (B. D. Harries & S. J. Higgins eds. 1984); Transcription And Translation (B. D. Hames & S. J. Higgins eds. 1984); Culture Of Animal Cells (R. I. Freshney, Alan R. Liss, Inc., 1987); Immobilized Cells And Enzymes (IRL Press, 1986); B. Perbal, A Practical Guide To Molecular Cloning (1984); the series, Methods In ENZYMOLOGY (J. Abelson and M. Simon, eds.-in-chief, Academic Press, Inc., New York), specifically, Vols.154 and 155 (Wu et al. eds.) and Vol. 185, “Gene Expression Technology” (D. Goeddel, ed.); Gene Transfer Vectors For Mammalian Cells (J. H. Miller and M. P. Calos eds., 1987, Cold Spring Harbor Laboratory); Immunochemical Methods In Cell And Molecular Biology (Mayer and Walker, eds., Academic Press, London, 1987); Handbook Of Experimental Immunology, Volumes I-IV (D. M. Weir and C. C. Blackwell, eds., 1986); and Manipulating the Mouse Embryo, (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1986).
In a general aspect, the present invention relates to methods for encapsulating an endonuclease reagent, comprising the steps of:
The particles are formed from by the association of macromolecular structures as shown in
The elementary structures that build up the capsules by microfluidic mixing are preferably “biodegradable matrix”, meaning that that they can be made of various materials that can be degraded or eliminated by action of the enzymes naturally present into the body, preferably into the human body.
By “diameter range” is meant that the diameter is not strictly uniform. It corresponds to a statistical measure (distribution of the diameter of a number of particles) centered on a major value. This value is generally comprised between 50 and 150 nm, and more generally preferably set between 50 and 100 nm, more preferably between 50 and 90 nm, and even more preferably between 60 and 80 nm.
By “endonuclease reagent” is meant a nucleic acid molecule that contributes to an endonuclease catalytic reaction in the target cell, itself or as a subunit of a complex, preferably leading to the cleavage of a nucleic acid sequence target. The “endonuclease reagents” of the invention are generally sequence-specific reagents, meaning that they can induce DNA cleavage in the cells at predetermined loci, referred to by extension as “gene targets”, by specific recognition of a nucleic acid “target sequence”. Said target sequence is usually selected to be rare or unique in the cell's genome, and more extensively in the human genome, as determined by using the available human genome databases and related common software.
“Rare-cutting endonucleases” are sequence-specific endonuclease reagents of choice, insofar as their recognition sequences generally range from 10 to 50 successive base pairs, preferably from 12 to 30 bp, and more preferably from 14 to 20 bp.
According to a preferred aspect of the invention, said endonuclease reagent is a nucleic acid encoding an “engineered” or “programmable” rare-cutting endonuclease, such as a homing endonuclease as described for instance by Arnould S., et al. (WO2004067736), a zing finger nuclease as described, for instance, by Urnov F., et al. (Highly efficient endogenous human gene correction using designed zinc-finger nucleases (2005) Nature 435:646-651), a TALE-Nuclease as described, for instance, by Mussolino et al. (A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity (2011) Nucl. Acids Res. 39(21):9283-9293), or a MegaTAL nuclease as described, for instance by Boissel et al. (MegaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering (2013) Nucleic Acids Research 42 (4):2591-2601).
According to the invention, the endonuclease reagent is preferentially under RNA form to allow transient endonuclease activity of said reagent into the target cell and make the entire capsule biodegradable in-vivo. Even more preferably, the endonuclease reagent is under the form of a mRNA for the expression of the rare cutting endonuclease into the cells. The endonuclease under mRNA form is preferably synthetized with a cap to enhance its stability according to techniques well known in the art, as described, for instance, by Kore A. L., et al. (Locked nucleic acid (LNA)-modified dinucleotide mRNA cap analogue: synthesis, enzymatic incorporation, and utilization (2009) J Am Chem Soc. 131(18):6364-5).
Due to their higher specificity, TALE-nuclease have proven to be particularly appropriate for therapeutic applications, especially under heterodimeric forms—i.e. working by pairs with a “right” monomer (also referred to as “5′” or “forward”) and “left” monomer (also referred to as “3″” or “reverse”) as reported for instance by Mussolino et al. (TALEN® facilitate targeted genome editing in human cells with high specificity and low cytotoxicity (2014) Nucl. Acids Res. 42(10): 6762-6773). However, before the invention, it was difficult to deliver in-vivo pairs of TALE-nuclease, even using viral vectors, especially because TAL-nuclease are large proteins having long genetic sequences. Delivery of these reactive proteins in-vivo was therefore remaining a considerable challenge before the present invention. This was all the more challenging that the proteins are active and specific when they are simultaneously delivered into the cell nucleus. Otherwise, the activity may be lost or the reagents may become less specific increasing the risk of off-site mutations.
The inventors have more particularly sought how to efficiently target cccDNA (covalently closed circular DNA), an intracellular viral replication intermediate of some viruses, which forms persistence reservoir and key obstacle for a cure of viral disease.
The cccDNA of HBV is at the origin of some common forms of chronic hepatitis B. Upon infection, cccDNA is generated as a plasmid-like episome in the host cell nucleus from the protein-linked relaxed circular (RC) DNA genome in incoming virions. It has a fundamental role as template for all viral RNAs, and in the production of new virions in the liver cells (Nassal et al., HBV cccDNA: viral persistence reservoir and key obstacle for a cure of chronic hepatitis B. (2015) Gut 64 (12):1972-1984). Beyond the difficulty to deliver specific TALE-nucleases into the nucleus of liver cells, it must be recalled that HBV comprises different genotypes, at least 24 subtypes, displaying genome variability, which are reported to respond to treatment in different ways (Palumbo E., Hepatitis B genotypes and response to antiviral therapy: a review. (2007). American Journal of Therapeutics 14 (3): 306-9). As detailed in Example 1 herein, the inventors have designed specific TALE-nucleases that are able to target both the cccDNA of the main HBV subtypes, namely at least type A, B and C. The sequences of the successful TALE-nucleases used by the inventors to target HBV are listed in Table 7.
The present application claims any of the polypeptide or polynucleotide sequences having at least 80% identity, preferably at least 90%, more preferably 95%, and even more preferably 99% identity with any sequences referred to in Table 7. The present application claims the polynucleotides encoding said sequences, especially under RNA form.
The present invention more broadly provides a method for delivering in-vivo two endonuclease reagents under RNA form, preferably under mRNA, form to be expressed simultaneously into a cell.
Accordingly, the invention has also for object a pair of heterodimeric TALE- nucleases, preferably those targeting the cccDNA of HBV such as those referred in Table 2, which are encapsulated according to the method described herein to target liver cells—i.e.: into a biodegradable delivery capsule for gene targeting of a cell in vivo, characterized in that a endonuclease reagent under RNA form is complexed with at least one polar domain, which is linked to biodegradable conjugate(s) of hydrophobic monomers to form spherical particles as previously described.
According to another embodiment, the endonuclease reagent is a RNA-guide to be used in conjunction with a RNA guided endonuclease, such as Cas9 or Cpf1, as per, inter alia, the teaching by Doudna, J., and Chapentier, E., (The new frontier of genome engineering with CRISPR-Cas9 (2014) Science 346 (6213):1077), which is incorporated herein by reference.
According to a preferred aspect the RNA guide is complexed with its associated RNA-guided endonuclease protein into the hydrophilic domain of the capsule. Alternatively the RNA-guided endonuclease protein can be retained within the hydrophilic core of the micelle structure (situation where the elementary structures have a second distal hydrophilic domain as illustrated in
According to another embodiment, at least two different endonuclease reagents are encapsulated under RNA form into the particles, which means that, for instance, a RNA guide and mRNA encoding a RNA guided endonuclease can be both complexed with the distal hydrophilic domain of the matrix.
The present method provides that the core hydrophobic domain can be a biodegradable conjugate of hydrophobic monomers.
According to one aspect of the invention, said hydrophobic monomers conjugate comprise aminolipids, such as ionized cationic lipid 1,2-dilinoleyloxy-3-dimethylaminopropane (DLinDMA) as described elsewhere, for instance, by Hafez, I. M. et al. (On the mechanism whereby cationic lipids promote intracellular delivery of the polynucleic acids (2001) Gene Therapy 8:1188-1196). Said aminolipids can be advantageously mixed with PEG-lipids, since endogenous apolipoprotein E (Apo E) specifically targets these delivery systems to hepatocytes by Apo E-dependent, receptor mediated endocytosis. The core hydrophobic domain can also include structural lipids such as cholesterol and saturated phosphatidylcholine. Apo E mediated endocytosis is one of the mechanism by which capsules comprising hydrophobic domain with PEG-lipids more particularly target liver cells by mimicking intermediate-density lipoprotein (IDL).
According to an alternative aspect of the invention, said hydrophobic domain comprises a polymer, such as poly-N,N-di(C1-C6)alkyl-amino(C1-C6)alkyl-ethacrylate, poly-N,N-di(C1-C6)alkyl-amino(C1-C6)alkyl-methacrylate, or poly-N,N-di(C1-C6)alkyl-amino(C1-C6)alkyl-acrylate, or a combination thereof. Preferentially, said hydrophobic domain comprises monomers including at least (C2-C8)alkyl-ethacrylate, a (C2-C8)alkyl-methacrylate, or a (C2-C8)alkyl-acrylate, which can be mixed with carboxylic acid monomers and tertiary amino monomers.
According to the present invention, a proximal polar “targeting domain” can be covalently linked to the core hydrophobic domain to specifically target desired cell type or tissue. Such targeting domain can be linked through usual peptide linker, such as Gly-rich linkers (GSn linkers) according to standard procedures known in the art. By “targeting domain” is meant any molecule that may be inserted or linked to the matrix providing more affinity of the capsule to a cell type, more generally to a specific cell surface marker.
Said targeting domain are mostly ligand or binding domains that are reported to have some affinity with cell surface receptors or antigens. Binding domains can be fusion proteins comprising ScFvs from antibodies generated against a cell surface antigen.
According to a preferred embodiment of the invention, the targeting domain recognizes a cell surface antigen from a LDL or VLDL receptor, which are abundantly present at the surface of liver cells, allowing easier internalization of the delivery capsule. According to another embodiment, the targeting domain has affinity with heparan sulfate proteoglycans.
According to another aspect of the invention N-acetylgalactosamine ligand is used as a targeting domain as a ligand of for asialoglycoprotein receptors (ASGP-r). Galactoside-containing cluster ligands, in particular glycopeptides containing N-acetyl-D-galactosamine (GaINAc) have high affinity to ASGP-r, which are found in abundance in mammalian parenchymal liver cells. Such ligands may be conjugated with the core hydrophobic domain to improve the efficiency of delivery to diseased liver cells as previously described by Wu Y. T., et al. (A new N-acetylgalactosamine containing peptide as a targeting vehicle for mammalian hepatocytes via asialoglycoprotein receptor endocytosis (2004) Curr Drug Deliv. April; 1(2):119-27).
As per the method described above, the invention provides with biodegradable delivery capsule for performing gene targeting into a cell in-vivo. These delivery capsules, are, at least in part, characterized in that a RNA endonuclease reagent is complexed with at least one polar domain, which can be linked to biodegradable conjugate(s) of hydrophobic monomers, under the form of spherical particles of 50 to 100 nm diameter range. The structure of these delivery capsules allowed the inclusion of at least two RNA endonuclease reagents, such as TALE nucleases, which was surprising given the reduced size of the particles.
According to one aspect, said biodegradable matrix that is complexed with the RNA endonuclease reagents comprises at least two polar domains, in such a manner that the inner core particle is hydrophilic. The inner core particle may then encapsulate a further endonuclease reagent, in particular under polypeptide form, such as a RNA or DNA-guided endonuclease, for instance, a Cas9 or Cpf1 protein.
Various combinations of reagents can be included in the biodegradable delivery capsules of the present invention, as illustrated in
The present invention is also drawn to a medicament or pharmaceutical compositions permitting the safe injection in-vivo of the above biodegradable delivery systems in view of editing a target gene. By “pharmaceutically injectable medium” is meant a suitable pharmaceutical carrier, which are well known in the art, such as phosphate buffered saline solutions, water, emulsions, such as oil/water emulsions, various types of wetting agents, sterile solutions, etc. Injections according to the present invention can be intracerebral, intramuscular, inside spinal chord or subcutaneous.
Preparations for intravenous administration include sterile aqueous or non-aqueous solutions, suspensions, and emulsions. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media. Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's, or fixed oils. Intravenous vehicles include fluid and nutrient replenishes, electrolyte replenishers (such as those based on Ringer's dextrose), and the like. Preservatives and other additives may also be present such as, for example, antimicrobials, anti-oxidants, chelating agents, and inert gases and the like. In addition, the pharmaceutical composition of the present disclosure might comprise proteinaceous carriers, like, e.g., serum albumin or immunoglobulin, preferably of human origin.
The pharmaceutical compositions according to the present invention can have many different therapeutic indications. Examples of indications are those referred to in Table 1. Specifically, Table 1 lists particular target genes in connection with several diseases, which can be treated using the endonuclease delivery means according to the present invention. One particular aspect of this approach is the gene editing of these specific target genes in view of obtaining the treatment of their associated disease in vivo.
As a preferred embodiment is the therapeutic use of the endonuclease reagents of the present invention to target in-vivo the genetic sequences expressing microRNAs involved into drug resistance in cancer treatment, especially after prolonged cycles of chemotherapy. Proposed targets in this respect are sequence encoding miRNA genes, especially those from let7, miR-21, mir-26, mir-10, mir-34 and/or mir-122 families. Drug resistance is a major problem in the treatment of cancer patients. Resistance can develop after prolonged cycles of chemotherapy or can be present intrinsically in the patient. There is an emerging role of microRNAs (miRNAs) in resistance to cancer treatments. miRNAs are small non-coding RNAs that are evolutionarily conserved and also involved as regulators of gene expression through the silencing of mRNA targets. They are involved in many different cancer types and a plethora of mechanisms have been postulated for the roles that miRNAs play in the development of drug resistance. Hence, miRNA-based gene therapy may provide a novel approach for the future of cancer therapy. This review focuses on an overview of recent findings on the role of miRNAs in the resistance to chemotherapy in different tumors.
According to a preferred embodiment of the invention, the biodegradable endonuclease delivery capsules are used against infection agents' genomes, in particular those agents that presents a DNA intermediate into the liver. By “DNA intermediate into the liver” is meant that the infectious agent has, even temporarily, at least one intermediate stage of its replication taking place into a hepatic cell under a DNA form.
HBV is such as infectious agent that presents a DNA intermediate as per its cccDNA, which forms a reservoir for the virus lodged into hepatic cells. Chronic hepatitis is mostly due to this cccDNA remaining in hepatic cells.
One aspect of the present invention is to provide with new endonuclease reagents, especially TALE-nucleases (TALEN presented in Table 1) under RNA form for encapsulation into delivery particles for in-vivo targeting of HBV into liver cells. Preferred target sequences and TALEN monomers are those identified by the inventors in Example 1, through the cloning of large pieces of cccDNA into the genome of HEK293 cells (
Also, the present invention claims TAL-nuclease monomer, which polypeptide sequence has at least 80% identity with any of SEQ ID NO.1 to 20, which are, useful for treating HBV related infections, and more particularly those having at least 80% identity with SEQ ID NO. 1, 2, 3, 4, 5, 6, 9, 10, 13, 14, 15, 16, 17 and 18 (TALEN 1212, 1213, 1214, 2559, 2561, 2562, and 2563 respectively displaying more than 40% activity in Example 1).
With respect to antiviral treatments, and in particular those related to HBV, the endonuclease reagents of the present invention can be advantageously used in combination with other antiviral molecules, which do not target cccDNA, in particular those selected from: lamivudine (Epivir), entecavir (Baraclude), adefovir (Hepsera), tenofovir (Viread), Telbivudine (Tyzeka, Sebivo), Pegylated Interferon (Pegasys) or Interferon Alpha (Intron A).
A further aspect of the present invention is a method for delivering an endonuclease reagent into a cell in vivo, comprising the step of:
More broadly, the present invention can be regarded as a method for gene editing a target gene into a cell in-vivo, comprising the steps of introducing into the blood stream of an animal a biodegradable delivery capsule comprising an endonuclease reagent under RNA form.
Other Definitions
Where a numerical limit or range is stated herein, the endpoints are included. Also, all values and subranges within a numerical limit or range are specifically included as if explicitly written out.
Having generally described this invention, a further understanding can be obtained by reference to certain specific examples, which are provided herein for purposes of illustration only, and are not intended to be limiting unless otherwise specified.
Design of TAL-Nucleases Targeting HBV Subtypes cccDNA
Hepatitis B virus (HBV) is a member of the Hepadnaviridae family of viruses. Infection with HBV can lead to cirrhosis and hepatocellular carcinoma. The genome of HBV is made of circular DNA, which is not fully double-stranded. One end of the full length strand is linked to the viral DNA polymerase. The genome is -3000 nucleotides long (for the full-length strand) and -2000 nucleotides long (for the short length-strand). The partially double-stranded DNA is rendered fully double-stranded by completion of the (+) sense strand and removal of a protein molecule from the (−) sense strand and a short sequence of RNA from the (+) sense strand. Non-coding bases are removed from the ends of the (−) sense strand and the ends are rejoined. There are four known genes encoded by the genome, called C, X, P, and S. The core protein is coded for by gene C (HBcAg), and its start codon is preceded by an upstream in-frame AUG start codon from which the pre-core protein is produced. HBeAg is produced by proteolytic processing of the pre-core protein. The DNA polymerase is encoded by gene P. Gene S is the gene that codes for the surface antigen (HBsAg). The function of the protein coded for by gene X is not fully understood but it is associated with the development of liver cancer. It stimulates genes that promote cell growth and inactivates growth regulating molecules.
The life cycle of hepatitis B virus is complex. Hepatitis B is one of a few known pararetroviruses: non-retroviruses that still use reverse transcription in their replication process. The virus gains entry into the cell by binding to NTCP on the surface and being endocytosed. Because the virus multiplies via RNA made by a host enzyme, the viral genomic DNA has to be transferred to the cell nucleus by cellular chaperones. The partially double stranded viral DNA is then made fully double stranded by viral polymerase and transformed into covalently closed circular DNA (cccDNA). This cccDNA serves as a template for transcription of four viral mRNAs by host RNA polymerase. The largest mRNA, (which is longer than the viral genome), is used to make the new copies of the genome and to make the capsid core protein and the viral DNA polymerase. These four viral transcripts undergo additional processing and go on to form progeny virions that are released from the cell or returned to the nucleus and re-cycled to produce more copies. The long mRNA is then transported back to the cytoplasm where the virion P protein (the DNA polymerase) synthesizes DNA via its reverse transcriptase activity.
The goal of the project was to generate TAL-nucleases able to cut HBV cccDNA and decrease its level in cell culture and in vivo. It should also cut the Relaxed Circular DNA (RC DNA), therefore acting of two different pools of virus. It could also cut integrated HBV partial genomes that are most often found in hepatocarcinomas.
There are no known inhibitors of the cccDNA. Some inhibitors are claimed to inhibit the formation of the cccDNA but none are targeting the pool of long lasting episomal reservoir of HBV in patients. The destruction of this pool could be a tool toward the cure of HBV.
HBV genome is difficult to express in cells line due to the complexity of its replication process and its toxicity. Also cells that produce HBV are difficult to transfect. We therefore decide to generate a stable cell line in 293 cells containing reference HBV genome (ayw) integrated at a known locus using a cGPS approach as described in WO2010046786, so that endonuclease reagent activity could be monitored in an easy and non -infectious manner.
HBV HEK 293 cells were very useful to select efficient TALE-nucleases targeting HBV. Cells M1-1000, M801-1800 and M1601-2006 were used to test TALE-nucleases: TALEN T002559-2564 (set 1) and TALEN T001212-1215 (set2). All of them were able to cut their target, with different level of efficiency. We were able to generate at least one very efficient TALEN per gene.
PCR on Transfected cGPS
The activity of the above TALENs was measured by transfecting plasmids in the above HBV 293 cGPS cells. 1.5 millions of each kind of HBV cGPS HEK 293 cells were plated in T25 the evening before transfection. 2 μg of each set of appropriate of plasmids (so 4 μg per TALEN, see table 1 and table 2) were transfected using Mirus TranslT-293 transfection reagent for 3 to 4 days. A control GFP was transfected in parallel (4 μg) for all cell lines and the efficiency of the transfection was monitored with a fluorescent microscope and estimated at ˜95%. Genomic DNA was then extracted using the Zymo Research quick-gDNA miniprep kit and PCR.
T7 Endonuclease Assay on HBV cGPS Cells Tranfected with TALENs
PCR products were annealed slowly, treated by T7 Endonuclease, run on a 10% polyacrylamide gel and stained with Sybergreen (T7 assay). One expects that the TALEN cut and NHEJ repair would result in the formation of a population of genomic DNA (and hence PCR product) that do not overlap at the surroundings of the TALEN cut site. After annealing those fragment would form a bulge that could be cleaved by the Endonuclease T7 and create fragments of expected sizes. Results are shown in
All the TALEN tested had an estimated efficiency of more than 10%, while 6 were more than 40% active.
HBV HEK 293 cells were very useful to select efficient TALENs targeting HBV. We were able to create at least one very efficient TALEN per gene. The activity of T002561 (which cuts S and P), T001212 (which cuts X and P), T002559 (which cuts C and P) was more than 40% based on T7 assay and are therefore eligible for being encapsulated for in-vivo targeting of liver cells.
In-Vivo Targeting of Factor VII Gene into the Genome of Liver Cells
The liver is a key organ for most metabolic pathways and therefore numerous metabolic inherited diseases have their origin in this organ. It is an attractive target for in vivo gene transfer studies due to the accessibility of the hepatocytes via the blood stream. The liver is the largest organ in the body and a highly vascularized organ. It is the only organ in the body to have two circulation systems, the systemic with the hepatic artery that brings oxygenated blood directly from the heart and the portal vein that brings nutrients from the gut and supplies 70% of the blood flow to the liver. In addition, it has a system of ducts that transports toxins out of the liver via bile into the small intestine, which is of importance for liver gene therapy applications since it allows hepatocytes to excrete bile salts, copper, bilirubin, etc, which cause liver diseases. Candidate diseases for liver gene therapy include primary liver diseases in which hepatocytes are injured and genetic defects altering a specific function of the hepatocyte but causing extrahepatic manifestations.
As a proof of principle, the liver has been chosen as a target organ in view of inactivating in-vivo mouse factor VII . Mouse Factor VII is a secreted protein secreted by liver cells, which can be easily quantitated in the blood. Inactivation of the gene in mouse liver is expected to lead to a decrease of the secreted protein into the circulating blood as described elsewhere (Akin, A. et al. (2009) Development of Lipidoid—siRNA Formulations. Molecular Therapy 17 5: 872-879.)
TAL-nucleases were engineered at the DNA level using the golden gate cloning assembly method described by Weber E., et al. (Assembly of Designer TAL Effectors by Golden Gate Cloning (2011) PLoS ONE 6(5): e19722) and cloned into a mammalian expression vector under the control of a pEF1alpha long promoter and tested in a human cell line by using a T7 experiment as described in Example 1.
Transcripts of mRNA encoding respectively forward (SEQ ID NO:21 or 23) and reverse (SEQ ID NO: 20 or 22) of the most efficient TALEN monomer pairs were produced using standard procedure (Ambion kit, Thermo Fisher Scientific). The capped transcripts were complexed with ionized cationic lipid 1,2-dilinoleyloxy-3-dimethylaminopropane (DLinDMA) and PEG- lipids to generate 80 nm range diameter range nanoparticles for systemic delivery to the liver. Controls were PBS (negative control) and siRNA against Factor VII (positive control from Ambion, #4457292 Thermofisher) as such siRNA have proven efficiency in previous studies.
The injection volume was 10 mL/kg (i.e for one mouse weighing 20 g, 200 μL of dosing solution is administered). Injection were at 2 mg/kg, of a 0.2 mg/ml solution, so that 200 μl were injected for a 20 g mouse, intravenously (IV, bolus) into the caudal vein of mice.
The treatment starts on Day 0 (Do) using sixteen (18) healthy female CD-1 mice.
The treatment schedule is as follows:
The treatment schedule is summarized in the table hereafter:
Blood was collected on D0 (just before IV treatment) and then on D3, D5, D10, D15, D20 and D25. All mice were terminated on D25. Approximately 150-200 μL of blood was collected at each time point, plasma was then flash-frozen in liquid nitrogen and stored at −80° C. Liver from each mouse was collected at the time of termination, flash-frozen in liquid nitrogen and stored at −80° C. Factor VII activity in the collected plasma was measured using BIOPHEN FVII kit #221304.
Gene modifications were measured in livers by extracting genomic DNA on powdered frozen liver using ZR Genomic DNA™-Tissue MidiPrep from ZymoResearch # D3110, then performing a T7 assay and deep sequencing on the PCR product of the locus of interest.
Results show in
| Number | Date | Country | Kind |
|---|---|---|---|
| PA 2016 70111 | Feb 2016 | DK | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2017/054264 | 2/24/2017 | WO | 00 |
