EP3331571A1 - Compositions and methods to treat viral infections - Google Patents
Compositions and methods to treat viral infectionsInfo
- Publication number
- EP3331571A1 EP3331571A1 EP16804107.7A EP16804107A EP3331571A1 EP 3331571 A1 EP3331571 A1 EP 3331571A1 EP 16804107 A EP16804107 A EP 16804107A EP 3331571 A1 EP3331571 A1 EP 3331571A1
- Authority
- EP
- European Patent Office
- Prior art keywords
- nuclease
- nucleic acid
- composition
- genome
- cmv
- Prior art date
- Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
- Withdrawn
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Classifications
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K9/00—Medicinal preparations characterised by special physical form
- A61K9/08—Solutions
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
- A61P31/12—Antivirals
- A61P31/20—Antivirals for DNA viruses
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
- A61P31/12—Antivirals
- A61P31/20—Antivirals for DNA viruses
- A61P31/22—Antivirals for DNA viruses for herpes viruses
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K9/00—Medicinal preparations characterised by special physical form
- A61K9/0012—Galenical forms characterised by the site of application
- A61K9/0014—Skin, i.e. galenical aspects of topical compositions
Definitions
- the invention generally relates to treatment of viral infections and cleaving foreign nucleic acids in cells.
- HSV herpes simplex virus
- oral herpes may cause oral herpes, which manifest as blisters around face or mouth, or genital herpes that manifest as blisters that can break open and result in small ulcers. Tingling or shooting pains may occur before the blisters appear.
- HSV has the ability to lie dormant within a cell indefinitely in a latent infection and not be fully eradicated even after treatment. Because latent infections can evade immune surveillance and reactivate the lytic cycle at any time, there is a persistent risk to an infected individual of outbreak and the pain and suffering associated with it.
- HSV-1 and HSV-2 with HSV-1 infection much more prevalent than HSV-2 infection.
- HSV-1 infection much more prevalent than HSV-2 infection.
- About 65% of persons in the United States have antibodies to HSV-1 and about 16% of Americans between the ages of 14 and 49 are infected with HSV-2.
- Cytomegalovirus is an example of another problematic virus. Some people get infected when they receive an organ transplant. The CMV infection disseminates to the lungs, liver, pancreas, kidneys, stomach, intestine, brain, and parathyroid glands, causing organ failure and even death. When disseminated to the eye, the virus can cause retinal detachment and blindness. Additionally, a fetus may be infected with cytomegalovirus (CMV) in utero, ultimately causing hearing loss, vision impairment, mental retardation, coordination problems, and death. Even when born healthy, a baby infected with CMV must be monitored throughout the developmental years for hearing or vision loss, or signs of mental impairment.
- CMV cytomegalovirus
- the invention provides methods and compositions for treating viral infections.
- a nuclease is used to cleave viral nucleic acid in an infected cell.
- the nuclease cleaves viral nucleic acid in a sequence-specific manner and thus does not cleave genes or other important genomic features from a genome of the infected host.
- the nuclease is a CRISPR-associated protein such as Cas9 and is delivered to the infected cells as a
- nuclease can be delivered encoded on a plasmid or as mRNA to be expressed within the target cells. Methods and compositions may be used to treat a patient or may be used to treat tissues, cells, or organs ex vivo.
- Embodiments of the invention relate to HSV.
- the invention provides compositions and methods for selectively treating HSV infection using a guided nuclease system that targets a specific region of the HSV genome such as oriS, UL9, RL2, or LAT.
- Methods of the invention may be used to remove even latent HSV genetic material from a host organism, without interfering with the integrity of the host's genetic material.
- a nuclease may be targeted to HSV nucleic acid where it can then disrupt the nucleic acid, thereby interfering with viral replication or transcription or even excising the viral genetic material from the host genome.
- the nuclease may be specifically targeted to remove only the HSV nucleic acid without acting on host material whether the viral nucleic acid exists as a particle within the cell or is integrated into the host genome.
- a sequence-specific moiety can include a guide RNA that targets viral genomic material for destruction by the nuclease and does not target the host cell genome.
- a CRISPR/Cas9 nuclease and guide RNA (gRNA) that together target and selectively edit or destroy viral genomic material is used.
- CRISPR clustered regularly interspaced short palindromic repeats
- the guide RNA localizes the CRISPR/Cas9 complex to a HSV target sequence, such as oriS, UL9, RL2, or LAT. Binding of the complex localizes the Cas9 endonuclease to the HSV genomic target sequence causing breaks in the viral genome.
- a HSV target sequence such as oriS, UL9, RL2, or LAT. Binding of the complex localizes the Cas9 endonuclease to the HSV genomic target sequence causing breaks in the viral genome.
- the guided nuclease system may be introduced into an infected host transdermally through application of, for instance, a topical solution.
- Topical solutions may be applied directly to infected tissue.
- the sequence specific moiety can target other nuclease systems to HSV nucleic acid including, for example, zinc finger nucleases, transcription activator-like effector nucleases (TALENs), meganucleases, or any other system that can be used to degrade or interfere with HSV nucleic acid without interfering with the regular function of the host's genetic material.
- TALENs transcription activator-like effector nucleases
- meganucleases or any other system that can be used to degrade or interfere with HSV nucleic acid without interfering with the regular function of the host's genetic material.
- compositions for treatment of a herpes simplex virus (HSV) infection comprising a vector encoding a nuclease and a sequence- specific targeting moiety complementary to HSV nucleic acid and capable of directing the nuclease to the HSV nucleic acid.
- HSV herpes simplex virus
- the HSV nucleic acid may comprise one or more of the following regions: origin of replication S (oriS), long unique region 9 (UL9), or long repeat region 2 (RL2).
- the composition may be configured to be administered transdermally, for example, through a topical solution.
- the nuclease may be a zinc-finger nuclease, a transcription activator-like effector nuclease, and a meganuclease.
- the nuclease may a Cas9 endonuclease and the sequence- specific binding module may comprise a guide RNA that specifically targets a portion of a viral genome.
- Compositions of the invention may be packaged for delivery to a human patient.
- the targeting sequence may be a guide RNA that has no match > 60% within a human genome.
- the vector may include a retrovirus, a lentivirus, an adenovirus, a herpesvirus, a poxvirus, an alphavirus, a vaccinia virus, an adeno-associated viruses, a plasmid, a nanoparticle, a cationic lipid, a cationic polymer, metallic nanoparticle, a nanorod, a liposome, microbubbles, a cell-penetrating peptide, or a lipo sphere.
- the invention includes a method for treating an HSV infection including the step of introducing into a cell of a host, a vector encoding a nuclease and a sequence-specific targeting moiety complementary to HSV nucleic acid. Additional steps include causing the sequence- specific targeting moiety to target the nuclease to the HSV nucleic acid and to cleave the HSV nucleic acid.
- the HSV nucleic acid can include a portion of or all of one or more genomic regions including an origin of replication S (oriS), long unique region 9 (UL9) or long repeat region 2 (RL2).
- Methods of the invention may include transdermally administering the vector to the host and transdermal administration may include applying a topical solution comprising the vector.
- the nuclease may be a zinc-finger nuclease, a transcription activator-like effector nuclease, or a meganuclease.
- the nuclease may include a Cas9 endonuclease and the sequence-specific binding module may include a guide RNA that specifically targets a portion of a viral genome.
- the host may be a living human subject and the steps may be performed in vivo.
- the targeting sequence may be a guide RNA and have no match > 60% within a human genome.
- the vector may include a retrovirus, a lentivirus, an adenovirus, a herpesvirus, a poxvirus, an alphavirus, a vaccinia virus, an adeno-associated viruses, a plasmid, a nanoparticle, a cationic lipid, a cationic polymer, metallic nanoparticle, a nanorod, a liposome, microbubbles, a cell-penetrating peptide, or a liposphere.
- compositions and methods of the invention can accordingly be used to treat an HSV infection through targeted disruption of HSV genomic function or by digestion of viral nucleic acid via one or multiple breaks caused by targeting sites such as oriS, UL9, RL2, or LAT for
- the invention provides a composition for treatment of a herpes simplex virus (HSV) infection.
- the composition includes a ribonucleoprotein that includes: a nuclease; and a sequence-specific targeting moiety complementary to HSV nucleic acid and capable of directing the nuclease to the HSV nucleic acid.
- the HSV nucleic acid may include an origin of replication S (oriS) region, a long unique region 9 (UL9), a long repeat region 2 (RL2), or a combination thereof.
- the nuclease comprises a Cas9 endonuclease and the sequence-specific binding module comprises a guide RNA that specifically targets a portion of a viral genome.
- the targeting sequence is a guide RNA and has no match > 60% within a human genome.
- composition may be configured to be administered transdermally.
- composition includes a pharmaceutically acceptable carrier for topical application to infected tissue.
- Embodiments of the invention relate to CMV.
- the invention provides methods for treating cytomegalovirus (CMV) infections in tissues, so that infected individuals will not suffer the effects of CMV infections, such as hearing/vision loss, mental impairment, multi-organ failure, and death.
- CMV infection is treated by using a nuclease that targets CMV nucleic acid.
- the nuclease cleaves and thus interferes with the function of the CMV nucleic acid, which prevents CMV from infecting the tissue or patient.
- the nuclease may be introduced into a patient with a CMV infection, or into an organ prior to transplant.
- a heart needed for a life-saving transplant may be exposed to the CMV targeted nuclease to incapacitate the CMV genome prior to transplantation.
- the heart transplant recipient does not need to choose between accepting the infected heart and passing, only to wait and hope that the next heart will be CMV-free.
- the invention provides compositions for treatment of a
- the composition comprise a nuclease; and a sequence- specific targeting moiety complementary to CMV nucleic acid and capable of directing the nuclease to the CMV nucleic acid.
- the invention provides methods for treating a cytomegalovirus (CMV) infection in an organ.
- the methods comprise introducing a nuclease that cleaves the CMV nucleic acid into an organ and then causing the nuclease to target and cleave CMV nucleic acid.
- the organ can be from a transplant donor, or the organ can be grown or created from cells.
- the organ is a heart, liver, kidney, eye, lung, pancreas, intestine, thymus, or any other biological tissue to be transplanted into a transplant recipient.
- preparing the nuclease for delivery can involve associating the nuclease with a viral or non- viral vector.
- the nuclease could be prepared for delivery into an organ by encasing or binding the nuclease within a liposome.
- the tissue may be a tissue that is to be used in transplantation.
- the tissue may be an organ supplied by a donor, to be transplanted into a recipient.
- the tissues of the organ are treated with the nuclease to cleave and incapacitate the CMV nucleic acid.
- the transplant donor is treated with or exposed to the nuclease.
- the donor receives the nuclease as a therapeutic agent to eliminate CMV from tissues within the patient.
- the nuclease may be delivered by oral, parenteral, inhalation, topical, rectal, or vaginal means.
- the transplant recipient is treated with or exposed to the nuclease following transplantation.
- the transplant recipient is treated with the nuclease to prevent CMV from spreading within and throughout the patient.
- the nuclease may be delivered by any known means in the art.
- the tissue is located within a patient.
- a patient may be treated with the CMV targeting nuclease to prevent infection.
- the patient may be a pregnant woman.
- the nuclease targets the CMV genome and destroys or disrupts the function of the virus.
- the pregnant woman does not pass the virus to the fetus in utero.
- the invention provides methods of treating a cytomegalovirus (CMV) infection in a fetus.
- the methods comprise providing a nuclease that cleaves CMV nucleic acid and preparing the nuclease for delivery into a pregnant woman. It should be appreciated that the nuclease may be delivered into the pregnant woman, the uterus of the pregnant women, or the fetus in utero, by techniques known in the art.
- nuclease may be used to cleave CMV nucleic acid.
- the nuclease may be a zinc finger nuclease, a transcription activator-like effector nuclease, or a meganuclease.
- the nuclease may be a structure specific nuclease or a sequence specific nuclease.
- the nuclease is a Cas9 endonuclease.
- the methods of the invention may further comprise cleaving the CMV nucleic acid using the nuclease.
- the methods comprise delivering to the cell or tissue a guide RNA that targets the nuclease to a portion of the CMV nucleic acid.
- a guide RNA targets the Cas9 endonuclease to a portion of the CMV nucleic acid.
- the guide RNA is designed to have no perfect match in a human genome.
- the guide RNAs may target the nuclease to a regulatory element in the genome of CMV.
- the nuclease may be delivered to the tissue by a viral vector.
- the viral vector may be retrovirus, lentivirus, adenovirus, herpesvirus, poxvirus, alphavirus, vaccinia virus or adeno- associated viruses.
- the nuclease may be delivered by a plasmid, a nanoparticle, a cationic lipid, a cationic polymer, metallic nanoparticle, a nanorod, a liposome, a cell-penetrating peptide, a liposphere, and polyethyleneglycol (PEG).
- a plasmid a nanoparticle, a cationic lipid, a cationic polymer, metallic nanoparticle, a nanorod, a liposome, a cell-penetrating peptide, a liposphere, and polyethyleneglycol (PEG).
- PEG polyethyleneglycol
- the nuclease is a CRISPR/Cas9 endonuclease.
- a guide RNA that specifically targets one or more portions of a genome of CMV within a cell or tissue of the transplant may be used.
- the CRISPR/Cas9 complex binds to and alters the CMV genome.
- the invention may make use of a CRISPR/Cas9 nuclease and guide RNA (gRNA) that together target and selectively edit or destroy CMV genomic material.
- the CRISPR (clustered regularly interspaced short palindromic repeats) is an element of the bacterial immune system that protects bacteria from phage infection.
- the guide RNA localizes the CRISPR/Cas9 complex to a CMV target sequence. Binding of the complex localizes the Cas9 endonuclease to the CMV genomic target sequence causing breaks in the CMV genome.
- the guide RNA is designed to target multiple sites on the CMV genome in order to disrupt the CMV nucleic acid and reduce the chance that it will functionally recombine.
- the presented methods allow for CMV genome destruction, which results in the inability of the virus to proliferate, with no observed cytotoxicity to the cells.
- Aspects of the invention provide for designing a CRISPR/gRNA/Cas9 complex to selectively target CMV genomic material (DNA or RNA), delivering the CRISPR/gRNA/Cas9 complex to a cell or tissue containing the CMV genome, and cutting the CMV genome in order to incapacitate the virus.
- the presented methods allows for targeted disruption of CMV genomic function or, in a preferred embodiment, digestion of CMV nucleic acid via multiple breaks caused by targeting multiple sites for nuclease action in the CMV genome.
- Aspects of the invention provide for transfection of a CRISPR/gRNA/Cas9 complex cocktail to completely suppressed CMV proliferation. Additional aspects and advantages of the invention will be apparent upon consideration of the following detailed description thereof.
- FIG. 1 diagrams a method of targeting an HSV infection.
- FIG. 2 is a map of an HSV genome.
- FIG. 3 shows amplicons of HSV genomic regions before and after digestion with cas9.
- FIG. 3 is a gel with lanes showing genomic DNA size bands for cells treated with the RL2, LATi, LATp, UL9, OriS, and US 12 guide sequences with and without Cas9.
- FIG. 4 shows the results of quantitative PCR assays showing different levels of decreasing of HSV DNA in the CRISPR treated samples.
- FIG. 5 shows the EGFP marker fused after the Cas9 protein, allowing selection of Cas9- positive cells.
- FIG. 6 shows that including an ori-P in the plasmid promoted active plasmid replication inside the cells, which increased the transfection efficiency to >60%.
- FIG. 7 is a diagram of an EBV genome, with structure-, transformation-, and latency- related targets called out.
- FIG. 8 shows the genome context around guide RNA sgEBV2 and PCR primer locations.
- FIG. 9 shows the large deletion induced by sgEBV2 (lanes 1-3 are before, 5 days after, and 7 days after sgEBV2 treatment, respectively).
- FIG. 10 shows the genome context around guide RNA sgEBV3/4/5 and PCR primer locations.
- FIG. 11 shows the large deletions induced by sgEBV3/5 and sgEBV4/5.
- Lane 1 and 2 are 3F/5R PCR amplicons before and 8 days after sgEBV3/5 treatment.
- Lane 3 and 4 are 4F/5R PCR amplicons before and 8 days after sgEBV4/5 treatment.
- FIG. 12 shows that Sanger sequencing confirmed genome cleavage and repair ligation 8 days after sgEBV3/5.
- FIG. 13 shows that Sanger sequencing confirmed genome cleavage and repair ligation 8 days after sgEBV4/5.
- FIG. 14 shows relative cell proliferation after targeting various combinations of regions in an EBV genome with guide RNAs.
- FIG. 15 gives flow cytometry scattering signals from before sgEBVl-7 treatments.
- FIG. 16 gives flow cytometry scattering signals from 5 days after sgEBVl-7 treatments
- FIG. 17 gives flow cytometry scattering signals from 8 days after sgEBVl-7 treatments.
- FIG. 18 shows Annexin V Alexa647 and DAPI staining results before sgEBVl-7 treatments.
- FIG. 19 shows Annexin V Alexa647 and DAPI staining results 5 days after sgEBVl -7 treatments.
- FIG. 20 shows Annexin V Alexa647 and DAPI staining results 8 days after sgEBVl -7 treatments.
- FIGS. 21 and 22 show microscopy revealed apoptotic cell morphology after sgEBVl -7 treatment.
- FIG. 23 shows nuclear morphology before sgEBVl-7 treatment.
- FIGS. 24-26 show nuclear morphology after sgEBVl -7 treatment.
- FIG. 27 shows EBV load after different CRISPR treatments by digital PCR.
- Cas9 and Cas9-oriP had two replicates, and sgEBVl-7 had 5 replicates.
- FIGS. 28 shows a single Raji cell as captured on a microfluidic chip.
- FIG. 29 shows a single sgEBVl-7 treated cell as captured on the chip.
- FIG. 30 is a histogram of EBV quantitative PCR Ct values from single cells before treatment.
- FIG. 31 is a histogram of EBV quantitative PCR Ct values from single live cells 7 days after sgEBVl -7 treatment.
- FIG. 32 represents SURVEYOR assay of EBV CRISPR (lanes numbered from left to right: Lane 1: NEB lOObp ladder; Lane 2: sgEBVl control; Lane 3: sgEBVl; Lane 4: sgEBV5 control; Lane 5: sgEBV5; Lane 6: sgEBV7 control; Lane 7: sgEBV7; Lane 8: sgEBV4).
- FIG. 33 shows that the CRISPR treatments were not cytotoxic to the EBV-negative Burkitt's lymphoma cell line DG-75
- FIG. 34 shows that the CRISPR treatments were not cytotoxic to primary human lung fibroblasts EVIR90.
- FIG. 35 shows ZFN being used to cut viral nucleic acid.
- FIG. 36 shows a composition for treating a viral infection.
- FIG. 37 depicts a flow chart of embodiments of the invention for targeting CMV.
- FIG. 38 is a map of a CMV genome.
- FIG. 39 depicts results from an in vitro CRISPR endonuclease assay, showing PCR amplicons from CMV genome and the corresponding products from in vitro CRISPR digestion (shown in pairs).
- FIG. 40 depicts results from an in vitro CRISPR endonuclease assay, showing PCR amplicons from CMV genome and the corresponding products from in vitro CRISPR digestion (shown in pairs).
- FIG. 41 depicts results from an in vitro CRISPR endonuclease assay, showing PCR amplicons from CMV genome and the corresponding products from in vitro CRISPR digestion (shown in pairs).
- FIG. 42 shows a method 3201 for treating a cell 3237 to remove foreign nucleic acid.
- Embodiments of the invention relate to compositions and methods for treating HSV infections including HSV-1 and HSV-2 infections using guided nuclease systems targeted to specific regions of the HSV genome such as RL2, LAT, UL9, or OriS.
- Compositions of the invention disrupt HSV viral nucleic acid in host cells through nuclease activity without affecting the host's genome. Through disruption of the HSV genome in infected host cells, methods and compositions of the invention may eradicate even latent HSV infections.
- embodiments of the invention related to methods for treating cytomegalovirus (CMV).
- Methods of the invention are used to incapacitate or disrupt CMV within a cell, a tissue, or a patient by systematically causing large or repeated insertions or deletions in the CMV genome, reducing the probability of reconstructing the full genome.
- the insertions or deletions in the genome incapacitates or destroys the virus, thus treating CMV.
- the nuclease may be a CRISPR/Cas9 complex.
- the nuclease is guided by a sequence, such as a guided RNA.
- tissues, such as organs are treated with the nuclease prior to transplantation.
- a transplant donor or recipient are treated before and after a transplantation surgery.
- a patient infected with CMV is treated with the nuclease.
- FIG. 1 diagrams a method of targeting an HSV infection.
- the method includes obtaining a targetable nuclease (e.g., as a protein or a gene for a nuclease). Any suitable nuclease can be used such as ZFN, TALENs, or meganucleases. In a preferred embodiment, the nuclease is Cas9.
- a sequence is provided that targets the nuclease to specific targets on the HSV genome such as oriS, UL9, RL2, or LAT.
- the nuclease gene and encoded gRNAs may be provided in a DNA vector, such as a plasmid or an adenovirus based vector, and the vector may further optionally include a promoter.
- That composition is then introduced into the HSV-infected cells. Any suitable transfection or delivery method may be used.
- the genes are expressed and the Cas9 enzyme uses the gRNA to target, and cleave, the HSV genome. Since the gRNA is specific to the HSV genome with no match to the human genome according to methods and criteria described herein, the method leaves the host genome intact and does not interfere with normal human genetic function.
- FIG. 2 shows the HSV genome and the HSV oriS palindrome dimer (oriS), RL2-ICP0 (RL2), LAT Intron (LATi), LAT promoter (LATp), UL9, and US 12 genes which may be targeted by CRISPR guide RNAs.
- FIG. 3 shows amplicons of HSV genomic regions before and after digestion with cas9 and corresponding guide RNAs.
- T7 in vitro transcription was used to produce the complete guide RNA with scaffold for RL2, LATi, LATp, UL9, oriS, and US 12. Flanking regions of the genome targets were PCR amplified from HSV2 strain G genomic DNA (from ATCC). Cas9 protein (from PNA Bio), guide RNA and target DNA were mixed and incubated for in vitro
- FIG. 3 shows PCR amplicons of RL2, LATi, LATp, UL9, oriS, and US 12 before and after digestion with cas9 and the guide RNA targeting each respective genomic region.
- FIG. 37 depicts a flow chart of embodiments of the invention for targeting CMV.
- the method 100 comprises introducing a nuclease 105 that targets the CMV genome.
- the nuclease can be introduced into an organ or a pregnant woman.
- the organ or the fetus can be suspected of having a CMV infection.
- the method further comprises causing the nuclease to target and cleave 110 a CMV nucleic acid.
- the nuclease is able to bind to and alter the CMV genome. i. Treating infected cell
- Cells may be treated with a nuclease encoded in a nucleic acid (e.g., delivered as mRNA or a plasmid) or delivered in active form.
- a nucleic acid e.g., delivered as mRNA or a plasmid
- active form e.g., a CRISPR-associated protein such as Cas9
- RNP active ribonucleoprotein
- FIG. 42 shows a method 3201 for treating a cell 3237 to remove foreign nucleic acid such as a viral nucleic acid 3251 from a herpes simplex virus.
- the method 3201 may be used to treat an infection, or the method 3201 may be used in vitro in research and development to remove foreign nucleic acid from subject cells such as cells from a human.
- the method 3201 includes the steps of: forming 3225 a ribonucleoprotein (RNP) 3231 that includes a nuclease 3205 and an RNA 3213; obtaining a cell 3237 from a donor; delivering 3245 (preferably in vitro) the RNP 3231 to the cell 3237; and cleaving viral nucleic acid 3251 within the cell 3237 with the RNP 3231.
- the method 3201 may include providing the cell 3237 for transplantation into a patient.
- the delivering 3245 may include electroporation, or the RNP may be packaged in a liposome for the delivering 3245.
- the viral nucleic acid 3251 will exist as an episomal viral genome, i.e., an episome or episomal vector, of a virus.
- the RNA 3213 has a portion that is substantially complementary to a target within a viral nucleic acid 3251 and preferably not substantially complementary to any location on a human genome.
- the virus is a herpes family virus such as one selected from the group consisting of HSV-1, HSV-2, Varicella zoster virus, Epstein-Barr virus, and Cytomegalovirus. The virus may be in a latent stage in the cell.
- the nuclease 3205 is a Crisper-associated protein such as, preferably, Cas9.
- the RNA 3213 may be a single guide RNA (sgRNA) (providing the functionality of crRNA and tracrRNA).
- the nuclease 3205 and the RNA 3213 are delivered to the cell as the RNP 3231.
- the cell 3237 has the viral nucleic acid 3251 therein, and the method further comprises cleaving the viral nucleic acid using the nuclease.
- RNP is preferable (e.g., to plasmid DNA) for clinical applications, particularly for parenteral delivery.
- RNP is the active pre-formed drug which offers advantages to DNA (AAV) or mRNA. No need to transcribe, translate, or assemble drug components within cell. Delivery of RNP 3231 may offer improved drug properties, e.g. earlier onset activity and controlled clearance (toxicity).
- FIG. 36 shows a composition for treating a viral infection according to certain embodiments.
- the composition preferably includes a vector (which may be a plasmid, linear DNA, or a viral vector) that codes for a nuclease and a targeting moiety (e.g., a gRNA) that targets the nuclease to HSV and may be complimentary to a genomic region of HSV such as RL2, LAT, UL9, or OriS.
- the composition may optionally include one or more of a promoter, replication origin, other elements, or combinations thereof as described further herein. ii. Nuclease
- Methods of the invention include using a programmable or targetable nuclease to specifically target viral nucleic acid for destruction.
- Any suitable targeting nuclease can be used including, for example, zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), clustered regularly interspaced short palindromic repeat (CRISPR) nucleases, meganucleases, other endo- or exo-nucleases, or combinations thereof.
- ZFNs zinc-finger nucleases
- TALENs transcription activator-like effector nucleases
- CRISPR clustered regularly interspaced short palindromic repeat
- CRISPR methodologies employ a nuclease, CRISPR-associated (Cas9), that complexes with small RNAs as guides (gRNAs) to cleave DNA in a sequence-specific manner upstream of the protospacer adjacent motif (PAM) in any genomic location.
- CRISPR may use separate guide RNAs known as the crRNA and tracrRNA. These two separate RNAs have been combined into a single RNA to enable site- specific mammalian genome cutting through the design of a short guide RNA.
- Cas9 and guide RNA (gRNA) may be synthesized by known methods.
- Cas9/guide- RNA uses a non-specific DNA cleavage protein Cas9, and an RNA oligo to hybridize to target and recruit the Cas9/gRNA complex.
- gRNA guide- RNA
- CRISPR Clustered Regularly Interspaced Short Palindromic Repeats
- the Cas9 endonuclease causes a double strand break in at least two locations in the genome. These two double strand breaks cause a fragment of the genome to be deleted. Even if viral repair pathways anneal the two ends, there will still be a deletion in the genome. One or more deletions using the mechanism will incapacitate the viral genome. The result is that the host cell will be free of viral infection.
- nucleases cleave the genome of the target virus.
- a nuclease is an enzyme capable of cleaving the phosphodiester bonds between the nucleotide subunits of nucleic acids.
- Endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain. Some, such as Deoxyribonuclease I, cut DNA relatively nonspecifically (without regard to sequence), while many, typically called restriction endonucleases or restriction enzymes, cleave only at very specific nucleotide sequences. In a preferred
- the Cas9 nuclease is incorporated into the compositions and methods of the invention, however, it should be appreciated that any nuclease may be utilized.
- the Cas9 nuclease is used to cleave the genome.
- the Cas9 nuclease is capable of creating a double strand break in the genome.
- the Cas9 nuclease has two functional domains: RuvC and HNH, each cutting a different strand. When both of these domains are active, the Cas9 causes double strand breaks in the genome.
- insertions into the genome can be designed to cause incapacitation, or altered genomic expression. Additionally, insertions/deletions are also used to introduce a premature stop codon either by creating one at the double strand break or by shifting the reading frame to create one downstream of the double strand break. Any of these outcomes of the NHEJ repair pathway can be leveraged to disrupt the target gene.
- the changes introduced by the use of the CRISPR/gRNA/Cas9 system are permanent to the genome.
- At least one insertion is caused by the
- CRISPR/gRNA/Cas9 complex In a preferred embodiment, numerous insertions are caused in the genome, thereby incapacitating the virus. In an aspect of the invention, the number of insertions lowers the probability that the genome may be repaired.
- At least one deletion is caused by the
- CRISPR/gRNA/Cas9 complex In a preferred embodiment, numerous deletions are caused in the genome, thereby incapacitating the virus. In an aspect of the invention, the number of deletions lowers the probability that the genome may be repaired. In a highly-preferred embodiment, the CRISPR/Cas9/gRNA system of the invention causes significant genomic disruption, resulting in effective destruction of the viral genome, while leaving the host genome intact.
- TALENs uses a nonspecific DNA-cleaving nuclease fused to a DNA-binding domain that can be to target essentially any sequence.
- target sites are identified and expression vectors are made.
- Linearized expression vectors e.g., by Notl
- a commercially available kit may be use such as the
- mMESSAGE mMACHINE SP6 transcription kit from Life Technologies (Carlsbad, CA). See Joung & Sander, 2013, TALENs: a widely applicable technology for targeted genome editing, Nat Rev Mol Cell Bio 14:49-55.
- TALENs and CRISPR methods provide one-to-one relationship to the target sites, i.e. one unit of the tandem repeat in the TALE domain recognizes one nucleotide in the target site, and the crRNA, gRNA, or sgRNA of CRISPR/Cas system hybridizes to the complementary sequence in the DNA target.
- Methods can include using a pair of TALENs or a Cas9 protein with one gRNA to generate double-strand breaks in the target. The breaks are then repaired via nonhomologous end-joining or homologous recombination (HR).
- FIG. 35 shows ZFN being used to cut viral nucleic acid.
- the ZFN method includes introducing into the infected host cell at least one vector (e.g., RNA molecule) encoding a targeted ZFN 305 and, optionally, at least one accessory polynucleotide.
- a vector e.g., RNA molecule
- the cell includes target sequence 311.
- the cell is incubated to allow expression of the ZFN 305, wherein a double- stranded break 317 is introduced into the targeted chromosomal sequence 311 by the ZFN 305.
- a donor polynucleotide or exchange polynucleotide 321 is introduced. Swapping a portion of the viral nucleic acid with irrelevant sequence can fully interfere transcription or replication of the viral nucleic acid.
- Target DNA 311 along with exchange polynucleotide 321 may be repaired by an error-prone non-homologous end-joining DNA repair process or a homology-directed DNA repair process.
- a ZFN comprises a DNA binding domain (i.e., zinc finger) and a cleavage domain (i.e., nuclease) and this gene may be introduced as mRNA (e.g., 5' capped,
- Zinc finger binding domains may be engineered to recognize and bind to any nucleic acid sequence of choice. See, e.g., Qu et al., 2013, Zinc-finger- nucleases mediate specific and efficient excision of HIV- 1 proviral DAN from infected and latently infected human T cells, Nucl Ac Res 41(16):7771-7782, incorporated by reference.
- An engineered zinc finger binding domain may have a novel binding specificity compared to a naturally-occurring zinc finger protein. Engineering methods include, but are not limited to, rational design and various types of selection.
- a zinc finger binding domain may be designed to recognize a target DNA sequence via zinc finger recognition regions (i.e., zinc fingers).
- Exemplary methods of selecting a zinc finger recognition region may include phage display and two-hybrid systems, and are disclosed in U.S. Pat. 5,789,538; U.S. Pat. 5,925,523; U.S. Pat. 6,007,988; U.S. Pat. 6,013,453; U.S. Pat. 6,410,248; U.S. Pat. 6,140,466; U.S. Pat. 6,200,759; and U.S. Pat. 6,242,568, each of which is incorporated by reference.
- a ZFN also includes a cleavage domain.
- the cleavage domain portion of the ZFNs may be obtained from any suitable endonuclease or exonuclease such as restriction endonucleases and homing endonucleases. See, for example, Belfort & Roberts, 1997, Homing endonucleases: keeping the house in order, Nucleic Acids Res 25(17):3379-3388.
- a cleavage domain may be derived from an enzyme that requires dimerization for cleavage activity. Two ZFNs may be required for cleavage, as each nuclease comprises a monomer of the active enzyme dimer.
- a single ZFN may comprise both monomers to create an active enzyme dimer.
- Restriction endonucleases present may be capable of sequence-specific binding and cleavage of DNA at or near the site of binding.
- Certain restriction enzymes e.g., Type IIS
- Fokl active as a dimer, catalyzes double-stranded cleavage of DNA, at 9 nucleotides from its recognition site on one strand and 13 nucleotides from its recognition site on the other.
- the Fokl enzyme used in a ZFN may be considered a cleavage monomer.
- two ZFNs each comprising a Fokl cleavage monomer, may be used to reconstitute an active enzyme dimer.
- a Fokl cleavage domain two ZFNs, each comprising a Fokl cleavage monomer, may be used to reconstitute an active enzyme dimer.
- Virus targeting using ZFN may include introducing at least one donor polynucleotide comprising a sequence into the cell.
- a donor polynucleotide preferably includes the sequence to be introduced flanked by an upstream and downstream sequence that share sequence similarity with either side of the site of integration in the chromosome.
- the upstream and downstream sequences in the donor polynucleotide are selected to promote recombination between the chromosomal sequence of interest and the donor polynucleotide.
- the donor polynucleotide preferably includes the sequence to be introduced flanked by an upstream and downstream sequence that share sequence similarity with either side of the site of integration in the chromosome.
- the upstream and downstream sequences in the donor polynucleotide are selected to promote recombination between the chromosomal sequence of interest and the donor polynucleotide.
- the donor polynucleotide preferably includes the sequence to be introduced flanked by an upstream and downstream
- the polynucleotide will be DNA.
- the donor polynucleotide may be a DNA plasmid, a bacterial artificial chromosome (BAC), a yeast artificial chromosome (YAC), a viral vector, a linear piece of DNA, a PCR fragment, a naked nucleic acid, and may employ a delivery vehicle such as a liposome.
- the sequence of the donor polynucleotide may include exons, introns, regulatory sequences, or combinations thereof.
- the double stranded break is repaired via homologous recombination with the donor polynucleotide such that the desired sequence is integrated into the chromosome.
- a double stranded break introduced into the target sequence by the ZFN is repaired, via homologous recombination with the exchange
- ZFN methods can include using a vector to deliver a nucleic acid molecule encoding a ZFN and, optionally, at least one exchange polynucleotide or at least one donor polynucleotide to the infected cell.
- Meganucleases are endodeoxyribonucleases characterized by a large recognition site (double- stranded DNA sequences of 12 to 40 base pairs); as a result this site generally occurs only once in any given genome. For example, the 18-base pair sequence recognized by the I-Scel meganuclease would on average require a genome twenty times the size of the human genome to be found once by chance (although sequences with a single mismatch occur about three times per human-sized genome). Meganucleases are therefore considered to be the most specific naturally occurring restriction enzymes.
- LAGLIDADG Meganucleases can be divided into five families based on sequence and structure motifs: LAGLIDADG, GIY-YIG, HNH, His-Cys box and PD-(D/E)XK.
- the most well studied family is that of the LAGLIDADG proteins, which have been found in all kingdoms of life, generally encoded within introns or inteins although freestanding members also exist.
- the sequence motif, LAGLIDADG represents an essential element for enzymatic activity. Some proteins contained only one such motif, while others contained two; in both cases the motifs were followed by -75-200 amino acid residues having little to no sequence similarity with other family members.
- Crystal structures illustrates mode of sequence specificity and cleavage mechanism for the LAGLIDADG family: (i) specificity contacts arise from the burial of extended ⁇ -strands into the major groove of the DNA, with the DNA binding saddle having a pitch and contour mimicking the helical twist of the DNA; (ii) full hydrogen bonding potential between the protein and DNA is never fully realized; (iii) cleavage to generate the characteristic 4-nt 3'-OH overhangs occurs across the minor groove, wherein the scissile phosphate bonds are brought closer to the protein catalytic core by a distortion of the DNA in the central "4-base” region; (iv) cleavage occurs via a proposed two-metal mechanism, sometimes involving a unique "metal sharing” paradigm; (v) and finally, additional affinity and/or specificity contacts can arise from "adapted" scaffolds, in regions outside the core ⁇ / ⁇ fold. See Silva et al., 2011,
- a template sequence is inserted into the genome.
- a DNA repair template containing the desired sequence must be present during homology directed repair (HDR).
- the DNA template is normally transfected into the cell along with the gRNA/Cas9. The length and binding position of each homology arm is dependent on the size of the change being introduced.
- HDR can introduce significant changes at the Cas9 induced double strand break.
- Some embodiments of the invention may utilize modified version of a nuclease.
- Modified versions of the Cas9 enzyme containing a single inactive catalytic domain, either RuvC- or HNH-, are called 'nickases' . With only one active nuclease domain, the Cas9 nickase cuts only one strand of the target DNA, creating a single-strand break or 'nick'. Similar to the inactive dCas9 (RuvC- and HNH-), a Cas9 nickase is still able to bind DNA based on gRNA specificity, though nickases will only cut one of the DNA strands.
- the majority of CRISPR plasmids are derived from S. pyogenes and the RuvC domain can be inactivated by a DIOA mutation and the HNH domain can be inactivated by an H840A mutation.
- a single- strand break, or nick is normally quickly repaired through the HDR pathway, using the intact complementary DNA strand as the template.
- two proximal, opposite strand nicks introduced by a Cas9 nickase are treated as a double strand break, in what is often referred to as a 'double nick' or 'dual nickase' CRISPR system.
- a double-nick induced double strain break can be repaired by either NHEJ or HDR depending on the desired effect on the gene target.
- insertions and deletions are caused by the CRISPR/Cas9 complex.
- a deletion is caused by positioning two double strand breaks proximate to one another, thereby causing a fragment of the genome to be deleted.
- a nuclease may use the targeting specificity of a guide RNA (gRNA).
- gRNA guide RNA
- guide RNAs or single guide RNAs are specifically designed to target a virus genome.
- a CRISPR/Cas9 gene editing complex of the invention works optimally with a guide RNA that targets the viral genome.
- Guide RNA gRNA
- sgRNA single guide RNA
- crRNA crisprRNA
- tracrRNA transactivating RNA
- any other targeting oligo or any combination thereof
- CRISPR/Cas9/gRNA complexes are designed to target specific viruses within a cell. It should be appreciated that any virus can be targeted using the composition of the invention. Identification of specific regions of the virus genome aids in development and designing of CRISPR/Cas9/gRNA complexes.
- the CRISPR/Cas9/gRNA complexes are designed to target latent viruses within a cell. Once transfected within a cell, the CRISPR/Cas9/gRNA complexes cause repeated insertions or deletions to render the genome incapacitated, or due to number of insertions or deletions, the probability of repair is significantly reduced.
- the Epstein-Barr virus also called human herpesvirus 4 (HHV-4) is inactivated in cells by a CRISPR/Cas9/gRNA complex of the invention.
- EBV is a virus of the herpes family, and is one of the most common viruses in humans. The virus is approximately 122 nm to 180 nm in diameter and is composed of a double helix of DNA wrapped in a protein capsid.
- the Raji cell line serves as an appropriate in vitro model.
- the Raji cell line is the first continuous human cell line from hematopoietic origin and cell lines produce an unusual strain of Epstein-Barr virus while being one of the most extensively studied EBV models.
- CRISPR/Cas9 complex with specificity for EBV is needed.
- the design of EBV-targeting CRISPR/Cas9 plasmids consisting of a U6 promoter driven chimeric guide RNA (sgRNA) and a ubiquitous promoter driven Cas9 that were obtained from Addgene, Inc.
- sgRNA U6 promoter driven chimeric guide RNA
- Cas9 nucleases Commercially available guide RNAs and Cas9 nucleases may be used with the present invention.
- An EGFP marker fused after the Cas9 protein allowed selection of Cas9-positive cells.
- guide RNAs are designed, whether or not commercially purchased, to target a specific viral genome.
- the viral genome is identified and guide RNA to target selected portions of the viral genome are developed and incorporated into the composition of the invention.
- a reference genome of a particular strain of the virus is selected for guide RNA design.
- guide RNAs that target the EBV genome are a component of the system in the present example.
- the reference genome from strain B95-8 was used as a design guide.
- selected regions, or genes are targeted. For example, six regions can be targeted with seven guide RNA designs for different genome editing purposes.
- FIG. 7 is a diagram of an EBV genome, with structure-, transformation-, and latency- related targets called out.
- FIG. 7 additionally shows where sgEBVl, sgEBV2, sgEBV3, sgEBV4/5, sgEBV6, and sgEBV7 target the EBV genome.
- EBNA1 In relation to EBV, EBNA1 is the only nuclear Epstein-Barr virus (EBV) protein expressed in both latent and lytic modes of infection. While EBNA1 is known to play several important roles in latent infection, EBNA1 is crucial for many EBV functions including gene regulation and latent genome replication. Therefore, guide RNAs sgEBV4 and sgEBV5 were selected to target both ends of the EBNA1 coding region in order to excise this whole region of the genome. These "structural" targets enable systematic digestion of the EBV genome into smaller pieces. EBNA3C and LMP1 are essential for host cell transformation, and guide RNAs sgEBV3 and sgEBV7 were designed to target the 5' exons of these two proteins respectively. iv. Introduce to cell
- Methods of the invention include introducing into a cell a nuclease and a sequence- specific targeting moiety.
- the nuclease is targeted to viral nucleic acid by means of the sequence-specific targeting moiety where it then cleaves the viral nucleic acid without interfering with a host genome.
- Any suitable method can be used to deliver the nuclease to the infected cell or tissue.
- the nuclease or the gene encoding the nuclease may be delivered by injection, orally, or by hydrodynamic delivery.
- the nuclease or the gene encoding the nuclease may be delivered to systematic circulation or may be delivered or otherwise localized to a specific tissue type.
- the nuclease or gene encoding the nuclease may be modified or
- tissue-specific promoter so that the encoded nuclease is preferentially or only transcribed in certain tissue types.
- specific CRISPR/Cas9/gRNA complexes are introduced into a cell.
- a guide RNA is designed to target at least one category of sequences of the viral genome.
- this invention can also be used to control actively replicating viruses by targeting the viral genome before it is packaged or after it is ejected.
- a cocktail of guide RNAs may be introduced into a cell.
- the guide RNAs are designed to target numerous categories of sequences of the viral genome. By targeting several areas along the genome, the double strand break at multiple locations fragments the genome, lowering the possibility of repair. Even with repair mechanisms, the large deletions render the virus incapacitated.
- RNAs are added to create a cocktail to target different categories of sequences.
- two, five, seven or eleven guide RNAs may be present in a CRISPR cocktail targeting three different categories of sequences.
- any number of gRNAs may be introduced into a cocktail to target categories of sequences.
- the categories of sequences are important for genome structure, host cell transformation, and infection latency, respectively.
- in vitro experiments allow for the determination of the most essential targets within a viral genome. For example, to understand the most essential targets for effective incapacitation of a genome, subsets of guide RNAs are transfected into model cells. Assays can determine which guide RNAs or which cocktail is the most effective at targeting essential categories of sequences.
- RNAs in the CRISPR cocktail targeted three different categories of sequences which are identified as being important for EBV genome structure, host cell transformation, and infection latency, respectively.
- Raji cells were transfected with subsets of guide RNAs.
- FIG. 14 shows relative cell proliferation after targeting various combinations of regions in an EBV genome with guide RNAs.
- sgEBV4/5 reduced the EBV genome by 85%, they could not suppress cell proliferation as effectively as the full cocktail (FIG. 14).
- Guide RNAs targeting the structural sequences sgEBVl/2/6) could stop cell proliferation completely, despite not eliminating the full EBV load (26% decrease).
- the residual EBV genome signature in sgEBV 1/2/6 was not due to intact genomes but to free-floating DNA that has been digested out of the EBV genome, i.e. as a false positive.
- CRISPR/Cas9/gRNA complexes are constructed, the complexes are introduced into a cell. It should be appreciated that complexes can be introduced into cells in an in vitro model or an in vivo model.
- CRISPR/Cas9/gRNA complexes are designed to not leave intact genomes of a virus after transfection and complexes are designed for efficient transfection.
- aspects of the invention allow for CRISPR/Cas9/gRNA to be transfected into cells by various methods, including viral vectors and non-viral vectors.
- Viral vectors may include retroviruses, lentiviruses, adenoviruses, and adeno-associated viruses.
- any viral vector may be incorporated into the present invention to effectuate delivery of the CRISPR/Cas9/gRNA complex into a cell. Some viral vectors may be more effective than others, depending on the CRISPR/Cas9/gRNA complex designed for digestion or incapacitation.
- the vectors contain essential components such as origin of replication, which is necessary for the replication and maintenance of the vector in the host cell.
- viral vectors are used as delivery vectors to deliver the complexes into a cell.
- Use of viral vectors as delivery vectors are known in the art. See for example U.S. Pub. 2009/0017543 to Wilkes et al., the contents of which are incorporated by reference.
- a retrovirus is a single-stranded RNA virus that stores its nucleic acid in the form of an mRNA genome (including the 5' cap and 3' PolyA tail) and targets a host cell as an obligate parasite.
- retroviruses have been used to introduce nucleic acids into a cell. Once inside the host cell cytoplasm the virus uses its own reverse transcriptase enzyme to produce DNA from its RNA genome, the reverse of the usual pattern, thus retro (backwards). This new DNA is then incorporated into the host cell genome by an integrase enzyme, at which point the retroviral DNA is referred to as a provirus.
- the recombinant retroviruses such as the Moloney murine leukemia virus have the ability to integrate into the host genome in a stable fashion. They contain a reverse transcriptase that allows integration into the host genome. Retroviral vectors can either be replication-competent or replication-defective. In some embodiments of the invention, retroviruses are incorporated to effectuate transfection into a cell, however the CRISPR/Cas9/gRNA complexes are designed to target the viral genome.
- lentiviruses which are a subclass of retroviruses, are used as viral vectors.
- Lentiviruses can be adapted as delivery vehicles (vectors) given their ability to integrate into the genome of non-dividing cells, which is the unique feature of lentiviruses as other retroviruses can infect only dividing cells.
- the viral genome in the form of RNA is reverse-transcribed when the virus enters the cell to produce DNA, which is then inserted into the genome at a random position by the viral integrase enzyme.
- the vector now called a provirus, remains in the genome and is passed on to the progeny of the cell when it divides.
- Adenoviral DNA does not integrate into the genome and is not replicated during cell division.
- Adenovirus and the related AAV would be potential approaches as delivery vectors since they do not integrate into the host's genome.
- only the viral genome to be targeted is effected by the CRISPR/Cas9/gRNA complexes, and not the host's cells.
- Adeno-associated virus is a small virus that infects humans and some other primate species. AAV can infect both dividing and non-dividing cells and may incorporate its genome into that of the host cell.
- scAAV self-complementary adeno-associated virus
- AAV packages a single strand of DNA and requires the process of second-strand synthesis
- scAAV packages both strands which anneal together to form double stranded DNA.
- scAAV carries many characteristics of its AAV counterpart.
- Methods of the invention may incorporate herpesvirus, poxvirus, alphavirus, or vaccinia virus as a means of delivery vectors.
- non-viral vectors may be used to effectuate transfection.
- Methods of non-viral delivery of nucleic acids include lipofection, nucleofection, microinjection, biolistics, virosomes, liposomes, immunoliposomes, polycation or lipid:nucleic acid conjugates, naked DNA, artificial virions, and agent-enhanced uptake of DNA. Lipofection is described in e.g., U.S. Pat. Nos.
- Cationic and neutral lipids that are suitable for efficient receptor-recognition lipofection of polynucleotides include those described in U.S. Pat. 7,166,298 to lessee or U.S. Pat. 6,890,554 to Jesse, the contents of each of which are incorporated by reference. Delivery can be to cells (e.g. in vitro or ex vivo administration) or target tissues (e.g. in vivo administration).
- Synthetic vectors are typically based on cationic lipids or polymers which can complex with negatively charged nucleic acids to form particles with a diameter in the order of 100 nm.
- the complex protects nucleic acid from degradation by nuclease.
- cellular and local delivery strategies have to deal with the need for internalization, release, and distribution in the proper subcellular compartment. Systemic delivery strategies encounter additional hurdles, for example, strong interaction of cationic delivery vehicles with blood components, uptake by the reticuloendothelial system, kidney filtration, toxicity and targeting ability of the carriers to the cells of interest.
- Modifying the surfaces of the cationic non-virals can minimize their interaction with blood components, reduce reticuloendothelial system uptake, decrease their toxicity and increase their binding affinity with the target cells.
- Binding of plasma proteins is the primary mechanism for RES to recognize the circulating nanoparticles.
- macrophages such as the Kupffer cells in the liver, recognize the opsonized nanoparticles via the scavenger receptor.
- non-viral vectors are modified to effectuate targeted delivery and transfection.
- PEGylation i.e. modifying the surface with
- polyethyleneglycol is the predominant method used to reduce the opsonization and aggregation of non-viral vectors and minimize the clearance by reticuloendothelial system, leading to a prolonged circulation lifetime after intravenous (i.v.) administration.
- PEGylated nanoparticles are therefore often referred as "stealth" nanoparticles. The nanoparticles that are not rapidly cleared from the circulation will have a chance to encounter infected cells.
- PEG on the surface can decrease the uptake by target cells and reduce the biological activity. Therefore, to attach targeting ligand to the distal end of the PEGylated component is necessary; the ligand is projected beyond the PEG "shield" to allow binding to receptors on the target cell surface.
- cationic liposome is used as gene carrier, the application of neutral helper lipid is helpful for the release of nucleic acid, besides promoting hexagonal phase formation to enable endosomal escape.
- neutral or anionic liposomes are developed for systemic delivery of nucleic acids and obtaining therapeutic effect in experimental animal model.
- Vectors may be incorporated into topical or intravenous formulations which may comprise a liquid or solid filler, diluent, excipient, solvent or encapsulating material, involved in carrying or transporting the subject agents from one organ, or portion of the body, to another organ, or portion of the body.
- Each carrier should be compatible with the other ingredients of the formulation.
- compositions of the invention may be encapsulated in hydrogels.
- composition as disclosed herein can comprise lipid-based formulations. Any of the known lipid-based drug delivery systems can be used in the practice of the invention. For instance, multivesicular liposomes, multilamellar liposomes and unilamellar liposomes can all be used so long as a sustained release rate of the encapsulated active compound can be established. Such formulations may be used to modify the release profile of the guided nuclease compositions. Methods of making controlled release multivesicular liposome drug delivery systems are described in PCT Application Publication Nos: WO 9703652, WO 9513796, and WO 9423697, the contents of which are incorporated herein by reference.
- Synthetic membrane vesicles may comprise a combination of phospholipids, usually in combination with steroids, especially cholesterol. Other phospholipids or other lipids may also be used. Examples of lipids useful in synthetic membrane vesicle production include
- phosphatidylglycerols phosphatidylcholines, phosphatidylserines, phosphatidylethanolamines, sphingolipids, cerebrosides, and gangliosides, with preferable embodiments including egg phosphatidylcholine, dipalmitoylphosphatidylcholine, distearoylphosphatidyleholine,
- dioleoylphosphatidylcholine dipalmitoylphosphatidylglycerol, and
- dioleoylpho sphatidylglycerol dioleoylpho sphatidylglycerol .
- compositions of the invention such variables as the efficiency of compound encapsulation, labiality of the compound, homogeneity and size of the resulting population of vesicles, active compound-to-lipid ratio, permeability, instability of the preparation, and pharmaceutical acceptability of the formulation should be considered.
- guided nuclease systems of the invention can be delivered in a vesicle, in particular a liposome (see Langer (1990) Science 249: 1527-1533), the contents of which are incorporated by reference in their entirety for all purposes).
- guided nuclease systems can be delivered in a controlled release system.
- a pump may be used (see Langer (1990) supra).
- polymeric materials can be used (see Howard et al. (1989) J. Neurosurg. 71 : 105, the contents of which are incorporated by reference in their entirety for all purposes).
- a vector of the invention can be administered so that it becomes intracellular, e.g., by use of a retroviral vector (see, for example, U.S. Pat. No. 4,980,286), or by direct injection, or by use of microparticle bombardment (e.g., a gene gun; Biolistic, Dupont), or coating with lipids or cell- surface receptors or transfecting agents, or by administering it in linkage to a homeobox-like peptide which is known to enter the nucleus (see e.g., Joliot et al., 1991, Proc. Natl. Acad. Sci. USA 88: 1864-1868), the contents of which are incorporated by reference in their entirety for all purposes.
- a nucleic acid can be introduced intracellularly and incorporated within host cell DNA for expression, by homologous recombination.
- targeted controlled-release systems responding to the unique environments of tissues and external stimuli are utilized.
- Gold nanorods have strong absorption bands in the near-infrared region, and the absorbed light energy is then converted into heat by gold nanorods, the so-called 'photothermal effect'. Because the near- infrared light can penetrate deeply into tissues, the surface of gold nanorod could be modified with nucleic acids for controlled release. When the modified gold nanorods are irradiated by near-infrared light, nucleic acids are released due to thermo-denaturation induced by the photothermal effect. The amount of nucleic acids released is dependent upon the power and exposure time of light irradiation.
- liposomes are used to effectuate transfection into a cell or tissue.
- the pharmacology of a liposomal formulation of nucleic acid is largely determined by the extent to which the nucleic acid is encapsulated inside the liposome bilayer. Encapsulated nucleic acid is protected from nuclease degradation, while those merely associated with the surface of the liposome is not protected. Encapsulated nucleic acid shares the extended circulation lifetime and biodistribution of the intact liposome, while those that are surface associated adopt the pharmacology of naked nucleic acid once they disassociate from the liposome.
- the complexes of the invention are encapsulated in a liposome.
- nucleic acids Unlike small molecule drugs, nucleic acids cannot cross intact lipid bilayers, predominantly due to the large size and hydrophilic nature of the nucleic acid. Therefore, nucleic acids may be entrapped within liposomes with conventional passive loading technologies, such as ethanol drop method (as in SALP), reverse-phase evaporation method, and ethanol dilution method (as in SNALP).
- L-PEI linear polyethylenimine
- L-PEI linear polyethylenimine
- Ultrasound shows tissue-permeabilizing effect. It is non-invasive and site- specific, and could make it possible to destroy tumor cells after systemic delivery, while leave nontargeted organs unaffected. Ultrasound-mediated microbubbles destruction has been proposed as an innovative method for noninvasive delivering of drugs and nucleic acids to different tissues. Microbubbles are used to carry a drug or gene until a specific area of interest is reached, and then ultrasound is used to burst the microbubbles, causing site- specific delivery of the bioactive materials.
- microbubbles for delivery of nucleic acids is based on the hypothesis that destruction of DNA-loaded microbubbles by a focused ultrasound beam during their microvascular transit through the target area will result in localized transduction upon disruption of the microbubble shell while sparing non-targeted areas.
- Magnetic nanoparticles are usually entrapped in gene vectors for imaging the delivery of nucleic acid.
- Nucleic acid carriers can be responsive to both ultrasound and magnetic fields, i.e., magnetic and acoustically active lipospheres (MAALs).
- MAALs magnetic and acoustically active lipospheres
- the basic premise is that therapeutic agents are attached to, or encapsulated within, a magnetic micro- or nanoparticle. These particles may have magnetic cores with a polymer or metal coating which can be functionalized, or may consist of porous polymers that contain magnetic nanoparticles precipitated within the pores. By functionalizing the polymer or metal coating it is possible to attach, for example, cytotoxic drugs for targeted chemotherapy or therapeutic DNA to correct a genetic defect.
- the particle/therapeutic agent complex is injected into the bloodstream, often using a catheter to position the injection site near the target.
- Magnetic fields generally from high-field, high- gradient, rare earth magnets are focused over the target site and the forces on the particles as they enter the field allow them to be captured and extravasated at the target.
- Synthetic cationic polymer-based nanoparticles (-100 nm diameter) have been developed that offer enhanced transfection efficiency combined with reduced cytotoxicity, as compared to traditional liposomes.
- the incorporation of distinct layers composed of lipid molecules with varying physical and chemical characteristics into the polymer nanoparticle formulation resulted in improved efficiency through better fusion with cell membrane and entry into the cell, enhanced release of molecules inside the cell, and reduced intracellular degradation of nanoparticle complexes.
- the complexes are conjugated to nano-systems for systemic therapy, such as liposomes, albumin-based particles, PEGylated proteins, biodegradable polymer-drug composites, polymeric micelles, dendrimers, among others.
- nano-systems for systemic therapy such as liposomes, albumin-based particles, PEGylated proteins, biodegradable polymer-drug composites, polymeric micelles, dendrimers, among others.
- nano-systems for systemic therapy such as liposomes, albumin-based particles, PEGylated proteins, biodegradable polymer-drug composites, polymeric micelles, dendrimers, among others.
- nano-systems for systemic therapy such as liposomes, albumin-based particles, PEGylated proteins, biodegradable polymer-drug composites, polymeric micelles, dendrimers, among others.
- liposomal anthracyclines have achieved highly efficient encapsulation, and include versions with greatly prolonged circulation such as liposomal daunorubicin and pegylated liposomal doxorubicin. See Krishna et al., Carboxymethylcellulose-sodium based transdermal drug delivery system for propranolol, J Pharm Pharmacol. 1996 Apr; 48(4):367-70.
- Liposomal delivery systems provide stable formulation, provide improved
- pharmaceutically active compound is heparin or a fragment thereof contained in a defined lipid system comprising at least one amphiphatic and polar lipid component and at least one nonpolar lipid component.
- Liposomes and polymerosomes can contain a plurality of solutions and compounds.
- the complexes of the invention are coupled to or encapsulated in polymersomes.
- polymersomes are tiny hollow spheres that enclose a solution, made using amphiphilic synthetic block copolymers to form the vesicle membrane.
- Common polymersomes contain an aqueous solution in their core and are useful for encapsulating and protecting sensitive molecules, such as drugs, enzymes, other proteins and peptides, and DNA and RNA fragments.
- the polymersome membrane provides a physical barrier that isolates the encapsulated material from external materials, such as those found in biological systems.
- Polymerosomes can be generated from double emulsions by known techniques, see Lorenceau et al., 2005, Generation of Polymerosomes from Double-Emulsions, Langmuir 21(20):9183-6, incorporated by reference.
- a gene gun is a device for injecting cells with genetic information, where the payload may be an elemental particle of a heavy metal coated with plasmid DNA. This technique may also be referred to as bioballistics or biolistics. Gene guns have also been used to deliver DNA vaccines. The gene gun is able to transfect cells with a wide variety of organic and non-organic species, such as DNA plasmids, fluorescent proteins, dyes, etc.
- aspects of the invention provide for numerous uses of delivery vectors. Selection of the delivery vector is based upon the cell or tissue targeted and the specific makeup of the
- CRISPR/Cas9/gPvNA CRISPR/Cas9/gPvNA.
- nucleofection a combination of electrical parameters generated by a device called Nucleofector, with cell-type specific reagents to transfer a substrate directly into the cell nucleus and the cytoplasm
- the Lonza pmax promoter drives Cas9 expression as it offered strong expression within Raji cells.
- obvious EGFP signals were observed from a small proportion of cells through fluorescent microscopy.
- FIG. 6 shows that including an ori-P in the plasmid promoted active plasmid replication inside the cells, which increased the transfection efficiency to >60%.
- the left panel shows that untreated cells and cells treated with a Cas9 exhibited similarly low number of cells with fluorescent markers.
- the right panels shows that the oriP promoted higher transfection.
- aspects of the invention utilize the CRISPR/Cas9/gRNA complexes for the targeted delivery.
- Common known pathways include transdermal, transmucal, nasal, ocular and pulmonary routes.
- Drug delivery systems may include liposomes, proliposomes, microspheres, gels, prodrugs, cyclodextrins, etc.
- Aspects of the invention utilize nanoparticles composed of biodegradable polymers to be transferred into an aerosol for targeting of specific sites or cell populations in the lung, providing for the release of the drug in a predetermined manner and degradation within an acceptable period of time.
- Controlled-release technology such as transdermal and transmucosal controlled-release delivery systems, nasal and buccal aerosol sprays, drug-impregnated lozenges, encapsulated cells, oral soft gels, iontophoretic devices to administer drugs through skin, and a variety of programmable, implanted drug-delivery devices are used in conjunction with the complexes of the invention of accomplishing targeted and controlled delivery.
- the CMV targeting nuclease can be delivered into a cell, organ, patient, or fetus by the techniques described herein and by techniques known in the art.
- the CMV targeting nucleases of the invention may be prepared for delivery by association (binding, encapsulating, etc.) with vectors and/or guided RNAs.
- the placenta is both a drug target and a drug barrier.
- the nuclease can be introduced into the amniotic sac or into the fetus.
- the nuclease can be introduced into the amniotic sac or into the fetus by injection.
- the fetus may be treated for CMV infection using the methods of the invention after birth, using any known technique in the art for delivering a therapeutic to an infant.
- the CRISPR/Cas9/gRNA complexes target the viral genome.
- the complexes are targeted to viral genomes.
- this invention can also be used to control actively replicating viruses by targeting the viral genome before it is packaged or after it is ejected.
- methods and compositions of the invention use a nuclease such as Cas9 to target latent viral genomes, thereby reducing the chances of proliferation.
- the nuclease may form a complex with a gRNA (e.g., crRNA + tracrRNA or sgRNA).
- the complex cuts the viral nucleic acid in a targeted fashion to incapacitate the viral genome.
- the Cas9 endonuclease causes a double strand break in the viral genome.
- the double strand breaks are designed so that small deletions are caused, or small fragments are removed from the genome so that even if natural repair mechanisms join the genome together, the genome is render incapacitated.
- the CRISPR/Cas9/gRNA complexes act on the viral genome, genes, transcripts, or other viral nucleic acid.
- the double-strand DNA breaks generated by CRISPR are repaired with small deletions. These deletions will disrupt the protein coding and hence create knockout effects.
- the nuclease may be delivered into an infected cell by transfection.
- the infected cell can be transfected with DNA that encodes Cas9 and gRNA (on a single piece or separate pieces).
- the gRNAs are designed to localize the Cas9 endonuclease at one or several locations along the viral genome.
- the Cas9 endonuclease causes double strand breaks in the genome, causing small fragments to be deleted from the viral genome. Even with repair mechanisms, the deletions render the viral genome incapacitated.
- Cells and tissues treated with a nuclease according to the methods of the invention are then provided for transplantation.
- organs are treated with the nuclease to render the tissue CMV free, prior to transplantation.
- the nucleases are prepared for use in organs for transplant.
- Organ transplantation is the moving of an organ from one body to another or from a donor site to another location on the person's own body, to replace the recipient's damaged or absent organ.
- Organ can also be created or re-grown from the person's own cells (stem cells, or cells extracted from the failing organs) or from cells of another person.
- Organs can either be from a living or cadaveric source.
- Organs that can be transplanted are the heart, kidneys, liver, lungs, pancreas, intestine, and thymus.
- Tissues include bones, tendons (both referred to as musculoskeletal grafts), cornea, skin, heart valves, nerves and veins. Cornea and musculoskeletal grafts are commonly transplanted tissues, or organs.
- method and compositions of the invention can be used to target viral nucleic acid without interfering with host genetic material.
- Methods and compositions of the invention employ a targeting moiety such as a guide RNA that has a sequence that hybridizes to a target within the viral sequence.
- Methods and compositions of the invention may further use a targeted nuclease such as the cas9 enzyme, or a vector encoding such a nuclease, which uses the gRNA to bind exclusively to the viral genome and make double stranded cuts, thereby removing the viral sequence from the host.
- the sequence for the gRNA, or the guide sequence can be determined by examination of the viral sequence to find regions of about 20 nucleotides that are adjacent to a protospacer adjacent motif (PAM) and that do not also appear in the host genome adjacent to the protospacer motif.
- PAM protospacer adjacent motif
- a guide sequence that satisfies certain similarity criteria (e.g., at least 60% identical with identity biased toward regions closer to the PAM) so that a gRNA/cas9 complex made according to the guide sequence will bind to and digest specified features or targets in the viral sequence without interfering with the host genome.
- the guide RNA corresponds to a nucleotide string next to a protospacer adjacent motif (PAM) (e.g., NGG, where N is any nucleotide) in the viral sequence.
- PAM protospacer adjacent motif
- the host genome lacks any region that (1) matches the nucleotide string according to a predetermined similarity criteria and (2) is also adjacent to the PAM.
- the predetermined similarity criteria may include, for example, a requirement of at least 12 matching nucleotides within 20 nucleotides 5' to the PAM and may also include a requirement of at least 7 matching nucleotides within 10 nucleotides 5' to the PAM.
- An annotated viral genome e.g., from GenBank
- GenBank may be used to identify features of the viral sequence and finding the nucleotide string next to a protospacer adjacent motif (PAM) in the viral sequence within a selected feature (e.g., a viral replication origin, a terminal repeat, a replication factor binding site, a promoter, a coding sequence, or a repetitive region) of the viral sequence.
- the viral sequence and the annotations may be obtained from a genome database.
- selection of the sequence to be the template for the guide RNA may favor the candidate target closest to, or at the 5' most end of, a targeted feature as the guide sequence.
- the selection may preferentially favor sequences with neutral (e.g., 40% to 60%) GC content.
- a targeting moiety (such as a guide RNA) preferably binds to targets within certain categories such as (i) latency related targets, (ii) infection and symptom related targets, and (iii) structure related targets.
- a first category of targets for gRNA includes latency-related targets.
- the viral genome requires certain features in order to maintain the latency. These features include, but not limited to, master transcription regulators, latency-specific promoters, signaling proteins communicating with the host cells, etc. If the host cells are dividing during latency, the viral genome requires a replication system to maintain genome copy level. Viral replication origin, terminal repeats, and replication factors binding to the replication origin are great targets. Once the functions of these features are disrupted, the viruses may reactivate, which can be treated by conventional antiviral therapies.
- a second category of targets for gRNA includes infection-related and symptom-related targets.
- Virus produces various molecules to facilitate infection. Once gained entrance to the host cells, the virus may start lytic cycle, which can cause cell death and tissue damage (HBV).
- HBV cell death and tissue damage
- cell products E6 and E7 proteins
- E6 and E7 proteins can transform the host cells and cause cancers. Disrupting the key genome sequences (promoters, coding sequences, etc) producing these molecules can prevent further infection, and/or relieve symptoms, if not curing the disease.
- a third category of targets for gRNA includes structure-related targets.
- Viral genome may contain repetitive regions to support genome integration, replication, or other functions. Targeting repetitive regions can break the viral genome into multiple pieces, which physically destroys the genome.
- the targeting moiety is a guide RNA.
- Each cas protein requires a specific PAM next to the targeted sequence (not in the guide RNA). This is the same as for human genome editing.
- the current understanding the guide RNA/nuclease complex binds to PAM first, then searches for homology between guide RNA and target genome.
- the guide RNA will preferably target conserved regions. As PAM is important to initial sequence recognition, it is also essential to have PAM in the conserved region.
- methods of the invention are used to deliver a nucleic acid to cells.
- the nucleic acid delivered to the cells may include a gRNA having the determined guide sequence or the nucleic acid may include a vector, such as a plasmid, that encodes an enzyme that will act against the target genetic material. Expression of that enzyme allows it to degrade or otherwise interfere with the target genetic material.
- the enzyme may be a nuclease such as the Cas9 endonuclease and the nucleic acid may also encode one or more gRNA having the determined guide sequence.
- the gRNA targets the nuclease to the target genetic material.
- the target genetic material includes the genome of a virus
- gRNAs complementary to parts of that genome can guide the degredation of that genome by the nuclease, thereby preventing any further replication or even removing any intact viral genome from the cells entirely. By these means, latent viral infections can be targeted for eradication.
- the host cells may grow at different rate, based on the specific cell type. High nuclease expression is necessary for fast replicating cells, whereas low expression help avoiding off-target cutting in non-infected cells. Control of nuclease expression can be achieved through several aspects. If the nuclease is expressed from a vector, having the viral replication origin in the vector can increase the vector copy number dramatically, only in the infected cells. Each promoter has different activities in different tissues. Gene transcription can be tuned by choosing different promoters. Transcript and protein stability can also be tuned by incorporating stabilizing or destabilizing (ubiquitin targeting sequence, etc) motif into the sequence.
- promoters may be used for the gRNA sequence, the nuclease (e.g., cas9), other elements, or combinations thereof.
- the gRNA is driven by a U6 promoter.
- a vector may be designed that includes a promoter for protein expression (e.g., using a promoter as described in the vector sold under the trademark PMAXCLONING by Lonza Group Ltd (Basel, Switzerland).
- a vector may be a plasmid (e.g., created by synthesis instrument 255 and recombinant DNA lab equipment).
- the plasmid includes a U6 promoter driven gRNA or chimeric guide RNA (sgRNA) and a ubiquitous promoter-driven cas9.
- the vector may include a marker such as EGFP fused after the cas9 protein to allow for later selection of cas9+ cells.
- cas9 can use a gRNA (similar to the CRISPR RNA (crRNA) of the original bacterial system) with a complementary trans-activating crRNA (tracrRNA) to target viral sequences complementary to the gRNA.
- crRNA CRISPR RNA
- tracrRNA complementary trans-activating crRNA
- cas9 can be programmed with a single RNA molecule, a chimera of the gRNA and tracrRNA.
- the single guide RNA (sgRNA) can be encoded in a plasmid and transcription of the sgRNA can provide the programming of cas9 and the function of the tracrRNA. See Jinek, 2012, A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity, Science 337:816-821 and especially figure 5A therein for background.
- compositions of the invention may be used to target viral nucleic acid in an infected host without adversely influencing the host genome.
- RNA-guided Cas9 nucleases DNA targeting specificity of RNA-guided Cas9 nucleases, Nature Biotechnology 31(9):827-832; and Jinek, 2012, A programmable dual- RNA-guided DNA endonuclease in adaptive bacterial immunity, Science 337:816-821, the contents of each of which are incorporated by reference. Since the targeted locations are selected to be within certain categories such as (i) latency related targets, (ii) infection and symptom related targets, or (iii) structure related targets, cleavage of those sequences inactivates the virus and removes it from the host.
- the targeting RNA (the gRNA or sgRNA) is designed to satisfy according to similarity criteria that matches the target in the viral genetic sequence without any off-target matching the host genome, the latent viral genetic material is removed from the host without any interference with the host genome. ii. Apoptotic pathway
- an aspect of the invention contemplates administration of a vector containing a promoter which is active in the latent viral state, wherein the promoter drives a cell-killing gene.
- HSV is a particularly interesting target for this approach as it has been estimated that only thousands to tens of thousands neurons are latently infected. See Hoshino et al., 2008, The number of herpes simplex virus -infected neurons and the number of viral genome copies per neuron correlate with latent viral load in ganglia, Virology 372(l):56-63, incorporated by reference.
- cell-killing genes include both (1) targetable nucleases that are targeted to the cell genome; and (2) apoptosis effectors such as BAX and BAK and proteins that destroy the integrity of the cell or mitochondrial membrane, such as alpha hemolysin.
- apoptosis effectors such as BAX and BAK and proteins that destroy the integrity of the cell or mitochondrial membrane, such as alpha hemolysin.
- the invention provides methods and therapeutics that can be used to cause the death of host cells but only those cells that are infected.
- the treatment can include delivering a gene for a protein that causes cell death, where the gene is under control of a viral regulatory element such as a promoter from the genome of the infecting virus or the gene is encoded in a vector that includes a viral origin of replication. Where the virus is present, the gene will be expressed and the gene product will cause the death of the cell.
- the gene can code for a protein important in apoptosis, or the gene can code for a nuclease that digests the host genome.
- the apoptotic embodiments may be used to remove infected cells from within a sample that contains a mix of infected and uninfected cells.
- a composition may be provided that includes a viral-driven promoter, a targetable nuclease, and guide RNAs that target the cellular (e.g., human) genome.
- the nuclease will kill the cells.
- the sample will be left containing only uninfected cells.
- An apoptosis protein may be used as the therapeutic.
- the therapeutic may be provided encoded within a vector, in which the vector also encodes a sequence that causes the therapeutic to be expressed within a cell that is infected by a virus.
- the sequence may be a regulatory element (e.g., a promoter and an origin of replication) from the genome of the virus.
- the therapeutic may provide a mechanism that selectively causes death of virus -infected cells.
- a protein may be used that restores a deficient apoptotic pathway in the cell.
- the gene may be, for example, BAX, BAK, BCL-2, or alpha-hemolysin.
- the therapeutic induces apoptosis in the cell that is infected by the virus and does not induce apoptosis in an uninfected cell.
- the invention provides a composition that includes a viral vector, plasmid, or other coding nucleic acid that encodes at least one gene that promotes apoptosis and at least one promoter associated a viral genome.
- Apoptosis regulator Bcl-2 is a family of proteins that govern mitochondrial outer membrane permeabilization (MOMP) and include pro-apoptotic proteins such as Bax, BAD, Bak, Bok, Bcl-rambo, Bcl-xs and BOK/Mtd.
- Apoptosis regulator BAX also known as bcl-2-like protein 4 is a protein that in humans is encoded by the BAX gene. BAX is a member of the Bcl-2 gene family. This protein forms a heterodimer with BCL2, and functions as an apoptotic activator. This protein is reported to interact with, and increase the opening of, the mitochondrial voltage-dependent anion channel (VDAC), which leads to the loss in membrane potential and the release of cytochrome c.
- VDAC mitochondrial voltage-dependent anion channel
- Bcl-2 homologous antagonist/killer is a protein that in humans is encoded by the BAK1 gene on chromosome 6. This protein localizes to mitochondria, and functions to induce apoptosis. It interacts with and accelerates the opening of the mitochondrial voltage-dependent anion channel, which leads to a loss in membrane potential and the release of cytochrome c.
- Human genes encoding proteins that belong to this family include: BAK1, BAX, BCL2, BCL2A1, BCL2L1, BCL2L2, BCL2L10, BCL2L13, BCL2L14, BOK, and MCL1.
- T7 in vitro transcription produced the complete guide RNA with scaffold. Flanking regions of the genome targets were PCR amplified from HSV2 strain G genomic DNA (from ATCC). Cas9 protein (from PNA Bio), guide RNA and target DNA were mixed and incubated for in vitro endonuclease assay.
- each HSV2 amplicon mentioned above into an expression vector.
- the same guide RNA sequences (RL2, LATi, LATp, UL9, OriS, and US 12) were also cloned into a CRISPR plasmid, containing CMV promoter driven cas9 and U6 promoter driven sgRNA scaffold.
- RL2, LATi, LATp, UL9, OriS, and US 12 were also cloned into a CRISPR plasmid, containing CMV promoter driven cas9 and U6 promoter driven sgRNA scaffold.
- Lipofectamine 2000 72 hours after transfection, cells were harvested for genomic DNA isolation.
- FIG. 3 is a gel with lanes showing genomic DNA size bands for cells treated with the RL2, LATi, LATp, UL9, OriS, and US 12 guide sequences with and without Cas9.
- FIG. 4 shows the results of quantitative PCR assays showing different levels of decreasing of HSV DNA in the CRISPR treated samples.
- In vivo anti-HSV treatment with a transient cell model We used a CRISPR plasmid with a scrambled sgRNA sequence as control. DNA sample input was normalized with each control sample. OriS demonstrated the highest viral DNA elimination activity followed by RL2, UL9, and LATi.
- Burkitt's lymphoma cell lines Raji, Namalwa, and DG-75 were obtained from ATCC and cultured in RPMI 1640 supplemented with 10% FBS and PSA, following ATCC
- Human primary lung fibroblast IMR-90 was obtained from Coriell and cultured in Advanced DMEM/F-12 supplemented with 10% FBS and PSA.
- Plasmids consisting of a U6 promoter driven chimeric guide RNA (sgRNA) and a ubiquitous promoter driven Cas9 were obtained from addgene, as described by Cong L et al. (2013) Multiplex Genome Engineering Using CRISPR/Cas Systems. Science 339:819-823. An EGFP marker fused after the Cas9 protein allowed selection of Cas9-positive cells (FIG. 6).
- sgRNA U6 promoter driven chimeric guide RNA
- Cas9 ubiquitous promoter driven Cas9
- pX458 from Addgene, Inc.
- a modified CMV promoter with a synthetic intron (pmax) was PCR amplified from Lonza control plasmid pmax-GFP.
- a modified guide RNA sgRNA(F+E) was ordered from IDT.
- EBV replication origin oriP was PCR amplified from B95-8 transformed lymphoblastoid cell line GM 12891.
- EBV sgRNA based on the B95-8 reference, and ordered DNA oligos from IDT. The original sgRNA place holder in pX458 serves as the negative control.
- Lymphocytes are known for being resistant to lipofection, and therefore we used nucleofection for DNA delivery into Raji cells.
- Nucleofector II for DNA delivery 5 million Raji or DG-75 cells were transfected with 5 ug plasmids in each 100-ul reaction. Cell line Kit V and program M-013 were used following Lonza recommendation. For IMR-90, 1 million cells were transfected with 5 ug plasmids in 100 ul Solution V, with program T-030 or X-005. 24 hours after nucleofection, we observed obvious EGFP signals from a small proportion of cells through fluorescent microscopy. The EGFP- positive cell population decreased dramatically after that, however, and we measured ⁇ 10% transfection efficiency 48 hours after nucleofection (FIG. 6). We attributed this transfection efficiency decrease to the plasmid dilution with cell division.
- the CRISPR plasmid To actively maintain the plasmid level within the host cells, we redesigned the CRISPR plasmid to include the EBV origin of replication sequence, oriP. With active plasmid replication inside the cells, the transfection efficiency rose to >60% (FIG. 6).
- RNA- guided endonuclease provides a therapeutic strategy to cure latent herpesviridae infection, PNAS 111(36): 13157-13162 and in the Supporting Information to that article published online at the PNAS website, and the contents of both of those documents are incorporated by reference for all purposes.
- EBNAl is crucial for many EBV functions including gene regulation and latent genome replication.
- Guide RNA sgEBV4 and sgEBV5 to both ends of the EBNAl coding region in order to excise this whole region of the genome.
- Guide RNAs sgEBVl, 2 and 6 fall in repeat regions, so that the success rate of at least one CRISPR cut is multiplied.
- These "structural" targets enable systematic digestion of the EBV genome into smaller pieces.
- EBNA3C and LMP1 are essential for host cell transformation, and we designed guide RNAs sgEBV3 and sgEBW were designed to target the 5' exons of these two proteins respectively.
- FIGS. 8-13 represent CRISPR/Cas9 induced large deletions.
- FIG. 8 shows the genome context around guide RNA sgEBV2 and PCR primer locations.
- FIG. 9 shows the large deletion induced by sgEBV2.
- Lane 1-3 are before, 5 days after, and 7 days after sgEBV2 treatment, respectively.
- FIG. 10 shows the genome context around guide RNA sgEBV3/4/5 and PCR primer locations.
- FIG. 11 shows the large deletions induced by sgEBV3/5 and sgEBV4/5.
- Lane 1 and 2 are 3F/5R PCR amplicons before and 8 days after sgEBV3/5 treatment.
- Lane 3 and 4 are 4F/5R PCR amplicons before and 8 days after sgEBV4/5 treatment.
- FIGS. 12 and 13 show that Sanger sequencing confirmed genome cleavage and repair ligation 8 days after sgEBV3/5 (FIG. 12) and sgEBV4/5 (FIG. 13) treatment. Areas 690 and 700 (FIG. 12) and areas 690 and 700 (FIG. 13) indicate the two ends before repair ligation.
- FIG. 32 represents SURVEYOR assay of EBV CRISPR (lanes numbered from left to right: Lane 1: NEB lOObp ladder; Lane 2: sgEBVl control; Lane 3: sgEBVl; Lane 4: sgEBV5 control; Lane 5: sgEBV5; Lane 6: sgEBV7 control; Lane 7: sgEBV7; Lane 8: sgEBV4).
- Guide RNA sgEBV2 targets a region with twelve 125-bp repeat units (FIG. 8). PCR amplicon of the whole repeat region gave a ⁇ 1.8-kb band (FIG. 9). After 5 or 7 days of sgEBV2 transfection, we obtained ⁇ 0.4-kb bands from the same PCR amplification (FIG. 9). The ⁇ 1.4-kb deletion is the expected product of repair ligation between cuts in the first and the last repeat unit (FIG. 8).
- DNA sequences flanking sgRNA targets were PCR amplified with Phusion DNA polymerase. SURVEYOR assays were performed following manufacturer's instruction. DNA amplicons with large deletions were TOPO cloned and single colonies were used for Sanger sequencing. EBV load was measured with Taqman digital PCR on Fluidigm BioMark.
- Taqman assay targeting a conserved human locus was used for human DNA normalization. 1 ng of single-cell whole-genome amplification products from Fluidigm CI were used for EBV quantitative PCR.
- RNA- guided endonuclease provides a therapeutic strategy to cure latent herpesviridae infection, PNAS 111(36): 13157-13162 and in the Supporting Information to that article published online at the PNAS website, and the contents of both of those documents are incorporated by reference for all purposes.
- FIGS. 14-26 represent cell proliferation arrest with EBV genome destruction.
- FIG. 14 shows cell proliferation curves after different CRISPR treatments. Five independent sgEBVl-7 treatments are shown here.
- FIGS. 15-20 show flow cytometry scattering signals before (FIG. 15), 5 days after (FIG. 16) and 8 days after (FIG. 14) sgEBVl-7 treatments.
- FIG. 18-20 show
- Regions 300 and 200 correspond to subpopulation P3 and P4 in (FIGS. 15-17).
- FIGS. 21 and 22 show microscopy revealed apoptotic cell morphology after sgEBVl-7 treatment.
- FIG. 23 shows nuclear morphology before sgEBVl-7 treatment.
- FIGS. 24-26 show nuclear morphology after sgEBVl-7 treatment.
- FIG. 15 shows that flow cytometry scattering signals clearly revealed alterations in the cell morphology after sgEBVl-7 treatment, as the majority of the cells shrank in size with increasing granulation (P4 to P3 shift).
- FIG. 19 gives DAPI staining results showing that cells in population P3 also
- FIG. 33 shows that the CRISPR treatments were not cytotoxic to the EBV-negative Burkitt's lymphoma cell line DG-75
- FIG. 34 shows that the CRISPR treatments were not cytotoxic to primary human lung fibroblasts EVIR90.
- FIGS. 27-31 represent EBV load quantitation after CRISPR treatment.
- FIG. 27 shows EBV load after different CRISPR treatments by digital PCR.
- Cas9 and Cas9-oriP had two replicates, and sgEBVl-7 had 5 replicates.
- EBV load was quantified in different samples with digital PCR targeting EBNA1.
- Another Taqman assay targeting a conserved human somatic locus served as the internal control for human DNA normalization.
- each untreated Raji cell has 42 copies of EBV genome (FIG. 27).
- Cells treated with a Cas9 plasmid that lacked oriP or sgEBV did not have an obvious difference in EBV load difference from the untreated control.
- Cells treated with a Cas9- plasmid with oriP but no sgEBV had an EBV load that was reduced by -50%.
- the EBV load was measured at the single cell level by employing single-cell whole-genome amplification with an automated microfluidic system.
- Freshly cultured Raji cells were loaded onto the microfluidic chip and captured 81 single cells.
- the live cells were flow sorted eight days after transfection and captured 91 single cells.
- FIGS. 28 shows a single Raji cell as captured on a microfluidic chip.
- FIG. 29 shows a single sgEBVl-7 treated cell as captured on the chip.
- FIG. 30 is a histogram of EBV quantitative PCR Ct values from single cells before treatment.
- the dash line represents Ct values of one EBV genome per cell.
- a log-normal distribution of EBV load was displayed by the 69 untreated single-cell products that passed the quality control, with almost every cell displaying significant amounts of EBV genomic DNA.
- FIG. 31 is a histogram of EBV quantitative PCR Ct values from single live cells 7 days after sgEBVl-7 treatment. The dash line represents Ct values of one EBV genome per cell.
- FIG. 32 represents SURVEYOR assay of EBV CRISPR.
- Lane 1 (lanes numbered from left to right): NEB lOObp ladder; Lane 2: sgEBVl control; Lane 3: sgEBVl; Lane 4: sgEBV5 control; Lane 5: sgEBV5; Lane 6: sgEBV7 control; Lane 7: sgEBV7; Lane 8: sgEBV4.
- FIG. 33 represents CRISPR cytotoxicity test with EBV-negative Burkitt's lymphoma DG-75.
- FIG. 34 represents CRISPR cytotoxicity test with primary human lung fibroblast IMR-90.
- the seven guide RNAs in our CRISPR cocktail target three different categories of sequences which are important for EBV genome structure, host cell transformation, and infection latency, respectively. To understand the most essential targets for effective EBV treatment, we transfected Raji cells with subsets of guide RNAs.
Abstract
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US10323236B2 (en) | 2011-07-22 | 2019-06-18 | President And Fellows Of Harvard College | Evaluation and improvement of nuclease cleavage specificity |
US9163284B2 (en) | 2013-08-09 | 2015-10-20 | President And Fellows Of Harvard College | Methods for identifying a target site of a Cas9 nuclease |
US9359599B2 (en) | 2013-08-22 | 2016-06-07 | President And Fellows Of Harvard College | Engineered transcription activator-like effector (TALE) domains and uses thereof |
US9340799B2 (en) | 2013-09-06 | 2016-05-17 | President And Fellows Of Harvard College | MRNA-sensing switchable gRNAs |
US9737604B2 (en) | 2013-09-06 | 2017-08-22 | President And Fellows Of Harvard College | Use of cationic lipids to deliver CAS9 |
US9322037B2 (en) | 2013-09-06 | 2016-04-26 | President And Fellows Of Harvard College | Cas9-FokI fusion proteins and uses thereof |
US20150165054A1 (en) | 2013-12-12 | 2015-06-18 | President And Fellows Of Harvard College | Methods for correcting caspase-9 point mutations |
US10077453B2 (en) | 2014-07-30 | 2018-09-18 | President And Fellows Of Harvard College | CAS9 proteins including ligand-dependent inteins |
EP3324999A1 (en) * | 2015-05-29 | 2018-05-30 | Agenovir Corporation | Compositions and methods for cell targeted hpv treatment |
WO2017070633A2 (en) | 2015-10-23 | 2017-04-27 | President And Fellows Of Harvard College | Evolved cas9 proteins for gene editing |
SG11201900907YA (en) | 2016-08-03 | 2019-02-27 | Harvard College | Adenosine nucleobase editors and uses thereof |
EP3497214B1 (en) | 2016-08-09 | 2023-06-28 | President and Fellows of Harvard College | Programmable cas9-recombinase fusion proteins and uses thereof |
WO2018039438A1 (en) | 2016-08-24 | 2018-03-01 | President And Fellows Of Harvard College | Incorporation of unnatural amino acids into proteins using base editing |
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WO2018119359A1 (en) | 2016-12-23 | 2018-06-28 | President And Fellows Of Harvard College | Editing of ccr5 receptor gene to protect against hiv infection |
US11898179B2 (en) | 2017-03-09 | 2024-02-13 | President And Fellows Of Harvard College | Suppression of pain by gene editing |
US11542496B2 (en) | 2017-03-10 | 2023-01-03 | President And Fellows Of Harvard College | Cytosine to guanine base editor |
IL306092A (en) | 2017-03-23 | 2023-11-01 | Harvard College | Nucleobase editors comprising nucleic acid programmable dna binding proteins |
US11560566B2 (en) | 2017-05-12 | 2023-01-24 | President And Fellows Of Harvard College | Aptazyme-embedded guide RNAs for use with CRISPR-Cas9 in genome editing and transcriptional activation |
US11732274B2 (en) | 2017-07-28 | 2023-08-22 | President And Fellows Of Harvard College | Methods and compositions for evolving base editors using phage-assisted continuous evolution (PACE) |
US11319532B2 (en) | 2017-08-30 | 2022-05-03 | President And Fellows Of Harvard College | High efficiency base editors comprising Gam |
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