Patent Application
20220009968
The present disclosure relates to a composition for enhancing the cell permeability and gene correction efficiency of Cas protein and guide RNA. More specifically, the composition of the present disclosure can be used for clinical therapy or cell therapy because it can provide higher gene correction efficiency by delivering genetic scissors into cells in the form of a protein-based RNP complex and can reduce the off-target effect.
The gene editing technologies include the first generation zinc-finger nucleases (ZFNs), the second generation transcription activator-like effector nucleases (TALENs) and the third generation genetic scissors Cas9 and Cpf1 derived from the CRISPR/Cas system.
The CRISPR/Cas system has originated from the adaptive immunity of microorganisms. It has originated from the immune system which remembers the DNA fragments of a bacteriophage when infected by the bacteriophage and cleaves them with the nuclease Cas9 (CRISPR-associated protein 9: RNA-guided DNA endonuclease enzyme) which serves as genetic scissors when infected again by the bacteriophage. It can conveniently cleave and correct a specific base sequence in a genome that can be recognized by guide RNA (gRNA). However, the third generation genetic scissors has the off-targeting problem of cleaving genes other than the target gene because they are expressed continuously in cells.
Especially, the early gene editing system using Cas9 plasmid requires verification of safety with regard to antibiotic resistance, immune response, etc. when delivered into the body. Although a delivery system prepared in vitro from protein-based genetic scissors (Cas9) and guide RNA was proposed recently as an alternative, it also has the problems of the efficiency of intracellular delivery and the stability of the protein and RNA (Ramakrishna S et al., 2014).
Therefore, the development of a biocompatible protein-based gene correction technology with decreased risk of off-targeting is necessary. For development of novel genetic scissors that can be stably applied to clinical therapy and cell therapy, effective intracellular delivery and reduced cytotoxicity are necessary. However, since the efficiency of intracellular delivery of the Cas9 protein-RNA complex (ribonucleoprotein: RNP) is very limited with around 10%, the existing gene correction technology is limited.
The present disclosure is directed to providing a cell-penetrating peptide for a Cas protein-RNA complex (ribonucleoprotein: RNP).
The present disclosure is also directed to providing a composition for gene correction, which contains a Cas protein-RNA complex (ribonucleoprotein: RNP).
The present disclosure is also directed to providing a method for preparing a non-human transformant using the composition.
The present disclosure provides a cell-penetrating peptide for a Cas protein-RNA complex (ribonucleoprotein: RNP), which is represented by General Formula 1.
Arg-Arg-Arg-Trp-Cys-Lys-Arg-Arg-Arg-Ala-Ser-[Gly]m[His-Glu]n [General Formula 1]
In the above formula, m is an integer from 3 to 7, and n is an integer from 5 to 15.
In General Formula 1, m may be an integer from 9 to 15. More specifically, m may be an integer from 10 to 12.
The cell-penetrating peptide for a Cas protein-RNA complex (ribonucleoprotein: RNP) may be represented by SEQ ID NO 6.
The present disclosure also provides a composition for gene correction, which contains a complex (RNP) including: a) a Cas protein to which a cell-penetrating peptide represented by General Formula 1 is bound; and b) a guide RNA
Arg-Arg-Arg-Trp-Cys-Lys-Arg-Arg-Arg-Ala-Ser-[Gly]m[His-Glu]n [General Formula 1]
wherein m is an integer from 3 to 7, and n is an integer from 5 to 15.
In General Formula 1, m may be an integer from 9 to 15. More specifically m may be an integer from 10 to 12.
The Cas protein may be represented by SEQ ID NO 9.
The guide RNA may be a dual RNA or a single-stranded guide RNA (sgRNA) including crRNA and tracrRNA.
The composition may induce targeted mutation of single or multiple genes in a prokaryotic cell, a eukaryotic cell or a non-human eukaryotic organism.
The present disclosure also provides a method for preparing a non-human transformant, which includes 1) a step of introducing the composition for gene correction into an isolated prokaryotic cell, eukaryotic cell or non-human eukaryotic organism by a method selected from local injection, microinjection, electroporation and lipofection.
The present disclosure also provides a non-human transformant prepared by the method.
The present disclosure relates to a composition for gene correction, which contains a complex (RNP) of a Cas protein to which a cell-penetrating peptide is bound and a guide RNA. The currently available CRISPR-Cas-based gene correction technology has the problems of difficult intracellular injection in a complex form, unverified stability and low efficiency even after injection, and the off-target problem. In contrast, the composition for gene correction of the present disclosure can be usefully used for gene therapy due to remarkably high intracellular delivery efficiency, inhibited off-target, and ensured stability.
The inventors of the present disclosure have made efforts to develop an effective gene correction technology capable of overcoming the limitation of the CRISPR-Cas-based gene correction technology and replacing the same. As a result, they have designed a specific gene correction technology utilizing a cell-penetrating peptide in order to effectively deliver a Cas protein-RNA complex (ribonucleoprotein: RNP) into cells, and have completed the present disclosure by identifying that the Cas protein-RNA complex (ribonucleoprotein: RNP) is delivered into cells.
An aspect of the present disclosure relates to a cell-penetrating peptide represented by General Formula 1 for a Cas protein-RNA complex (ribonucleoprotein: RNP).
Arg-Arg-Arg-Trp-Cys-Lys-Arg-Arg-Arg-Ala-Ser-[Gly]m[His-Glu]n [General Formula 1]
In the above formula, m may be an integer from 3 to 7, and n may be an integer from 5 to 15.
In the above formula, [Gly]m is a linker which connects peptides, and m may be an integer from 3 to 7, although not being specially limited thereto. If m is larger than 7, cell-penetrating effect may be unsatisfactory because the sequence length is excessively long. And, if it is smaller than 3, sufficient flexibility cannot be ensured. More specifically, m may be from 4 to 6.
If n in the above formula is an integer from 5 to 15, the cell-penetrating peptide may be used as a cell-penetrating peptide. Specifically, when n is an integer from 9 to 15, more specifically an integer from 10 to 12, masking and delivery efficiency are superior by 1.3-1.5 times or more. Further more specifically, n may be an integer which is 10 or larger.
In the present disclosure, a protein capable of providing a new Cas protein-RNA complex (ribonucleoprotein: RNP) by enhancing cell permeability and gene correction efficiency with decreased off-targeting and ensured stability was developed.
Since the cell-penetrating peptide for a Cas protein-RNA complex (ribonucleoprotein: RNP) having an amino acid sequence represented by General Formula 1 used in the present disclosure is the smallest peptide with the most superior delivery efficiency and masking efficiency, it can minimize any biological interference that may occur.
According to an exemplary embodiment, General Formula 1 may be represented by an amino acid sequence represented by any of SEQ ID NOS 10-17, specifically by any of SEQ ID NOS 15-17, most specifically by SEQ ID NO 15. Since the cell-penetrating peptide for a Cas protein-RNA complex (ribonucleoprotein: RNP) includes the attenuator HE in an adequate amount, it does not interfere with the formation of a Cas protein-RNA complex (ribonucleoprotein: RNP) at all. It was confirmed experimentally that, unlike the existing cell-penetrating peptide, the cell-penetrating peptide-bound Cas protein-RNA complex (ribonucleoprotein: RNP) of the present disclosure exhibits the best intracellular delivery efficiency and gene correction efficiency.
Another aspect of the present disclosure relates to a composition for gene correction, which contains a complex (RNP) including: a) a Cas protein to which a cell-penetrating peptide represented by General Formula 1 is bound; and b) a guide RNA.
Arg-Arg-Arg-Trp-Cys-Lys-Arg-Arg-Arg-Ala-Ser-[Gly]m[His-Glu]n [General Formula 1]
In the above formula, m is an integer from 3 to 7, and n is an integer from 5 to 15.
In the above formula, [Gly]m is a linker which connects peptides, and m may be an integer from 3 to 7, although not being specially limited thereto. If m is larger than 7, cell-penetrating effect may be unsatisfactory because the sequence length is excessively long. And, if it is smaller than 3, sufficient flexibility cannot be ensured. More specifically, m may be from 4 to 6.
If n in the above formula is an integer from 5 to 15, the cell-penetrating peptide may be used as a cell-penetrating peptide. Specifically, when n is an integer from 9 to 15, more specifically an integer from 10 to 12, masking and delivery efficiency are superior by 1.3-1.5 times or more. Further more specifically, n may be an integer which is 10 or larger.
The information about the Cas protein or gene may be obtained from a known database such as GenBank of the NCBI (National Center for Biotechnology Information). Specifically, the Cas protein may be Cas9 protein. In addition, the Cas protein may be a Cas protein derived from the genus Campylobacter, more specifically from Campylobacter jejuni. More specifically, it may be Cas9 protein. As a more specific example, it may be a protein having an amino acid sequence of SEQ ID NO 9, or a protein having the activity of the protein having the sequence and has homology thereto. In addition, the protein may have a sequence identity of at least 50%, 60%, 70%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% to SEQ ID NO 39, although not being limited thereto.
In addition, the term Cas protein is used in the present disclosure to include, in addition to the natural protein, all variants that may act as activated endonuclease or nickase in cooperation with a guide RNA. Activated endonuclease or nickase can cleave a target DNA and thus can lead to genome correction. In addition, an inactivated variant may lead to regulation of transcription or cleavage of target DNA.
The variant of the Cas protein may be a mutant of Cas9 in which the catalytic aspartate residue or histidine residue is changed with another arbitrary amino acid. Specifically, the another amino acid may be alanine, although not being limited thereto.
More specifically, the Cas protein, specifically the Cas9 protein derived from C. jejuni may be one in which the catalytic aspartic acid (D) at position 8 or the histidine (H) residue at position 559 is substituted with another amino acid. Specifically, the another amino acid may be alanine, although not being limited thereto. That is to say, a Cas9 nuclease protein prepared by introducing mutation to only one active site of the Cas9 nuclease protein may act as a nickase when bound to a guide RNA. The nickase is included in the category of RGEN because it may cause double-strand breakage (DSB) by cleaving both DNA strands on both sides when two nickases are used.
In the present disclosure, the term “inactivated Cas protein” refers to a Cas nuclease protein with all or part of the function of the nuclease inactivated. The inactivated Cas is also referred to as dCas.
The term “cleavage” used in the present disclosure includes the breakage of a covalent backbone of a nucleotide molecule.
The Cas protein to which the cell-penetrating peptide represented by General Formula 1 is bound a) is one which is developed to able to function in cells. Specifically, it may be one in which the cell-penetrating peptide represented by General Formula 1 is bound or connected to the Cas protein represented by SEQ ID NO 9. The cell-penetrating peptide may be represented specifically by SEQ ID NOS 10-17, more specifically by SEQ ID NOS 15-17, most specifically by SEQ ID NO 15. The Cas protein bound to the cell-penetrating peptide represented by SEQ ID NO 15 may be represented by SEQ ID NO 15.
If a peptide other than the cell-penetrating peptide represented by General Formula 1 is connected, gene correction efficiency and intracellular delivery efficiency are decreased significantly as demonstrated in the test examples described below and off-target ratio may increase even when the intracellular delivery efficiency is high.
The Cas protein or a nucleic acid encoding the same may further include a nuclear localization signal (NLS) for importing the Cas protein into the nucleus.
In addition, the nucleic acid encoding the Cas protein may further include a nuclear localization signal (NLS) sequence. Accordingly, an expression cassette including a nucleic acid encoding the Cas protein may include, in addition to a regulatory sequence such as a promoter sequence for expressing the Cas protein, an NLS sequence, although not being limited thereto.
The Cas protein may be linked to a tag which is advantageous for separation and/or purification. Examples of the tag that may be linked include a small peptide tag such as a His tag, a Flag tag, an S tag, etc., a GST (glutathione S-transferase) tag, an MBP (maltose-binding protein) tag, etc., although not being limited thereto.
In the present disclosure, an RNP refers to a ribonucleic acid protein in complex form in which a) a Cas protein to which a cell-penetrating peptide represented by General Formula 1 is bound; and b) a target DNA-specific guide RNA are bound.
In the present disclosure, the RNP may be applied to a cell in the form of a) a Cas protein to which a cell-penetrating peptide represented by General Formula 1 is bound or a nucleic acid encoding the same; and b) a target DNA-specific guide RNA or a DNA encoding the guide RNA, although not being limited thereto. The guide RNA or the DNA encoding the same and the Cas protein to which a cell-penetrating peptide represented by General Formula 1 is bound or a nucleic acid encoding the same a) may be applied to a cell either simultaneously or sequentially.
Accordingly, in the present disclosure, it is the most preferable in terms of stability, gene correction efficiency and delivery efficiency that an RNP complex consisting of a) a Cas protein to which a cell-penetrating peptide represented by General Formula 1 is bound; and b) a guide RNA is delivered into a cell. Particularly, this is advantageous in that there is no risk of genetic modification because a DNA vector is not used.
According to an exemplary embodiment, General Formula 1 may be selected from any of SEQ ID NOS 10-17, specifically from any of SEQ ID NOS 15-17. Most specifically, it may be represented by an amino acid sequence represented by SEQ ID NO 15. Since the cell-penetrating peptide for a Cas protein-RNA complex represented by SEQ ID NO 15 is the smallest peptide with the most superior delivery efficiency and masking efficiency, it can minimize any biological interference that may occur.
The “guide RNA” refers to an RNA which is specific to a target DNA. It may be combined with the Cas protein to guide the Cas protein to the target DNA. The guide RNA may be prepared to be specific to a target to be cleaved.
In the present disclosure, a guide RNA may be a dual RNA composed of two RNAs, i.e., a crRNA (CRISPR RNA) and a tracrRNA (trans-activating crRNA). Alternatively, the guide RNA may be a sgRNA (single-chain guide RNA) prepared from the fusion of a first part including a sequence capable of forming a base pair with a complementary strand of the target DNA and a second part including a sequence interacting with the Cas protein, more specifically the major parts of a crRNA and a tracrRNA.
The sequence capable of forming a base pair with the complementary strand of the target DNA may have a length of 17-23 bp, 18-23 bp or 19-23 bp, more specifically 20-23 bp, further more specifically 21-23 bp, although not being limited thereto. This applies to both a dual RNA and a sgRNA, more specifically to a sgRNA.
In addition, the guide RNA may have 1-3 additional nucleotides, more specifically 2 or 3 nucleotides, in front of the 5′-end of the sequence capable of forming a base pair with the complementary strand of the target DNA. For example, the nucleotide may be A, T, G or C. The guide RNA may have more specifically 1-3 guanines (G's), further more specifically 2 or 3 G′s. This applies to both a dual RNA and a sgRNA, more specifically to a sgRNA.
The sgRNA may include a region having a sequence complementary to the sequence in the target DNA (referred to as Spacer region, target DNA recognition sequence, base pairing region, etc.) and a hairpin structure for binding to the Cas protein. More specifically, it may include a region having a sequence complementary to the sequence in the target DNA, a hairpin structure for binding to the Cas protein, and a terminator sequence. The structures described above may be present sequentially from the 5′-end to the 3′-end, although not being limited thereto.
In the present disclosure, a guide RNA in any form may be used as long as the guide RNA incudes the major parts of a crRNA and a tracrRNA and a region complementary to the target DNA.
The guide RNA may include a first region capable of forming a base pair with the complementary strand of the target DNA sequence; and a second region having a stem or loop structure with a length of 13-18 bp (specifically 5-10 bp).
That is to say, the guide RNA may be selected adequately depending on the type of endonuclease capable of forming a complex depending on the target sequence and/or a microorganism from which it is derived. For example, the guide RNA may be one or more selected from a group consisting of a CRISPR RNA (crRNA), a trans-activating crRNA (tracrRNA) and a single-stranded guide RNA (sgRNA), and may be a double-stranded complex of CRISPR RNA (crRNA) and trans-activating crRNA (tracrRNA) or a single-stranded guide RNA (sgRNA) depending on the type of endonucleotide. The sgRNA may include crRNA and tracrRNA regions.
The composition may be for correction of a single or multiple target DNAs (or genes) in a prokaryotic cell, a eukaryotic cell or a non-human eukaryotic organism.
In the present disclosure, “gene correction (gene editing)” refers to the action of inducing mutation (deletion, substitution, and/or insertion) of one or more nucleotide by causing double-stranded DNA cleavage at the target site in a target gene. In an exemplary embodiment, the gene correction may include inactivation (knock-out) of a target gene by forming a stop codon at a target site or forming a codon encoding a non-wild-type amino acid, introduction of mutation to a non-coding DNA sequence not generating a protein, etc., although not being limited thereto.
In the present disclosure, the ‘target gene’ refers to a gene which is a target of gene correction, and the ‘target site (or target region)’ refers to the region where gene correction occurs in the target gene by Cas (or Cas9).
In the present disclosure, the ‘target sequence’ may be a base sequence of a region including a nucleotide (nt) hybridized by a guide RNA at the target site of the target gene.
The prokaryotic cell or eukaryotic cell may be an isolated cell. The eukaryotic cell may be a cell isolated from yeast, molds, protozoa, plants, higher plants, insects, amphibians or mammals such as CHO, HeLa, HEK 293 and COS-1 cells. The eukaryotic cell may be a cultured (in vitro) cell, a grafted cell, a primarily cultured cell (in vitro and ex vivo), an in vivo, or a mammalian cell isolated from a mammal including human.
The eukaryotic organism may be a eukaryotic cell (e.g., embryonic cell, stem cell, somatic cell, germ cell, etc.) derived from fungi such as yeast, eukaryotic animals (e.g., non-human primates such as monkey, dog, pig, cow, sheep, goat, mouse, rat, etc.) and/or eukaryotic plants (e.g., algae such as green algae, corn, bean, wheat, rice, etc.).
Another aspect of the present disclosure relates to a method for preparing a non-human transformant, which includes 1) a step of introducing the composition for gene correction into an isolated prokaryotic cell, eukaryotic cell or non-human eukaryotic organism by a method selected from local injection, microinjection, electroporation and lipofection.
When a non-human transformant is prepared by the method for preparing a non-human transformant of the present disclosure, the desired transformant can be obtained with high success rate. The success rate of the composition for gene correction of the present disclosure is remarkably improved over the existing composition for gene correction in that the transformant can be obtained successfully.
The present disclosure may provide a pharmaceutical composition containing the composition for gene correction. The pharmaceutical composition of the present disclosure contains a commonly used pharmaceutically acceptable carrier such as lactose, dextrose, sucrose, sorbitol, mannitol, starch, acacia gum, calcium phosphate, alginate, gelatin, calcium silicate, microcrystalline cellulose, polyvinylpyrrolidone, cellulose, water, syrup, methyl cellulose, methyl hydroxybenzoate, propyl hydroxybenzoate, talc, magnesium stearate, mineral oil, etc., although not being limited thereto. The pharmaceutical composition of the present disclosure may further contain, in addition to the above-described ingredients, a lubricant, a wetting agent, a sweetener, a flavorant, an emulsifier, a suspending agent, a preservative, etc. Suitable pharmaceutically acceptable carriers and preparations are described in detail in Remington's Pharmaceutical Sciences (19th ed., 1995).
The pharmaceutical composition of the present disclosure may be administered orally or parenterally. Specifically, it may be parenterally, e.g., by intravenous injection, topical injection, intraperitoneal injection, etc.
An adequate administration dosage of the pharmaceutical composition of the present disclosure varies depending on various factors such as preparation method, administration method, the age, body weight, sex, pathological condition and diet of a patient, administration time, administration route, excretion rate and response sensitivity. An ordinarily skilled physician will easily determine and prescribe an administration dosage effective for the desired treatment or prevention. According to a specific exemplary embodiment of the present disclosure, a daily administration dosage of the pharmaceutical composition of the present disclosure is 0.0001-100 mg/kg.
The pharmaceutical composition of the present disclosure may be prepared into a single-dose or multi-dose formulation using a pharmaceutically acceptable carrier and/or excipient according to methods that may be easily employed by those having ordinary knowledge in the art to which the present disclosure belongs. The formulation may be in the form of a solution in an oily or aqueous medium, a suspension, an emulsion, an extract, a powder, a granule, a tablet or a capsule, and may further contain a dispersant or a stabilizer.
Hereinafter, the present disclosure will be described in detail through examples. However, the following examples are for the purpose of illustrating the present disclosure more specifically only and it will be obvious to those having ordinary knowledge in the art that the scope of the present disclosure is not limited by the examples.
For cloning of a plasmid DNA (SEQ ID NOS 41-48;
Each plasmid DNA prepared in the step 1) was transformed into E. coli BL21 (DE3) star pLysS. Each colony was inoculated to 50 mL of LB liquid medium containing chloramphenicol (34 μg/mL) and ampicillin (50 μg/mL) antibiotics and, after culturing at 37° C. for 10 hours, was transferred to 500 mL of fresh LB liquid medium. The culturing was performed until OD600nm measured by a spectrophotometer reached between 0.4 and 0.6. After adding IPTG to a concentration of 0.2 mM and lowering temperature to 20° C., culturing was performed further at 150 rpm for 14 hours. After the culturing was completed, the culture was recovered and centrifuged. Then, after discarding the supernatant, the pellet was resuspended by adding a lysis buffer (0.5 M NaCl, 5 mM imidazole, 20 mM Tris-HCl, pH 8.0). After treating the resuspended solution with an ultrasonic cell disruptor (VCX-130; Sonics & Materials) and then centrifuging the same, the supernatant was separated. The separated supernatant was filtered through a 0.45-μm filter and purified using a 1 M imidazole solution using an AKTA prime protein purification system. Finally, the AP-HE-SpCas9 protein (SEQ ID NOS 10-17) was separated using a PD-10 desalting column. The protein was identified by 12% SDS-PAGE (
For cloning of a plasmid DNA (
In Table 1, Ala Ser is the restriction enzyme site (AS:Nhel).
Each plasmid DNA prepared in the step 1) was transformed into E. coli BL21 (DE3) star pLysS. Each colony was inoculated to 50 mL of LB liquid medium containing chloramphenicol (34 μg/mL) and ampicillin (50 μg/mL) antibiotics and, after culturing at 37° C. for 10 hours, was transferred to 500 mL of fresh LB liquid medium. The culturing was performed until OD600nm measured by a spectrophotometer reached between 0.4 and 0.6. After adding IPTG to a concentration of 0.2 mM and lowering temperature to 20° C., culturing was performed further at 150 rpm for 14 hours. After the culturing was completed, the culture was recovered and centrifuged. Then, after discarding the supernatant, the pellet was resuspended by adding a lysis buffer (0.5 M NaCl, 5 mM imidazole, 20 mM Tris-HCl, pH 8.0). After treating the resuspended solution with an ultrasonic cell disruptor (VCX-130; Sonics & Materials) and then centrifuging the same, the supernatant was separated. The separated supernatant was filtered through a 0.45-μm filter and purified using a 1 M imidazole solution using an AKTA prime protein purification system. Finally, the CPP-SpCas9 protein (SEQ ID NOS 19, 21, 23, 25, 27, 29 and 31) was separated using a PD-10 desalting column. The protein was identified by 12% SDS-PAGE (
For cloning of plasmid DNAs (
Each plasmid DNA prepared in the step 1) was transformed into E. coil BL21 (DE3) star pLysS. The obtained colony was inoculated to 50 mL of LB liquid medium containing chloramphenicol (34 μg/mL) and ampicillin (50 μg/mL) antibiotics and, after culturing at 37° C. for 10 hours, was transferred to 500 mL of fresh LB liquid medium. The culturing was performed until OD600nm measured by a spectrophotometer reached between 0.4 and 0.6. After adding IPTG to a concentration of 0.2 mM and lowering temperature to 20° C., culturing was performed further at 150 rpm for 14 hours. After the culturing was completed, the culture was recovered and centrifuged. Then, after discarding the supernatant, the pellet was resuspended by adding a lysis buffer (0.5 M NaCl, 5 mM imidazole, 20 mM Tris-HCl, pH 8.0). After treating the resuspended solution with an ultrasonic cell disruptor (VCX-130; Sonics & Materials) and then centrifuging the same, the supernatant was separated. The separated supernatant was filtered through a 0.45-μm filter and purified using a 1 M imidazole solution using an AKTA prime protein purification system. Finally, the CPP (AP, dNP2, R9, TAT)-AsCas12a (SEQ ID NOS 69, 70, 71 and 72) (Comparative Examples 8-11 in order) protein and the CPP (AP, dNP2, R9, TAT)-LbCas12a protein (SEQ ID NOS 73, 74, 75 and 76) (Comparative Examples 12-15 in order) were separated using a PD-10 desalting column. The proteins were identified by 12% SDS-PAGE (
Cell-penetrating ability was investigated through an experiment of delivering the AP-HE-SpCas9 protein purified in Example 6 into human HEK 293 T cells. After culturing HEK 293 T cells using DMEM, the cells were plated on a 96-well plate containing 25 μL of DMEM, with 2.5×105 cells per well. Then, the cells were mixed with the protein of an adequate concentration in 20 μL of D-PBS to a total volume of 200 μL and then incubated with the protein under various conditions.
After treating each well with a mixture of AP-HE-Cas9 (2 μM) and CQ (1, 10, 50, 100, 250, 500 μM), AP-HE-Cas9 (2 μM) alone or a control (2 μM), the cells were cultured for 2 hours in a 5% CO2 cell incubator at 37° C. The cultured cells were centrifuged and washed twice with a PBS buffer. Then, the protein adhering to the cell surface was removed by treating with a trypsin solution for 5 minutes. Then, after neutralizing using a DMEM solution and then washing with a PBS buffer, delivery efficiency was investigated by measuring intracellular fluorescence by flow cytometry (BD Science FACS Canto II). CQ stands for chloroquine, which was used as a lysosomal degradation inhibitor.
It was confirmed in Test Example 1 that the AP-HE-SpCas9 protein of the present disclosure (Example 6) is delivered well into cells. In this test example, the location of the protein after being delivered into the cells was investigated using a microscope.
After placing a 24-mm2 rectangular cover glass on each well of the 6-well plate and plating 1×105 HeLa cells, the cells were allowed to adhere to the cover glass by culturing in DMEM for 24 hours. Then, after removing the DMEM, 900 μL of fresh DMEM was added. Thereafter, the AP-HE-SpCas9 protein prepared in Example 6 was added after mixing with 50 μL of D-PBS to a concentration of 0.5 μM, 1 μM or 2 μM. Then, the cells were cultured for 2 hours at 37° C. in a 5% CO2 cell incubator. After the culturing was completed, the protein and DMEM were removed except the adhering cells and washed twice with a PBS buffer. Then, after fixing the cells in 1 mL of a 4% paraformaldehyde phosphate buffer solution (Wako) and washing again with a PBS buffer, F-actin was stained with a green fluorescent dye (Alexa Fluor 488-conjugated phalloidin; Invitrogen) and the nucleus was stained with Hoechst 33342 (Invitrogen). After washing twice with a PBS buffer and mounting on a slide glass, the location of the AP-HE-Cas9 protein of the present disclosure (Example 6) in the cells was investigated by fluorescence microscopy (Eclipse 50i, Nikon) or confocal microscopy (TCS SP5, Leica).
An AP-HE-Cas9 protein-RNA complex (ribonucleoprotein: RNP) was prepared by mixing the AP-HE-SpCas9 protein of Example 6 (5 μM) with sgRNA (5 μM) at a ratio of 1:1 and conducting reaction at room temperature for 10 minutes, and was named as AP-HE-Cas9 RNP. crRNP refers to a Cas9 protein-RNA complex (ribonucleoprotein: RNP) regardless of the type of the Cas9 protein.
It was investigated whether the AP-HE-SpCas9 protein of Example 6 prepared in the form of a Cas9 protein-RNA complex (ribonucleoprotein: RNP) exhibit gene correction effect in cells. For this, the RFP/GFP reporter system which express RFP and GFP at the same time when a specific gene is cleaved and T7 endonuclease 1 assay were used. Mouse HEK 293 T cells were cultured in DMEM. After placing 400 μL of DMEM on each well of a 24-well plate, 2.5×105 cells contained in 50 μL of DMEM were mixed. Then, CQ (50 μM) and AP-HE-Cas9 RNP were added such that the concentration corresponds to that of D-PBS present in 50 μL of the medium (on day 0). The final volume was adjusted to 500 μL.
On day 1 after the culturing, the HEK 293 T cells in each well were treated with 5 μM AP-HE-Cas9 RNP and, after culturing for 6 hours in a 5% CO2 cell incubator at 37° C., the medium was replaced with fresh DMEM.
The next day (on day 2), after treating each well with 5 μM AP-HE-Cas9 RNP and incubating for 6 hours in a 5% CO2 cell incubator at 37° C., the medium was replaced with fresh DMEM. On day 3 after the culturing, after treating with AP-HE RNP in the same manner as on day 2 and reacting for 6 hours, the culture was recovered and then centrifuged. After removing the supernatant, the remaining pellet was washed twice with a PBS buffer and the protein attached to the cell surface was removed by treating with trypsin for 5 minutes. After neutralizing by adding an RPMI solution and washing once again with a PBS buffer, gene correction efficiency was investigated by flow cytometry (BD Science FACS Canto II) and T7 endonulease 1 assay. As a control group, the cells were treated with 250 ng of the CCR5 sgRNA vector and 250 ng of the SpCas9 vector once a day.
It was investigated whether the AP-SpCas9 of Comparative Example 1 exhibits gene correction effect in cells. For this, the RFP/GFP reporter system which express RFP and GFP at the same time when a specific gene is cleaved and T7 endonuclease 1 assay were used. Mouse HEK 293 T cells were cultured in DMEM. After placing 400 μL of DMEM on each well of a 24-well plate, 2.5×105 cells contained in 50 μL of DMEM were mixed. Then, CQ (50 μM) and the AP-Cas9 of Comparative Example 1 were added such that the concentration corresponds to that of D-PBS present in 50 μL of the medium (on day 0). The final volume was adjusted to 500 μL.
Before the addition of the AP-Cas9 of Comparative Example 1, the HEK 293 T cells were transformed with lipofectamine with a sgRNA plasmid targeting the CCR5 gene.
On day 1 after the culturing, after delivering a sgRNA plasmid targeting the AP-Cas9 plasmid (Comparative Example 1-1) CCR5 gene to the HEK 293 T cells using lipofectamine and culturing for 24 hours in a 5% CO2 cell incubator at 37° C., the medium was replaced with fresh DMEM on day 2. Then, after treating each well with 5 μM AP-SpCas9 protein (Comparative Example 1) and incubating for 6 hours in a 5% CO2 cell incubator at 37° C., the medium was replaced with fresh DMEM. On day 3, after treating each well 5 μM AP-SpCas9 protein (Comparative Example 1) and incubating for 6 hours in a 5% CO2 cell incubator at 37° C., the medium was replaced with fresh DMEM. On day 4, after treating with AP-SpCas9 in the same manner as on day 3 and reacting for 6 hours, the culture was recovered and then centrifuged. After removing the supernatant, the remaining pellet was washed twice with a PBS buffer and the protein attached to the cell surface was removed by treating with trypsin for 5 minutes. After neutralizing by adding an RPMI solution and washing once again with a PBS buffer, gene correction efficiency was investigated by flow cytometry (BD Science FACS Canto II) and T7 endonulease 1 assay.
An AP Cas9 protein-RNA complex (ribonucleoprotein: RNP) was prepared by mixing the AP-SpCas9 of Comparative Example 1 protein (5 μM) and a sgRNA (5 μM) at a ratio of 1:1 and reacting at room temperature for 10 minutes, and it was named AP-Cas9 RNP. crRNP refers to a Cas9 protein-RNA complex (ribonucleoprotein: RNP) regardless of the type of the Cas9 protein.
It was investigated whether the AP-SpCas9 protein of Comparative Example 1 prepared in the form of a Cas9 protein-RNA complex (ribonucleoprotein: RNP) exhibit gene correction effect in cells. For this, the RFP/GFP reporter system which express RFP and GFP at the same time when a specific gene is cleaved and T7 endonuclease 1 assay were used. Mouse HEK 293 T cells were cultured in DMEM. After placing 400 μL of DMEM on each well of a 24-well plate, 2.5'105 cells contained in 50 μL of DMEM were mixed. Then, CQ (50 μM) and AP RNP were added such that the concentration corresponds to that of D-PBS present in 50 μL of the medium (on day 0). The final volume was adjusted to 500 μL.
On day 1 after the culturing, the HEK 293 T cells in each well were treated with 5 μM AP-Cas9 RNP and, after culturing for 6 hours in a 5% CO2 cell incubator at 37° C., the medium was replaced with fresh DMEM. The next day (on day 2), after treating the HEK 293 T cells with 5 μM AP-Cas9 RNP and incubating for 6 hours in a 5% CO2 cell incubator at 37° C., the medium was replaced with fresh DMEM. On day 3 after the culturing, after treating with AP-Cas9 RNP in the same manner as on day 2 and reacting for 6 hours, the culture was recovered and then centrifuged. After removing the supernatant, the remaining pellet was washed twice with a PBS buffer and the protein attached to the cell surface was removed by treating with trypsin for 5 minutes. After neutralizing by adding an RPMI solution and washing once again with a PBS buffer, gene correction efficiency was investigated by flow cytometry (BD Science FACS Canto II) and T7 endonulease 1 assay. As a control group, the cells were treated with 250 ng of the CCR5 sgRNA vector and 250 ng of the SpCas9 vector once a day.
The AP-HE-SpCas9 protein prepared in Example 6 of the present disclosure includes 10 HEs, which are attenuators, and functions to prevent the + charge of the cell-penetrating peptide. It was investigated in vitro whether the target DNA was cleaved by the AP-HE-SpCas9 protein of Example 1 of the present disclosure. First, a Cas9 protein-RNA complex (ribonucleoprotein: RNP) was prepared by mixing 50 nM of Cas9 (SEQ ID NO 9), the AP-Cas9 of Comparative Example 1 (SEQ ID NO 19) or the AP-HE-Cas9 of Example 6 (SEQ ID NO 15) with 50 nM of sgRNA and reacting at room temperature for 15 minutes. Then, it was investigated whether a target DNA is cleaved by agarose electrophoresis (0.8% agarose gel) by incubating 300 ng of the target DNA at 37° C. for 15, 30 or 60 minutes.
The AP-HE-SpCas9 protein prepared in Example 6 of the present disclosure includes 10 HEs, which are attenuators, and functions to prevent the + charge of the cell-penetrating peptide. It was investigated in vitro whether the target DNA was cleaved by the AP-HE-SpCas9 protein of Example 6 of the present disclosure. First, a Cas9 protein-RNA complex (ribonucleoprotein: RNP) was prepared by mixing 50 nM of Cas9 (SEQ ID NO 9), the TAT-Cas9 of Comparative Example 7 (SEQ ID NO 29), the TAT-HE-Cas9 of Comparative Example 6 (SEQ ID NO 31), the R9-Cas9 of Comparative Example 5 (SEQ ID NO 25), the R9-HE-Cas9 of Comparative Example 4 (SEQ ID NO 27), the dNP2-Cas9 of Comparative Example 3 (SEQ ID NO 21) or the dNP2-HE-Cas9 of Comparative Example 2 (SEQ ID NO 23) with 50 nM of sgRNA and reacting at room temperature for 15 minutes. Then, it was investigated whether a target DNA is cleaved by agarose electrophoresis (0.8% agarose gel) by incubating 300 ng of the target DNA at 37° C. for 15, 30 or 60 minutes.
That is to say, it can be seen that the gene correction effect is decreased on the contrary for the CPP (cell-penetrating peptide) with the HE sequence added, such as TAT, R9, dNP2, etc.
The gene correction efficiency of a target DNA in vitro was investigated using the AP-HE-Cas9 protein prepared in Examples 1-8 of the present disclosure. A Cas9 protein-RNA complex (ribonucleoprotein: RNP) was prepared by mixing 50 nM of the AP-HE-SpCas9 protein prepared in Examples 1-8 of the present disclosure with 50 nM of a sgRNA and conducting reaction at room temperature for 15 minutes.
After placing a 24-mm2 rectangular cover glass on each well of a 6-well plate and plating 1×105 HeLa cells, the cells were allowed to adhere to the cover glass by culturing in DMEM for 24 hours. Then, after removing the DMEM, 900 μL of fresh DMEM was added. Thereafter, the AP-HE-Cas9 protein prepared in Examples 1-8 was added to a concentration of 01, 2 or 5 μM, and the cells were cultured for 1 hour at 37° C. in a 5% CO2 cell incubator under different pH conditions (pH 7.4, 6.5, 6.0). The cultured cells were centrifuged and washed twice with a PBS buffer. Then, the protein attached to the cell surface was removed by treating with a trypsin solution for 5 minutes. Then, after neutralizing with DMEM and washing once again with a PBS buffer, delivery efficiency was investigated by measuring intracellular fluorescence by flow cytometry (BD Science FACS Canto II).
It can also be seen that the AP-HE10-Cas9 of Example 6 (SEQ ID NO 15) exhibits higher delivery efficiency than the AP-HE5-Cas9 of Example 1 (SEQ ID NO 10) at pH 7.4 and 6.5.
It was confirmed that the AP-HE10-Cas9 of Example 6 (SEQ ID NO 15) exhibits remarkably higher masking efficiency than the AP-HE5-Cas9 of Example 1 (SEQ ID NO 10), the AP-HE6-Cas9 of Example 2 (SEQ ID NO 11) or the AP-HE8-Cas9 of Example 4 (SEQ ID NO 13).
In addition, it can be seen that the AP-HE10-Cas9 of Example 6 (SEQ ID NO 15) exhibits higher delivery efficiency than the AP-HE5-Cas9 of Example 1 (SEQ ID NO 10), the AP-HE6-Cas9 of Example 2 (SEQ ID NO 11) or the AP-HE8-Cas9 of Example 4 (SEQ ID NO 13) at pH 7.4-6.0.
Meanwhile, the AP-HE10-Cas9 of Example 6 (SEQ ID NO 15) and the AP-HE5-Cas9 of Example 8 (SEQ ID NO 17) did not show significant difference in masking and delivery efficiency despite the difference in HE sequence length.
That is to say, whereas Example 6 having 10 HE sequences showed excellent masking efficiency as compared to Example 2 or 4 having 6 or 8 HE sequences under various pH conditions, the AP-HE-Cas9 of Example 6 and Example 9 showed little difference. Through this, it can be seen that there is no significant effect in increasing the number of HE sequences to more than 10, and that the AP-HE10-Cas9 of Example 6 is most preferred.
Although specific exemplary embodiments of the present disclosure have been described in detail above, it is obvious to those having ordinary knowledge in the art that such specific exemplary embodiments are only preferred examples and the scope of the present disclosure is not limited by them. Accordingly, it is to be noted that the substantial scope of the present disclosure is defined by the appended claims and their equivalents.
| Number | Date | Country | Kind |
|---|---|---|---|
| 10-2018-0170463 | Dec 2018 | KR | national |
| 10-2019-0174907 | Dec 2019 | KR | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/KR2019/018627 | 12/27/2019 | WO | 00 |
