CRISPR SYSTEM FOR GENOME EDITING

Abstract

A CRISPR-Cas system targeting a genomic target sequence in a eukaryotic cell and capable of promoting death of the eukaryotic cell is provided. A viral particle and an isolated eukaryotic cell including the CRISPR-Cas system, a method that uses the CRISPR-Cas system, and use of the CRISPR-Cas system as a medicament in the treatment of neoplastic diseases are also provided.

Claims

1. A non-naturally occurring or engineered Clustered Regularly Interspersed Short Palindromic Repeat (CRISPR)-CRISPR associated (Cas) (CRISPR-Cas) system targeting at least one genomic target sequence in a target cell, the CRISPR-Cas system comprising a viral expression vector which comprises: 1) a nucleotide sequence encoding an endonuclease enzyme capable of generating cohesive ends, said nucleotide sequence being operably linked to one or more regulatory sequences located on the viral expression vector; 2) a nucleotide sequence encoding a protein capable of promoting cell death, said nucleotide sequence not being operably linked to any regulatory sequence located on the viral expression vector; 3) a first target nucleotide sequence and a second target nucleotide sequence located, respectively, downstream of the 3′ end and upstream of the 5′ end of the nucleotide sequence encoding the protein capable of promoting cell death, both the first target nucleotide sequence and the second target nucleotide sequence being located downstream of the 3′ end of a Protospacer Adjacent Motif (PAM) nucleotide sequence; 4) a nucleotide sequence encoding a first guide RNA (first gRNA) operably linked to one or more regulatory sequences located on the viral expression vector, wherein said first gRNA comprises a first scaffold nucleotide sequence capable of binding the endonuclease enzyme and a first guide nucleotide sequence capable of hybridizing to the first target nucleotide sequence; and 5) a nucleotide sequence encoding a second guide RNA (second gRNA) operably linked to one or more regulatory sequences located on the viral expression vector, wherein said second gRNA comprises a second scaffold nucleotide sequence capable of binding the endonuclease enzyme and a second guide nucleotide sequence capable of hybridizing to the second target nucleotide sequence, wherein the first target nucleotide sequence corresponds to the at least one genomic target sequence in the target cell targeted by the CRISPR-Cas system.

2. The CRISPR-Cas system according to claim 1, wherein the first target nucleotide sequence and the second target nucleotide sequence are the same or different, and wherein the first target nucleotide sequence and the second target nucleotide sequence are selected so that protruding single-stranded portions of respective cohesive ends generated upon endonuclease enzyme cleavage are complementary sequences.

3. The CRISPR-Cas system according to claim 1, wherein the CRISPR-Cas system targets a first genomic target sequence and a second genomic target sequence, and wherein the first genomic target sequence corresponds to the first target nucleotide sequence and the second genomic target sequence corresponds to the second target nucleotide sequence.

4. The CRISPR-Cas system according to claim 1, wherein the endonuclease enzyme is selected from the group consisting of Cas12a and mutants thereof which are capable of binding to different PAM sequences.

5. The CRISPR-Cas system according to claim 1, wherein the protein capable of promoting cell death is thymidine kinase.

6. The CRISPR-Cas system according to claim 1, wherein the at least one genomic target sequence in the target cell targeted by the CRISPR-Cas system comprises one or more gene mutations.

7. The CRISPR-Cas system according to claim 6, wherein gene mutation is selected from the group consisting of TP53 gene mutations, KRAS/BRAF gene mutations, NRAS gene mutations, EGFR gene mutations in a region encoding the extracellular domain of the receptor, HER2 gene amplification, EML4/ALK translocation, and MET, PK3CA and ERB2 gene mutations, and any combination thereof.

8. The CRISPR-Cas system according to claim 1, wherein the viral expression vector further comprises a nucleotide sequence encoding an integrase enzyme, the nucleotide sequence comprising a mutation capable of suppressing activity of said integrase enzyme.

9. The CRISPR-Cas system according to claim 1, wherein the target cell is a eukaryotic cell.

10. A viral particle comprising the CRISPR-Cas system according to claim 1.

11. The viral particle according to claim 10, wherein the viral particle is selected from the group consisting of lentivirus, retrovirus, adenovirus and adeno-associated virus.

12. The viral particle according to claim 10, further comprising a chimeric capsid protein, said chimeric capsid protein comprising a domain capable of binding to at least one marker expressed on a surface of the target cell targeted by the CRISPR-Cas system.

13. The viral particle according to claim 12, wherein said domain is an antibody, a growth factor or a ligand.

14. The viral particle according to claim 12, wherein said at least one marker is selected from the group consisting of CD5, CD19, CD20, CD23, CD46, BCR protein, and any combination thereof.

15. An in vitro method for promoting apoptosis in a target cell, said method comprising the steps of: transducing the target cell with a non-naturally occurring or engineered Clustered Regularly Interspersed Short Palindromic Repeat (CRISPR)-CRISPR associated (Cas) (CRISPR-Cas) system targeting at least one genomic target sequence in a target cell, the CRISPR-Cas system comprising a viral expression vector which comprises: 1) a nucleotide sequence encoding an endonuclease enzyme capable of generating cohesive ends, said nucleotide sequence being operably linked to one or more regulatory sequences located on the viral expression vector; 2) a nucleotide sequence encoding a protein capable of promoting cell death, said nucleotide sequence not being operably linked to any regulatory sequence located on the viral expression vector; 3) a first target nucleotide sequence and a second target nucleotide sequence located, respectively, downstream of the 3′ end and upstream of the 5′ end of the nucleotide sequence encoding the protein capable of promoting cell death, both the first target nucleotide sequence and the second target nucleotide sequence being located downstream of the 3′ end of a Protospacer Adjacent Motif (PAM) nucleotide sequence; 4) a nucleotide sequence encoding a first guide RNA (first gRNA) operably linked to one or more regulatory sequences located on the viral expression vector, wherein said first gRNA comprises a first scaffold nucleotide sequence capable of binding the endonuclease enzyme and a first guide nucleotide sequence capable of hybridizing to the first target nucleotide sequence; and 5) a nucleotide sequence encoding a second guide RNA (second gRNA) operably linked to one or more regulatory sequences located on the viral expression vector, wherein said second gRNA comprises a second scaffold nucleotide sequence capable of binding the endonuclease enzyme and a second guide nucleotide sequence capable of hybridizing to the second target nucleotide sequence, wherein the first target nucleotide sequence corresponds to the at least one genomic target sequence in the target cell targeted by the CRISPR-Cas system and/or with at least one viral particle comprising said CRISPR-Cas system, and culturing the transduced cell under suitable conditions for inducing expression of the endonuclease enzyme and the first gRNA and second gRNA and for obtaining a first macromolecular complex comprising the endonuclease enzyme associated with said first gRNA and a second macromolecular complex comprising the endonuclease enzyme associated with said second gRNA.

16. The method according to claim 15, wherein the protein capable of promoting cell death is thymidine kinase.

17. The method according to claim 16, further comprising the step of contacting the target cell with a substrate of thymidine kinase.

18. The method according to claim 15, wherein the target cell is a eukaryotic cell.

19. An isolated target cell comprising a CRISPR-Cas system according to claim 1.

20. (canceled)

21. A method for treating, in a subject in need thereof, a disease selected from the group consisting of B-cell Chronic Lymphocytic Leukemia, non-Hodgkin lymphoma, myelodysplastic syndromes, myeloproliferative neoplasms, multiple myeloma, acute myeloid leukemia, acute lymphoblastic leukemia, lung squamous cell carcinoma, lung adenocarcinoma, ovarian cancer, colorectal cancer, esophageal cancer, head and neck cancer, laryngeal cancer, skin cancer, pancreatic cancer, stomach cancer, prostate cancer, liver cancer, brain tumour, bladder cancer, breast cancer, uterine cancer, soft tissue sarcoma, bone cancer, endocrine tumours and cervical cancer, the method comprising administering to said subject the CRISPR-Cas system of claim 1.

Description

[0057] The experimental section that follows is provided for illustration purposes only and does not limit the scope of the invention as defined in the appended claims. In the experimental section, reference is made to the accompanying drawings, wherein:

[0058] FIG. 1 is a schematic representation of the CRISPR system of the invention. (A) Representation of the structure of the viral expression vector according to the invention. (B-E) Mechanism of action of the CRISPR system of the invention: (B) transduction of the viral expression vector into the target cell carrying the target genomic mutation; (C) (i) expression of Cas12a and of the two gRNAs (gRNA I and gRNA II), and binding of the latter to the endonuclease to form a first and a second macromolecular complex; (ii) transfer of the first and second macromolecular complexes towards the target sequences (TARGET SEQ I and TARGET SEQ II) present on the vector and the cell genome, and DNA cleavage at these sequences with excision of the sequence encoding the TK enzyme, optionally linked to the enhanced green fluorescent protein (EGFP); (D) insertion of the EGFP-TK-encoding sequence into the double-stranded cut on the genomic target sequence by homologous repair; (E) administration to the modified target cell of ganciclovir, which is converted by the TK enzyme into a toxic compound that causes the death of the cell.

[0059] FIG. 2 illustrates charts showing cell death figures, as determined by FACS analysis, in the presence (+) and the absence (−) of ganciclovir (GCV) in HEK293 cell cultures engineered with the target mutation (A) and in wild-type HEK293 cell cultures (B), transfected with the lentiviral vector (LV+TK), untransfected (CTR), transfected with the lentiviral vector devoid of the EGFP-TK cassette (LV-TK), and transfected with the lentiviral vector constitutively encoding the EGFP-TK sequence (pEGFP+TK). After 3 days in the presence or the absence of Ganciclovir treatment (GCV, 0.1 mg/ml) a 70% reduction in the number of cells in the culture was detected in the mutated HEK293 cell sample transfected with the CRISPR system of the invention, and an 80% reduction was detected in the mutated and wild type HEK293 cell samples transfected with the lentiviral vector constitutively encoding the EGFP-TK sequence.

[0060] FIG. 3 is a schematic illustration of the cutting process performed by the enzyme Cas12a on the lentiviral vector and the target genome, showing that the mutation that introduces a stop codon remains after the correct integration of the EGFP-TK sequence (coding cassette) into the target genome 3′ (downstream) of said coding sequence so as to allow the translation of the suicidal gene. Two different gRNAs are used to guide Cas12a enzyme to the target sequences. gRNA(a): arbitrary sequence specific for the 5′ portion of the coding cassette; gRNA(b): mutated sequence specific for the mutated gene and the 3′ region of the coding cassette. (A) detail of the EGFP-TK (coding cassette) sequence present in the lentiviral vector. The Cas12a enzyme cleavage site that produces cohesive ends is indicated by a dashed line; (B) detail of the TP53 genomic sequence containing the target mutation. The Cas12a enzyme cleavage site that produces cohesive ends is indicated by a dashed line. The TGA stop codon is boxed and indicated with an asterisk. (C) scheme of insertion of the coding cassette excised from the lentiviral vector by the Cas12a enzyme within the TP53 genomic sequence containing the target mutation.

[0061] FIG. 4 shows the results of HEK293T cell infection by wild-type integrases compared to transfection with inactive integrase. (A) HEK293T cells infected with the lentivirus characterized by wild-type integrases show unchanged expression of the GFP reporter protein 4, 8, 11, 15 and 18 days after infection. (B) On the other hand, HEK293T cells infected with the lentivirus characterized by inactive integrase show decreased expression of the GFP reporter protein already 8 days after infection, and its total clearance 11 days after infection, as in the untreated control (C).

[0062] FIG. 5 shows the results of the qPCR analysis carried out to test the expression of the Cas12a enzyme 48 hours after infection (A) of HEK293 cells with the virus carrying wild-type integrases compared to (B) the virus with the inactive integrase. LV-TK: lentiviral vector without the EGFP-TK cassette, where the target sequences leading to cassette excision are absent. LV+TK: lentiviral vector with the EGFP-TK cassette carrying the target sequences leading to cassette excision. (A) No difference is detected in the expression of the Cas12a enzyme after infection with the wild-type integrase virus carrying LV-TK or LV+TK. (B) A significant difference in expression of the Cas12a enzyme is detected after infection with the inactive integrase virus carrying LV-TK or LV+TK. GFP virus with wild-type integrase and inactive integrase was used as a negative control since the GFP vector does not contain the sequence encoding Cas12a enzyme. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH): housekeeping gene.

EXAMPLE 1: SET-UP OF THE EXPERIMENTAL MODEL

[0063] Given the prominent role of the TP53 gene in cancer progression and drug resistance, the present inventors selected this experimental model to assess the efficacy and specificity of the CRISPR system of the invention. As previously described, the CRISPR system of the invention, through viral transduction, allows a gene encoding a cell death-promoting protein (for example, thymidine kinase, TK) to be inserted into a target cell, for example a tumour cell. Experiments carried out by the present inventors used tumour-specific TP53 gene mutations as the genomic target of the CRISPR system according to the invention, demonstrating that the action of this system induces cell death only in tumour cells, without causing any damage to normal cells. Table 1 lists tumours associated with TP53 gene mutations.

TABLE-US-00001 TABLE 1 Percentage of TP53 mutations in different types of tumours. Other % patients % patients % patients haematological with TP53 with TP53 with TP53 tumours mutation Solid tumours mutation Solid tumours mutation Non-Hodgkin's 66-11% .sup.   Squamous cell 81.0% Prostate 17.5% lymphoma lung Myelodysplastic 20-5%.sup.  Lung 46.0% Liver 31.9% syndromes adenocarcinoma Myeloproliferative 15% Ovary 47.8% Brain 27.0% neoplasms Multiple myeloma 10% Colon-rectum 43.2% Bladder 26.4% Acute myeloid  5% Esophagus 43.1% Breast 25.0% leukemia Acute lymphoblastic  3% Head and neck 40.6% Uterus 20.5% leukemia Larynx 40.4% Soft tissue 19.1% Skin 35.0% Bone tissue 14.6% Pancreas 32.6% Endocrine glands 14.6% Stomach 32.0% Cervix 5.8%

[0064] For experimental studies, a haematological tumour was selected, more specifically B-cell chronic lymphocytic leukemia. The CRISPR system according to the invention was first tested in vitro by using HEK293 and MCF7 cells engineered with the TP53 gene target mutation (c.548C>G; p.Ser183*), and B-CLL cells carrying TP53 gene mutations isolated from a patient.

[0065] In order to increase the specificity of the CRISPR system of the invention for B-CLL target cells, a pseudotyped HIV-derived lentiviral vector was designed and generated, which had lost its ability to integrate into the cell genome and was specifically targeted to B cells by using measles virus envelope glycoproteins and an anti-CD20/CD5 antibody (Funke S., et al, “Targeted cell entry of lentiviral vectors, (2008) Mol Ther. 16(8):1427-36). The various steps of the experimental approach followed by the present inventors are as described below.

Materials and Methods

EXAMPLE 2: ISOLATION OF PERIPHERAL BLOOD MONONUCLEAR CELLS (PBMCS) AND CELL CULTURE CONDITIONS

[0066] In order to prepare chronic lymphocytic leukemia lymphocytes, peripheral blood mononuclear cells (PBMCs) were isolated from leukemia patient blood samples. Blood samples were diluted with an equal volume of phosphate saline solution (pH 7.5) (PBS). The diluted blood was then carefully layered over a volume of human Pancoll (PAN Biotech) equal to the original blood sample volume. The sample was centrifuged at 350×g for 30 minutes at room temperature to obtain the formation of the PBMC layer. After centrifugation, the PBMC layer was transferred to 15 ml tubes with PBS. PBMCs were again centrifuged at 350×g for 20 minutes at room temperature. Subsequently, PBMCs were resuspended in complete growth medium.

[0067] HEK293 (ATCC CRL 3216), MCF7 (ATCC # HTB-22) and primary human fibroblast cells were maintained in Dulbecco's Modified Eagle's Medium (DMEM) (Invitrogen) with 10% heat-inactivated Fetal Bovine Serum (FBS) (Invitrogen) and 2 mM L-glutamine (Invitrogen). Primary human fibroblasts were isolated from skin biopsies from voluntary donors and cultured with DMEM, 10% FBS, 2 mM L-glutamine, 50 units/ml penicillin (Invitrogen) and 50 g/ml streptomycin (Invitrogen). PBMCs were grown in Roswell Park Memorial Institute (RPMI) medium, 10% FBS and 4 mM L-glutamine.

EXAMPLE 3: LENTIVIRAL CONSTRUCT, GRNA DESIGN AND CLONING

[0068] The lentivirus (LV) was purchased from Addgene and subsequently modified to insert the desired sequences essential for the correct functioning of the CRISPR system according to the invention. The first and second gRNA sequences were designed and selected by using the platform available on the Massachusetts Institute of Technology's (MIT) website (http://crispr.mit.edu). The nucleotide sequences encoding the first and second gRNAs consist of the sequence SEQ ID NO.2 (scaffold sequence: nucleotides (nt) 1-20; guide sequence: nt 21-43) and SEQ ID NO.3 (scaffold sequence: nt 1-20; guide sequence: nt 21-43), respectively. The nucleotide sequence of the second guide RNA, i.e. the gRNA whose target sequence is only present on the viral vector, was selected among sequences that are able to hybridize exclusively in the vicinity of the EGFP-HSV-TK sequence and not to other regions of the vector. The following sequences were inserted in the viral vector: the sequences encoding the first gRNA (SEQ ID NO.2) and the second gRNA (SEQ ID NO.3), the EGFP-HSV-TK cassette (SEQ ID NO.4), the sequence encoding Cas12a endonuclease (SEQ ID NO.5), the first target nucleotide sequence (SEQ ID NO.6) and the second target nucleotide sequence (SEQ ID NO.7). The following regulatory elements were also inserted: the U6 promoter sequence (SEQ ID NO.8), upstream of the sequences encoding the first and second gRNAs, as well as two PAM sequences, the first (5′-GATA-3′) downstream of the first target sequence, and the second (5′-TATC-3′) downstream of the second target sequence. The insertion of the aforementioned sequences was carried out by following a standard cloning protocol, typically comprising the following steps: cutting the DNA sequence with specific restriction enzymes, ligating the desired sequence, checking for the correct ligation, transforming in competent bacterial cells and extracting the plasmid DNA. EGFP-HSV-TK cassette was synthesized throughout and inserted in the lentiviral vector by using the KpnI restriction site. The nucleotide sequences of the gRNAs were initially synthesized as single-stranded DNA fragments and then phosphorylated and paired for subsequent insertion on the sides of the EGFP-HSV-TK cassette by using EcoRI (first gRNA) and BamHI (second gRNA) enzyme restriction sites. To confirm the correctness of the cloning, the DNA of the viral expression vector thus obtained was fully sequenced (sequence designated as SEQ ID NO.1).

EXAMPLE 4: RECOMBINANT VIRAL VECTOR DNA TRANSFORMATION, SELECTION AND ISOLATION

[0069] The DNA of the recombinant viral vector was transformed in E. coli DH5a competent cells (Invitrogen) following the supplier's instructions and isolated by using the “EndoFree Plasmid” kit (Qiagen), following the vendor's standard instructions. Transformed cells were selected with ampicillin antibiotic. EGFP lentiviral vector (Addgene, no. 21316) was used as a positive control for transduction.

EXAMPLE 5: HEK293 AND MCF-7 ENGINEERED WITH THE TP53 GENE MUTATION

[0070] Engineered HEK293 and MCF7 cell lines were obtained by randomly inserting a cassette including the specific TP53 gene mutation (c.548C>G; p.Ser183*) in their genome. The cassette with the point mutation (C>G) and the mCherry-bsr sequence was cloned into a plasmid as previously reported (Severi F. and Conticello SG. Flow-cytometric visualization of C>U mRNA editing reveals the dynamics of the process in live cells. RNA Biol. 2015; 12:389-397). The vector was transfected with lipofectamine 2000 (Invitrogen) into HEK293 and MCF7 cell lines by following the protocol illustrated in Example 3 section. Transfection efficiency was tested by mCherry expression.

EXAMPLE 6: VIRAL TRANSFECTION AND TRANSDUCTION

[0071] 1.2×10.sup.5 HEK293 and MCF7 cells, both also in the engineered form, were used for viral transfection and transduction experiments. The cells were cultured alone or co-cultured with primary fibroblasts and distributed in a 24-well plate. 24 hours later, the cells were Lipofectamine 2000-transfected (Invitrogen) with the lentiviral expression vector (2 μg total) or the EGFP lentiviral vector as a control by following the manufacturer's instructions. The cells were then analysed by flow cytometry and MTT cell proliferation assay 48 hours and 6 days post-transfection, respectively. In order to generate the HIV retroviral vector, approximately 5×10.sup.5 HEK293 cells were co-transfected by Lipofectamine 2000 with 200 ng of vesicular stomatitis virus G protein expression plasmid (VSV-G) and 1 μg of MLV GVPol expression plasmid. The supernatant containing the virus was collected, centrifuged and filtered 48 hours after transfection. A total of 5×10.sup.5 cells and 200 μl of virus was used for transduction in the presence of 5 μg/ml polybrene (Sigma).

EXAMPLE 7: OFF-TARGET ANALYSIS

[0072] The present inventors carried out specific investigations in order to demonstrate lower exposure of the cells to Cas12a enzyme effects in the CRISPR system of the invention. A first investigation analysed the persistence of the lentiviral genome in HEK293T cells infected with the inactive integrase compared to cells infected with a wild-type integrase system. By using the GFP protein as the reporter of the system, this experiment demonstrated the almost complete clearance of the viral genome from the cell culture within one week after infection compared to 100% of GFP-expressing cells after 18 days of infection using the wild-type integrase (FIG. 4). Cas12a expression mediated by the CRISPR system according to the invention was also compared to that mediated by an equivalent plasmid in which the target sequences leading to excision of the cassette had been removed, in the presence of mutated or wild-type integrase. The comparison shows a significant decrease in Cas12a expression in the CRISPR system object of the invention compared to the different control conditions (FIG. 5).

EXAMPLE 8: FLOW CYTOFLUORIMETRY ANALYSIS (FACS) AND CELL SELECTION TO VERIFY CAS EDITING AND DETECT CLONES DERIVED FROM A SINGLE MODIFIED CELL

[0073] The flow cytofluorimeter (BD) acquired 50,000 events/well. The data was analysed by FlowJo v7.5 cytofluorimetry software. For the analysis, HEK293 cells genetically modified with the CRISPR system of the invention were selected based on size and morphology; a second selection was then performed in order to detect GFP-positive cells in which the expression of the GFP protein is indicative of the correct integration of the HSV-TK sequence in the cell genome.

EXAMPLE 9: IN VITRO CELL ANALYSIS

[0074] The cells were distributed in triplicate in 48-well plates at a density of 0.8×10.sup.5 cells/well and transfected with and without HSV-TK lentivirus according to the invention. After 6 days, Ganciclovir (GCV), a thymidine kinase enzyme substrate, was administered to the cells at a concentration of 12 μM and left in contact with the cells for 4 hours. The HSV-TK gene product phosphorylates GCV into GCV triphosphate, which is incorporated into the DNA during cell replication, thereby inhibiting DNA synthesis and causing cell death. Cells were subsequently analysed with 3-[4,5-Dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide (MTT) to assess the percentage of cell viability after Ganciclovir addition and the mortality caused by administration of this compound. The MTT assay estimates the metabolic activity of the cells since the MTT assay is based on the conversion of the water soluble yellow MTT solution into insoluble purple crystals by living cells, which indicates mitochondrial activity.

Results

EXAMPLE 10: TRANSFECTION OF HEK293 AND MCF7 CELLS

[0075] HEK293 and MCF7 cell lines, specially engineered with the TP53 gene mutations, were co-cultured with human fibroblasts to establish a heterogeneous cell population. HEK293 and MCF7 cells were transfected using lipofectamine with the lentiviral vector according to the invention carrying sequences encoding the first and second gRNAs, and the Cas12a and TK enzymes, respectively. In order to verify the successful transfection, the TK gene sequence was linked, through a 2A peptide sequence, to a marker, in particular to the sequence expressing the enhanced green fluorescent protein (EGFP). Accordingly, GFP-positive cells are also TK-positive. The lentiviral vector devoid of the EGFP-TK cassette and the lentiviral vector constitutively encoding the EGFP-TK sequence were used as controls in the transfection experiments.

[0076] The results of the in vitro experiments were analysed by FACS 3 days after transfection. Cells were recovered by FACS in order to select positively transfected cells based on the EGFP expression, proportional to the amount of cells in which the genome editing mediated by the CRISPR-Cas system of the invention was successful. The FACS analysis demonstrated high efficiency of the CRISPR-Cas system of the invention since a high percentage of cells positive for the marker signal was found.

[0077] In order to verify the correct integration of the TK gene coding sequence in the target genomic locus, the DNA extracted from the FACS-recovered cells was amplified by using a set of primers specific for the sequence integrated into the genomic locus. An amplicon of the expected 822-bp length was obtained only in amplification reactions performed on DNA extracted from engineered cell lines transfected with the lentiviral vector according to the invention, thus indicating the successful integration of the TK gene coding sequence into the genomic site carrying the specific target mutation.

[0078] Subsequently, using the engineered HEK293 and MCF7 cells, the wild-type HEK293 and MCF7 cells transfected as described above, experiments were carried out in order to verify the functionality of the TK-encoding gene upon integration into the target genomic site. Briefly, six days after transfection, EGFP-positive cells were selected by FACS. The recovered cells were incubated in the presence and the absence of Ganciclovir at a concentration of 0.1 mg/ml. From a subsequent FACS analysis carried out after 3 days of incubation, a cell death value of 70% was reported in the mutated HEK293 sample transfected with the CRISPR system of the invention, and an 80% reduction was detected in the mutated and wild-type HEK293 samples transfected with the lentiviral vector constitutively encoding the EGFP-TK sequence (FIG. 2). Similar results were obtained with the MTT viability assay. In fact, the MTT colorimetric analysis revealed that a significant percentage of cells modified by the CRISPR system of the invention, compared to the control, died following treatment with ganciclovir, thus indicating that the TK-encoding sequence was correctly integrated into the target genomic locus and that the expressed enzyme is able to convert ganciclovir into a toxic compound harmful to cells.

EXAMPLE 11: CULTURE AND TRANSDUCTION OF TP53-GENE MUTATED AND NON-MUTATED LEUKEMIA LYMPHOCYTES

[0079] After the efficiency of the CRISPR system of the invention was confirmed in the analysed cell lines, the present inventors tested said system in primary cell lines. Lymphocytes isolated from blood samples from B-CLL patients, including both the leukemia lymphocytes carrying the specific TP53 gene mutation, which represents the genomic target sequence of the first gRNA encoded by the lentiviral vector of the invention, and non-TP53 mutated leukemia lymphocytes, were used as target cells. Since B lymphocytes are known from the literature to be difficult to transfect and transduce, electroporation was chosen as the method of transducing the lentiviral vector according to the invention into TP53-gene mutated and non-mutated leukemia B cells. Successful integration of the EGFP-TK cassette into the mutated genomic site exclusively in the lymphocyte population carrying the TP53-gene mutation was demonstrated by FACS analysis and DNA amplification, according to the methods illustrated in Example 8.

EXAMPLE 12: VIRAL PRODUCTION AND TRANSDUCTION

[0080] After the efficiency of the CRISPR system of the invention was demonstrated in in vitro cell lines, the present inventors generated viral particles capable of infecting target cells. Lentiviral particles (Addgene) were produced by following the standard viral production protocol indicated by the manufacturer. For this purpose, HEK293 cell line cells were transfected with a plasmid that enables viral protein packaging, a plasmid that drives the production of viral envelope proteins, and the lentiviral expression vector of the invention, together with a fourth plasmid encoding a modified Cas9 enzyme (dCas9) essential to avoid self-degradation of the lentiviral vector itself. In fact, in the absence of dCas9, the lentiviral vector, once inside the cell, expresses the guide RNAs and the Cas12a enzyme which, by being complexed into a macromolecular system, are able to excise the EGFP-TK cassette from the vector, resulting in the opening and degradation of the latter. On the other hand, in the presence of dCas9, which has lost its catalytic activity, this enzyme, guided by the gRNA molecules, binds to the target sequences on the vector preventing Cas12a from recognizing them. This endonuclease cannot therefore cut the double strand at target sites.

[0081] Alternatively, in order to avoid self-degradation of the lentiviral vector, a modified endonuclease (dCas12a) can be used. This strategy comprises transfecting a dCas12a-encoding plasmid into HEK293 cells, together with the plasmid that enables the packaging of viral proteins and a plasmid that drives the production of viral envelope proteins, both essential for the production of the virus. The role of the modified endonuclease is to bind to the guide RNA molecules, sequestering them, so that the operative Cas12a cannot target the target sites due to the low amount of free gRNAs available.

[0082] The present inventors employed the viral particles generated as described above to infect normal and TP53-gene mutated HEK293 and MCF7 cell lines. The presence of the correct integration of the EGFP-TK cassette in the target genomic site was verified by subjecting cell samples to FACS analysis 2 days after infection. The green fluorescence signals were localized exclusively in the target cells of the CRISPR system, i.e. in the mutated cells. These results were confirmed by amplifying genomic DNA extracted from the cells and detecting the presence of the expected 822-bp band only in virus-infected cells carrying the cassette with the mutation.