CN116042707A - T cell gene editing method and application - Google Patents

Abstract

The invention discloses a method for gene editing of isolated T cells, which takes degradable nano particles formed by protein serving as an inner core and macromolecule serving as an outer shell as a carrier to transfer Cas9/sgRNA of target T cell target genes into the T cells, and the target T cell genes are inactivated by gene editing. The invention also provides application of the CD7 and PD1 defective T cells prepared by the method in preparation of chimeric antigen receptor T cells. The method provided by the invention is simple, green, low in cost, good in biocompatibility and low in cytotoxicity. The method has high-efficiency cell uptake rate and gene editing rate, can realize quantitative control of a gene editing system, reduces off-target effect, and has wide application prospect in the fields of gene editing and treatment.

Description

T cell gene editing method and application

Technical Field

The invention discloses a gene editing method of T cells, and belongs to the technical field of cell engineering.

Background

For CRISPR gene editing applications, the direct delivery of the complex formed by Cas9 protein and sgRNA to cells can achieve higher specificity and safety. However, the difficulty of delivering Cas9/sgRNA complexes is greater. First, cas9 proteins and sgrnas are susceptible to inactivation by intracellular enzymatic degradation; secondly, while assembling Cas 9/sgrnas into a tight, stable structure that can be taken up by cells, it is necessary to consider dissociation and release of Cas 9/sgrnas within the cells, and too close binding of Cas 9/sgrnas to the vector also reduces its activity. However, the existing Cas9/sgRNA delivery vector generally has the problems of complex synthetic route, low gene editing efficiency, cytotoxicity caused by insufficient degradation of vector materials, and the like. And for suspension cells of specific structure, smaller size, such as primary T cells, no vector has been reported to be able to make Cas9/sgRNA delivery to produce gene editing T cells, while electrotransformation is more damaging to cells and depends on the specific equipment.

Chimeric antigen receptor T cells (CAR T) are currently one of the most effective ways to treat malignant tumors. Similar to other immunotherapies, the basic principle is to use the patient's own immune cells to eliminate cancer cells. Because some endogenous genes of the T cells can cause immune rejection reaction so as to limit the immune effect of the CAR T, the gene editing technology combined with the CAR T has wide application prospect in tumor immunotherapy. The use of genetically engineered T cells as a source of CAR T cells has the potential to potentiate the efficacy of CAR T in the treatment of cancer and infectious diseases.

CD7 and PD1 are two targets of clear clinical therapeutic interest associated with CAR T. CD7 is a transmembrane protein that is highly expressed in T cell malignancies and can be used as a CAR molecule target antigen for the treatment of T cell malignancies. Since normal T cells will also express CD7, expression of a CD7 specific CAR molecule will cause T cells to self-phase and thus hinder in vitro expansion of CAR T cells. Knockout on normal T cellsA kind of electronic deviceCD7The gene can prevent the self-phase killing and improve the treatment effect. PD1 is an immunosuppressive molecule expressed on T cells and used for regulating the immune activation degree, participating in suppressing continuous immune response in peripheral tissues and preventing autoimmune injury of the tissues, and protecting the immune system of a human body. Since PD-L1 (programmed death ligand 1) is usually highly expressed on the surface of tumor cells, immune checkpoint molecule PD1 on T cells and PD-L1 binding on tumor cells initiate programmed death of T cells, resulting in immune escape of tumor cells. Knocking out T cellsPD1The gene can weaken the immunosuppression signal and enhance the killing of the CAR T cells on tumor cells.

Existing delivery technologies of Cas 9/sgrnas on T cells have been reported only in electrotransport, so delivery systems that use degradable nanoparticles to achieve gene editing of T cells CD7 and PD1 to address the above limitations are a technical need in the art to facilitate the clinical application and development of CRISPR gene editing systems, especially for gene editing of T cells.

Disclosure of Invention

The present invention aims to overcome the disadvantages of the prior art and provides a method for gene editing of isolated T cells, the method comprising:

(1) Constructing degradable nano particles formed by proteins serving as inner cores and macromolecules serving as outer shells, wherein the macromolecules are formed by in-situ polymerization of primary amino groups of lysine in the proteins, electrically neutral monomers and cationic monomers in the presence of a free radical initiator after the primary amino groups of the lysine are modified and introduced into double bonds;

(2) Mixing the nanoparticle obtained in the step (1) with Cas9/sgRNA of a target T cell target gene to obtain a self-assembled complex formed by mixing the nanoparticle and the Cas9/sgRNA complex;

(3) Transferring the self-assembled complex obtained in step (2) into isolated T cells.

In a preferred embodiment, the cationic monomer of step (1) is ethyl 2- (dimethylamino) methacrylate, the charge neutral monomer is acrylamide, the free radical initiator is ammonium persulfate and tetramethyl ethylenediamine, and the modification of the primary amine group of lysine in the protein is an acrylation modification.

In a more preferred embodiment, the modification of the primary amine groups of lysine in the protein is performed using N-hydroxysuccinimide acrylate.

More preferably, the protein is any polypeptide having more than two lysine residues.

Still preferably, the protein is bovine serum albumin. Chemically modified (e.g., fluorescent molecular labeled) polypeptides are also included in embodiments of the invention, as long as the modification does not interfere with nanoparticle synthesis, as is well known to those of skill in the art.

More preferably, the bovine serum albumin: acrylamide: 2- (dimethylamino) ethyl methacrylate: ammonium persulfate: the molar ratio of the tetramethyl ethylenediamine is 1:3000:3000:250:1000.

in a preferred embodiment, the sequence of sgRNA in the Cas9/sgRNA in step (2) is shown in SEQ ID NO.1, and the gene of interest of the T cell is a gene encoding CD 7.

In another preferred embodiment, the sequence of sgRNA in the Cas9/sgRNA in step (2) is shown in SEQ ID NO.2, and the T cell gene of interest is a gene encoding PD 1.

Next, the present invention provides a CD 7-deficient T cell prepared according to the above method.

Third, the present invention provides a PD 1-deficient T cell prepared according to the above method.

Fourth, the present invention provides the use of the above-described CD 7-deficient T cells and/or PD 1-deficient T cells for the preparation of chimeric antigen receptor T cells.

Finally, the invention provides application of the T cells in preparing medicines for treating tumors or autoimmune diseases.

Compared with the existing T cell gene editing method, the method using the degradable nano-particles as the Cas9/sgRNA carrier has the following outstanding advantages:

1) The Cas9/sgRNA carrier provided by the invention utilizes protein to polymerize polymer in situ, and the material preparation method is simple, green and low in cost; the design thought with the protein as the inner core ensures that the material has good biocompatibility and low cytotoxicity.

2) The nano particles can well load the Cas9/sgRNA complex only by simple mixing, and can efficiently deliver the Cas9/sgRNA into cells without any other transfection reagent, thereby remarkably improving the cell uptake rate.

3) The cationic monomer of the polymer shell of the nanoparticle is designed to be 2- (dimethylamino) ethyl methacrylate with tertiary amino and ester bonds, the tertiary amino structure generates proton sponge effect to help endosome escape, and the ester bonds connected with the tertiary amino generate hydrolysis reaction at physiological temperature to degrade the cationic groups, so that the release of Cas9/sgRNA from a self-assembled complex is promoted. At the same time, components in the cytoplasm such as negatively charged proteins and amino acids compete for the nanoparticle binding site to Cas 9/sgrnas, further accelerating dissociation of Cas 9/sgrnas from the self-assembled complex in the cytoplasm. The nano-particles can realize high-level release of Cas9/sgRNA, and remarkably improve the gene editing effect.

4) In the application of T cell gene editing, the editing efficiency of the nano particle mediated Cas9/sgRNA compound on the target gene in the cell can reach 14%. Meanwhile, the method for directly presenting the Cas9/sgRNA complex is beneficial to realizing quantitative regulation and control of intracellular content and action time, and reduces off-target effect.

5) None of the existing Cas9/sgRNA delivery systems can be used for difficult transfected cell types such as primary T cells, except for electrotransport. The Cas9/sgRNA delivery system based on the degradable nano-particles provides a novel gene knockout method for primary T cells, and lays a foundation for the preparation of the next-generation immunotherapy such as general CAR T cells.

Drawings

Fig. 1 is a schematic representation of the preparation of nanoparticles and their Cas9/sgRNA delivery system.

Fig. 2 is a graph of the morphology and size of nanoparticles. (a) a transmission electron microscope image; (b) atomic force microscopy.

FIG. 3 is a comparison of structural properties of nanoparticles and core proteins. (a) a dynamic light scattering map; (b) Zeta potential patterns; (c) fourier infrared spectrogram; (d) ion chromatograms.

FIG. 4 shows uptake efficiency and gene editing efficiency of self-assembled complexes transfected into HEK293T cells at different molar ratios of nanoparticle and Cas 9/sgRNA. Uptake efficiency is expressed as the average fluorescence intensity of Cas9-AF647 taken up by cells after 12h, and gene editing efficiency is expressed as the percentage of EGFP negative cells after 4 days, where Cas9-AF647 is AF 64-labeled Cas9.

FIG. 5 shows (a) flow results, (b) fluorescent microscopy observations, and (c) sequencing and monoclonal sequencing analysis of DNA fragments near the genomic targeting site of the nanoparticle/Cas 9/sgRNA transfected HEK293T cells.

FIG. 6 shows (a) flow results, (b) fluorescent microscopy observations, and (c) sequencing and monoclonal sequencing analysis of DNA fragments near the genomic targeting site of the nanoparticle/Cas 9/sgRNA transfected A549 cells.

Fig. 7 is a transmission electron microscope topography of Cas 9/sgrnas and their self-assembled complexes with nanoparticles. (a) Cas9/sgRNA; (b) nanoparticle/Cas 9/sgRNA; (c) nanoparticle-37/Cas 9/sgRNA, wherein nanoparticle-37 is a nanoparticle after 10 days of standing at 37 ℃.

FIG. 8 (a) is a plot of Zeta potential changes of nanoparticles before and after 10 days of placement at 37 ℃; (b) Is a fluorescence spectrum diagram of NP-FITC/Cas9-RBITC/sgRNA in different media. Wherein the concentration of the protein medium is 0.4mg/ml; NP-FITC represents FITC-labeled nanoparticles; RNP-RBITC means complex formed by RBITC-labeled Cas9 and sgRNA.

Figure 9 is an in vitro CRISPR cleavage reaction of nanoparticle/Cas 9/sgrnas under different conditions.

FIG. 10 shows the internalization efficiency of cellular Cas9-AF647 as measured by flow cytometry 6h after transfection of non-activated T cells with nanoparticle/Cas 9-AF 647/sgRNA.

FIG. 11 shows the efficiency of T cell internalization and genome editing under different activation conditions. (a) Cell Cas9-AF647 internalization efficiency measured by flow cytometry after 6h of T cell activation by nanoparticle/Cas 9-AF647/sgRNA transfection; (b) Culturing was continued for 7 days after transfection of nanoparticle/Cas 9/CD7-sgRNA, APC expression of CD7 as measured by flow cytometry.

FIG. 12 shows the results of monoclonal Sanger sequencing of T cells targeting (a) CD7 and (b) PD1 genes. PAM is the primordial spacer adjacent motif.

FIG. 13 is a deep sequencing analysis of nanoparticle/Cas 9/CD7-sgRNA transfected T cells. (a) The frequency of base insertion at each site is expressed as the number of insertion Reads per site per total Reads; (b) The number of inserted Reads of a particular length is a percentage of the total number of inserted Reads; (c) The frequency of missing bases at each site is expressed as the number of missing Reads per site/total Reads; (d) The number of missing Reads of a particular length is a percentage of the total number of missing Reads.

FIG. 14 shows the sequences and frequencies of major deletions or insertions after nanoparticle/Cas 9/CD7-sgRNA transfection into T cells.

FIG. 15 is a deep sequencing analysis of nanoparticle/Cas 9/PD1-sgRNA transfected T cells. (a) The frequency of base insertion at each site is expressed as the number of insertion Reads per site per total Reads; (b) The number of inserted Reads of a particular length is a percentage of the total number of inserted Reads; (c) The frequency of missing bases at each site is expressed as the number of missing Reads per site/total Reads; (d) The number of missing Reads of a particular length is a percentage of the total number of missing Reads.

FIG. 16 is the sequence and frequency of major deletions or insertions following nanoparticle/Cas 9/PD1-sgRNA transfection into T cells.

Figure 17 is the effect of nanoparticle delivery system on activity of T cells.

Detailed Description

The invention will be further described with reference to specific embodiments, and advantages and features of the invention will become apparent from the description. These examples are only exemplary and do not limit the scope of the invention in any way, which is defined by the claims.

Example 1: preparation method of degradable nano particles

1) Bovine serum albumin (Sigma-Aldrich #SRE0096) was dissolved in a borate buffer of pH 8.5 at 100mM, and after centrifugation of the buffer four times through a 30kD ultrafiltration tube (Amicon #UFC5030 BK), the concentration was measured by the biquinolinecarboxylic acid (BCA) method and the protein was diluted to 10mg/ml with the buffer to give a stock solution of the reaction protein.

2) N-hydroxysuccinimide acrylate (Sigma-Aldrich #A8060) was dissolved in dimethyl sulfoxide (Sigma-Aldrich # 276855) to prepare a solution of 20mg/ml, and 5.1. Mu.l was mixed with 100. Mu.l of the reaction protein stock solution uniformly (wherein N-hydroxysuccinimide acrylate: bovine serum albumin = 40:1 molar ratio), and reacting for 6 hours at room temperature of 25 ℃ to obtain the protein solution A with the surface double bond modified.

3) Acrylamide (Sigma-Aldrich #A8887) was dissolved in deionized water to prepare 200mg/ml solution B; ammonium persulfate (Sigma-Aldrich #A3678) was dissolved in deionized water to prepare a solution C of 100 mg/ml; both ethyl 2- (dimethylamino) methacrylate (Sigma-Aldrich# 234907) and tetramethyl ethylenediamine (Sigma-Aldrich#T9281) are liquid reagents that can be used directly for the reaction.

4) After adding 300. Mu.l of pH 7.4 and 100mM phosphate buffer to the solution A system, 16. Mu.l of solution B, 7.6. Mu.l of ethyl 2- (dimethylamino) methacrylate, 8.6. Mu.l of solution C and 2.1. Mu.l of tetramethyl ethylenediamine were added and mixed uniformly (wherein, bovine serum albumin: acrylamide: 2- (dimethylamino) ethyl methacrylate: ammonium persulfate: tetramethyl ethylenediamine=1: 3000:3000:250:1000 molar ratio), at room temperature 25 ℃ for 4h.

5) The schematic of the reaction is shown in the first two steps of figure 1. After the polymerization reaction, the non-target reaction product components generally remain in the system, and thus purification is required. The product solution was centrifuged 4 times in a 30kD ultrafiltration tube with pH 7.4, 10mM Phosphate Buffer (PBS) to give 300. Mu.l of nanoparticle solution. The BCA concentration was 3.28mg/ml, and diluted to 1.5mg/ml with PBS.

Example 2: characterization of degradable nanoparticles

The nanoparticles were subjected to transmission electron microscopy (HT 7700, hitachi) And atomic force microscopy (Bruker) (fig. 2), it is known that the particles are spherical and have a particle size distribution of between a few nanometers and 20 nanometers. The average particle size of the nanoparticles, as measured by dynamic light scattering (Zetasizer Nano, malvern), was 10nm, which is much greater than the 5.5nm particle size value of the bovine serum albumin as the synthetic raw material (FIG. 3 a). The average Zeta potential of the nanoparticles was 9.7mV (b in FIG. 3), as compared to bovine serum albumin with Zeta potential of-20.8 mV, and the design of the cationic polymer surface modification was such that the electrical properties were altered. FIG. 3 c further shows that the nanoparticle is composed of a copolymer of ethyl 2- (dimethylamino) methacrylate and acrylamide coupled with a protein, since 2950cm can be observed in the infrared spectrum of the nanoparticle ^-1 （–CH ₃ and-CH ₂ C-H stretching vibration peak) of 2820cm ^-1 And 2780cm ^-1 （–N(CH ₃ ) ₂ C-H stretching vibration peak) of 1730cm ^-1 (C=O stretching vibration peak in ester bond), 1460cm ^-1 （–CH ₂ -bending vibration peak), 1395cm ^-1 （CH ₃ Bending vibration peak), 1148cm ^-1 (C-N and C-O stretching vibration peaks), which are characteristic absorption peaks of the ethyl 2- (dimethylamino) methacrylate unit. Furthermore, 1680cm ^-1 Is a characteristic absorption peak of c=o stretching vibration peak in amide bond, which belongs to the connection bond of acrylamide unit and bovine serum albumin with N-hydroxysuccinimide acrylate. 3317cm ^-1 Broad peak at and 1540cm ^-1 The small peaks at the positions respectively belong to N-H stretching vibration and bending vibration peaks of primary amino groups in the acrylamide units. FIG. 3d is an elution profile (equilibration solution pH 4.5, 10mM sodium acetate solution, elution solution pH 4.5, 10mM sodium acetate solution with 0.5M NaCl added) using a Dionex ICS-5000+ ion chromatography system and a TOSOH TSKgel CM-STAT column at 280 nm. The results further demonstrate that in situ growth of cationic polymers on the surface of the nucleoprotein imparts positive properties to the material. Furthermore, there is no distinct separation peak in the elution profile of the nanoparticles, which also confirms the relative uniformity of the nanoparticle material.

Example 3: experimental optimization and Gene editing results for nanoparticle delivery Cas9/sgRNA

In this embodiment, the Cas9 protein consists ofEscherichia coliBL21 (DE 3) expression purification, pET-NLS-Cas9-6xHis plasmid with the product number Addgene #62934.EGFP-sgRNA is transcribed and purified in vitro from a DNA template having the sequence: GTTTTTTTTAATACGACTCACTATAgggcgaggagctgttcaccgGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTT. cgRNA, which served as a control, did not target any gene, was also transcribed and purified in vitro from a DNA template of the sequence: GTTTTTTTTAATACGACTCACTATAgggtaaccgtgcggtcgtacGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTT. The cells used were laboratory-constructed expression single copiesEGFP- PESTHEK293T and A549 cell lines of the genes.

The nanoparticle prepared in example 1 above can be used to prepare Cas9/sgRNA delivery systems. The process is as follows:

1) Mixing the Cas9 protein and the sgRNA, and standing for 20min at room temperature to obtain the Cas9/sgRNA complex.

2) Mixing the nano particles with the Cas9/sgRNA complex solution, and standing at room temperature for 20min to obtain the self-assembled complex of the nano particles and the Cas 9/sgRNA.

3) The self-assembled complex is incubated with cells to produce a nanoparticle-based Cas9/sgRNA cell delivery system.

4) The effect of editing cellular genes produced by Cas9/sgRNA delivery systems based on the nanoparticles described above was evaluated.

The following are more specific experimental steps:

1.18 μl Cas9 protein (1354 μg/ml) and 1.59 μl were targetedEGFPEGFP-sgRNA (200 mug/ml) of the gene is mixed at room temperature at 25 ℃ (molar ratio is 1:1), and is kept stand for 20min, thus obtaining the Cas9/sgRNA complex. 2.2. Mu.l, 4.4. Mu.l, 8.8. Mu.l and 13.2. Mu.l of the nanoparticle (150. Mu.g/ml) were mixed with the Cas9/sgRNA complex prepared under the above conditions at room temperature of 25℃and allowed to stand for 20min to obtain self-assembled complexes at different molar ratios of nanoparticle to Cas9/sgRNA (molar ratios of 1:2, 1:1, 2:1 and 3:1, respectively). Nanoparticles are formedThe Cas9/sgRNA complex was added to serum-free DMEM medium to a final volume of 100 μl, with an amount of Cas9/sgRNA of 100nM. And adding the mixture into HEK293T cells growing to an exponential growth phase in a 96-well plate, transferring the culture medium into DMEM medium containing 10% of serum after 12 hours of transfection, and analyzing the fluorescent expression of EGFP (enhanced green fluorescent protein) of the cells by using a flow cytometer (Guava easyCyte HT, merck Millipore) after the culture is continued for 4 days, wherein EGFP negative cells are cells which are subjected to gene editing and lead to the non-expression of EGFP. The experimental control was to replace sgRNA with cgRNA that did not target any gene (200 μg/ml), and the difference in the final EGFP negative cell ratios of sgRNA and cgRNA was expressed as the gene editing efficiency.

Meanwhile, after incubation of Cas9 protein (100 kD ultrafiltration tube to pH 8.5, 100mM borate buffer) with AF647 fluorescent dye (Molecular probes#a 20006) at a molar ratio of 1:10 for 1h in the dark, the mixture was centrifuged 4 times with PBS in 100kD ultrafiltration tube to remove free AF647, yielding fluorescent dye-labeled Cas9-AF647. Self-assembled complexes of nanoparticles and Cas9-AF647/sgRNA in a molar ratio of 1:2-3:1 were obtained in the same procedure and incubated with HEK293T cells for 12h under the same conditions, and then analyzed for cellular AF647 fluorescence with a flow cytometer to evaluate the uptake efficiency of Cas9/sgRNA by the cells.

The above experimental results are shown in fig. 4, with an increase in the nanoparticle ratio generally enhancing the internalization efficiency of Cas 9/sgRNA. However, the internalization efficiency does not correspond exactly to the gene editing efficiency. This suggests that the partial complementarity between the nanoparticle and Cas 9/sgrnas is important for efficient presentation and implementation of CRISPR functions, probably due to the need for equilibrium of Cas9/sgRNA loading and release. When the molar ratio of the nano particles to the Cas9/sgRNA is 1:1, the gene editing effect is optimal. HEK293T and A549 cells were transfected with optimal conditions, respectively, and the cells after 4 days were characterized for intracellular EGFP fluorescent expression using flow cytometry and fluorescence microscopy. The flow chart shows that gene editing efficiencies reach 28% (fig. 5a, targeted and non-targeted nanoparticle delivery systems produce EGFP negative cell fractions of 34.4% and 6.04%, respectively) and 40% (fig. 6 a, targeted and non-targeted nanoparticle delivery systems produce EGFP negative cell fractions, respectively44.5% and 4.45%, respectively). It is also clear from fig. 5b and fig. 6b that the nanoparticle/Cas 9/sgRNA targeting system produced a number of cells without EGFP expression, while nanoparticle/Cas 9/cgRNA non-targeting system delivered had substantially no effect on fluorescence expression of the cells. This gap further demonstrates that nanoparticles as a presentation vector can achieve the gene knockout function of Cas 9/sgRNA. Extracting genome DNA of the cells, amplifying DNA fragments near the editing site by PCR, purifying and connecting the PCR product to pCloneEZ TOPO cloning vector (CloneSmarter#C5865), transferringEscherichia coliDH5 a. Direct Sanger sequencing of the PCR products and Sanger sequencing of more than 50 clones resulted in the results shown in FIG. 5c and FIG. 6 c, the set of peaks of the PCR products indicated that fragments containing different sequences, i.e., the targeting region resulted in gene editing; the monoclonal sequencing results show details of gene editing of insertions or deletions or single nucleotide variations.

Example 4: intracellular delivery mechanism study of nanoparticle-based Cas 9/sgrnas

1. Nanoparticle self stability

The nanoparticle placed at 37℃for 10 days was designated nanoparticle-37 as an experimental condition for evaluating the stability of the nanoparticle material itself.

The size of the Cas9/sgRNA complex was close to that of the nanoparticle as seen by transmission electron microscopy (a of fig. 7), and the nanoparticle/Cas 9/sgRNA was a regular spherical large aggregate (b of fig. 7). Whereas nanoparticle-37/Cas 9/sgrnas exhibit a dissociated, loose structure (C of fig. 7), indicating that an intracellular 37 ℃ environment can accelerate the dissociative release of Cas 9/sgrnas from aggregates.

The Zeta potential of the nanoparticles was significantly reduced from-8.4 mV to-1.9 mV at 37℃as measured by potentiometers (Zetasizer Nano, malvern) (FIG. 8 a). From this, it is known that the instability of the nanoparticle self structure is an important factor for its intracellular ability to release Cas 9/sgRNA.

2. Competitive binding from other molecules

Nanoparticles and Cas9 proteins were labeled with FITC fluorescent labeling reagent (Sigma-Aldrich #f3651) and RBITC (aladin #r 105502), respectively: after incubation of the Nanoparticles (NP) with FITC in the dark for 1h at a molar ratio of 1:4, the mixture was centrifuged 4 times in a 30kD ultrafiltration tube with PBS to remove free FITC, yielding FITC-labeled nanoparticles (NP-FITC). After incubation of Cas9 protein to RBITC in the dark for 1h at a molar ratio of 1:5, the mixture was centrifuged 4 times with PBS in a 100kD ultrafiltration tube to remove free RBITC, yielding RBITC-labeled Cas9 (Cas 9-RBITC). Mixing with sgRNA and standing for 20min to obtain RBITC marked Cas9/sgRNA (RNP-RBITC).

Self-assembly formation and dissociation release of nanoparticles with Cas 9/sgrnas was assessed by fluorescence resonance energy transfer by the fluorescent molecule pairs described above (b of fig. 8). Fluorescence spectra were recorded by a multifunctional microplate reader (SpectraMax Paradigm, molecular Devices) with excitation and emission wavelengths of 470nm and 505-750nm, respectively. When self-assembled, RNP-RBITC quenches the NP-FITC fluorescent moiety, giving a bimodal form to the fluorescence spectrum. Addition of bovine serum albumin or DMEM containing fetal bovine serum to the self-assembled complex solution triggered release of Cas9/sgRNA, which was manifested by a decrease in peak intensity at 580nm in the fluorescence spectrum. This suggests that abundant cytoplasmic proteins can trigger dissociation of Cas 9/sgrnas, possibly due to competition of negatively charged proteins for Cas 9/sgrnas for binding to nanoparticles.

3. In vitro enzyme assay mimics intracellular Cas9/sgRNA release mechanism

In this example, pcDNA3.1-EGFP plasmid was constructed by cloning EGFP sequence (GenBank: DQ 389577.1) into the multicloning site of plasmid pcDNA3.1 (+) (Invitrogen #V 79020). Since pcDNA3.1-EGFP contains EGFP-sgRNA targeting sequences, it can be used in Cas9/sgRNA mediated in vitro DNA digestion experiments to mimic the conditions of intracellular RNP release. Before in vitro DNA3.1-EGFP is subjected to in vitro DNA3.1-EGFP enzyme digestion with PvuI-HF (NEB#R3150S) to linearize the plasmid, so that double bands generated by further enzyme digestion of Cas9/sgRNA are easy to detect.

nanoparticle/Cas 9/sgRNA (molar ratio 1:1:1, final concentration 50 nM) was added to 250ng of linearized pcDNA3.1-EGFP, and the enzyme-free water or medium was added to a final volume of 20. Mu.L followed by incubation at 37℃for 1 h. Proteinase K (Sigma-Aldrich #P6556) was added and incubated for 30min to terminate the reaction, and the DNA was analyzed for CRISPR cleavage by 1% agarose gel electrophoresis. In FIG. 9, lane M is the DL15000 DNA molecular marker, lane 1 is the in vitro cleavage reaction of nanoparticle/Cas 9/sgRNA, lane 2 is the in vitro cleavage reaction of nanoparticle-37/Cas 9/sgRNA, lane 3 is the in vitro cleavage reaction of nanoparticle/Cas 9/sgRNA in DMEM, lane 4 is the in vitro cleavage reaction of nanoparticle-37/Cas 9/sgRNA in DMEM, and lane 5 is the in vitro cleavage reaction of nanoparticle-37/Cas 9/sgRNA in complete medium. The results indicate that the nanoparticle/Cas 9/sgrnas cannot directly exert CRISPR cleavage activity due to the excessively tight binding of the vector and the load; nanoparticle-37/Cas 9/sgrnas exhibit partial activity of Cas 9/sgrnas, further demonstrating that the effect of the environment at 37 ℃ on nanoparticle structure results in reduced binding of the load to the carrier. The nanoparticle/Cas 9/sgRNA also demonstrated partial gene editing activity in the presence of DMEM (anionic molecule containing negative amino acids). When fetal bovine serum is added to DMEM (rich in anionic molecules such as amino acids, proteins, etc., as a rough mimic of the cytoplasm), nanoparticle-37/Cas 9/sgRNA retains the complete cleavage function of Cas9/sgRNA, since anionic molecules such as negative proteins can also bind to the nanoparticle, competing with Cas 9/sgRNA. The above results mimic the principle that the cytosolic environment at 37 ℃ triggers the dissociation and release of the cargo from the carrier, thereby disrupting the target DNA.

Example 5: nanoparticle delivery of Cas 9/sgrnas to primary T cells

Chimeric antigen receptor T cells (CAR T) are currently one of the most effective ways to treat malignant tumors. Similar to other immunotherapies, the basic principle is to use the patient's own immune cells to eliminate cancer cells. Because some endogenous genes of the T cells can influence the immune effect of the CAR T, the gene editing technology combined with the CAR T has wide application prospect in tumor immunotherapy. The use of genetically edited T cells as a source of CAR T cells has the potential to potentiate the efficacy of CAR T in the treatment of cancer and infectious diseases.

Promotion of CAR T to the treatment of T cell malignancies is problematic because most of the target antigen is shared between normal and malignant cells, resulting in CAR T cells being self-killing. CD7 is a transmembrane protein that is highly expressed in acute T-lymphocyte leukemia and peripheral T-cell lymphoma, and thus CD7 is an attractive therapeutic target for T-cell malignancies. Since T cells that make CAR T will also themselves express CD7, expression of a CD7 specific CAR (CD 7-CAR) will cause T cells to self-kill, thus impeding expansion of CAR T cells. Whereas knockout of the CD7 gene can prevent this self-phase killing, CAR T targeted to treat T cell tumors can be made using this T cell. Thus, a CD 7-targeting gene editing system is of clear clinical significance.

In addition, since PD-L1 (programmed death ligand 1) is usually highly expressed on the surface of tumor cells, the binding of immune checkpoint molecule PD-1 (programmed death receptor 1) on T cells to PD-L1 highly expressed on tumor cells initiates programmed death of T cells, which leads to immune escape of tumor cells. On T cellsPD1The knockout of the gene can attenuate the immunosuppressive signal, thereby enhancing the killing of the tumor cells by the CAR T.

Existing delivery techniques of Cas 9/sgrnas on T cells have been reported only for electrotransport methods, and this example attempts to achieve gene editing of T cells CD7 and PD1 using the degradable nanoparticles of the present invention.

In this example, the sequence of CD7-sgRNA is shown as SEQ ID NO.1, the sequence of PD1-sgRNA is shown as SEQ ID NO.2, both sgRNAs are transcribed and purified in vitro by DNA templates, and the DNA template sequence of CD7-sgRNA is:

GTTTTTTTTAATACGACTCACTATAggagcaggtgatgttgacggGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTT。

the DNA template sequence of PD1-sgRNA is:

GTTTTTTTTAATACGACTCACTATAggccaggatggttcttaggtGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTT。

the lower case letters in the two sequences represent the 20bp sequence of the sgRNA-targeted T cell genome. T cells were cultured in X-VIVO 15 medium (LONZA#04-418Q), to which 100U/ml recombinant human interleukin 2 (PeproTech, # 200-02-100) and 5% fetal bovine serum were additionally added.

5.9 μl Cas9 protein (1354 μg/ml) and 15.9 μl were targetedCD7The CD7-sgRNA (200 mug/ml) of the gene is mixed at room temperature and 25 ℃ in a molar ratio of 1:2, and is kept stand for 20min, so that the Cas9/sgRNA complex is obtained. 33 μl of nanoparticle (150 μg/ml) was mixed with the Cas9/sgRNA complex prepared under the above conditions at room temperature of 25 ℃, and left to stand for 20min to obtain self-assembled nanoparticle/Cas 9/sgRNA complex (molar ratio 1.5:1:2, respectively, this ratio being better for T cell transfection). The nanoparticle/Cas 9/sgRNA complex was added to T cells in serum-free DMEM medium to a final volume of 500 μl, with an amount of Cas9 of 100nM. After 6h of transfection, the culture medium is changed into X-VIVO 15 culture medium, and after continuous culture for 7 days, the cells are stained with APC anti-human CD7 antibody (BioLegend # 343108), and then the expression condition of the CD7 cells is detected by a flow cytometry, and the CD7 negative cells areCD7Cells after gene knockout. Monoclonal sequencing was performed from genomic DNA (see example 3 experimental methods). Sanger sequencing results of 100 or more clones can be used to estimate the efficiency of gene editing on T cells and to show details of the edited insertions or deletions or single nucleotide variations.

After labeling Cas9 with AF647 (see example 3 preparation method), self-assembled complexes of nanoparticle/Cas 9-AF647/sgRNA were prepared and incubated with T cells for 6h under the same conditions, and then cell AF647 fluorescence was analyzed with a flow cytometer to evaluate the uptake efficiency of Cas9/sgRNA by T cells. Dynabeads [ CD3/CD28 CTS ™ (Gibco # 40203D) ] is a magnetic bead that binds anti-CD 3 and anti-CD 28 antibodies, providing the stimulation signal required for T cell activation and expansion. To investigate the effect of activation on T cells, we compared endocytosis and genome editing of cells upon activation in different situations. Cells are designated as the state of cell activation at the time of transfection (e.g., "AC-1D" means that cells were transfected for 24 hours of activation; activated cells were frozen and thawed for another activation, and "RE-3D" means that cells were transfected for 3 days of reactivation).

T cells not stimulated by magnetic bead activation were transfected for 6h under the above conditions, with an uptake efficiency of intracellular Cas9/sgRNA of only 67.7% (FIG. 10). In contrast, AF647 positive rate of all cells activated with magnetic beads (according to the specification, number of cells when added: number of magnetic beads = 1:3) was close to 100%, indicating that activation could significantly increase Cas9/sgRNA uptake (fig. 11 a). Meanwhile, the level of Cas9/sgRNA internalization of the reactivating cells was higher than that of the single activating cells, but the effect of activation for 1-3 days on internalization was not great (fig. 11 a). After the nanoparticle/Cas 9/sgRNA transfected cells were cultured for a further 7 days, the CD7 negative cell proportion was calculated by flow-through, effective gene editing was detected by both activated and reactivated cells, and the gene knockout efficiency was correlated with the uptake of Cas 9/sgRNA. About 13.3% of CD7 expression was reduced in transfected RE-3D cells compared to untransfected cells (b of FIG. 11). Sanger sequencing of 100 clones revealed that 15 clones had insertions or deletions (FIG. 12 a), and the gene editing efficiency (15%) was similar to that detected by flow.

When PD1-sgRNA targeting PD1 is used, T cells are also targetedPD1Gene production editing (b of FIG. 12). 27 insertions or deletions were made in 200 clones, with a gene editing efficiency of 13.5%. The insertion or deletion sequence of the primary T is longer (e.g., 16bp and 35bp insertions, 106bp, 127bp and 222bp deletions) as compared to the monoclonal sequencing data in the 293T or a549 cell line.

Example 6: deep sequencing results of T cells after nanoparticle-mediated gene editing

The PCR primers used in this example to amplify fragments near the CD7 targeting region were 5'-AGCTGCCTCAGGTAGATCCCA-3' and 5'-GATCTGCTCCATGCCCCGTA-3'; the PCR amplification primers for fragments near the PD1 targeting region were 5'-TCTGGGCGGTGCTACAACT-3' and 5'-AAGCCACACAGCTCAGGGT-3'. The genome DNA is amplified into a 250-280bp fragment by using a primer, and after the tail end of the fragment is repaired and the tail end of the A base is added, the two ends of the fragment are respectively connected with a connector to construct a DNA library. Double-ended sequencing was performed using a high throughput sequencing platform (NovaSeq 6000, illumina), 150bp each. The sequencing sequences (Reads) obtained by high throughput sequencing were aligned with reference sequences using the BWA tool (https:// sourceforge. Net/subjects/bio-BWA /), and analyzed using the SAMtools version 1.9 (http:// www.htslib.org /).

Analysis of the results of the deep sequencing sequence of the nanoparticle/Cas 9/CD7-sgRNA transfected T cells (RE-3D) in example 5 revealed that the frequency of insertions occurred highest at the 5 th site upstream of PAM, followed by the 4 th site upstream of PAM (fig. 13). The greatest probability of occurrence occurs when the length of the insertion sequence is 1, accounting for 87.3% of the total number of insertion Reads. The frequency of deletion of gene editing is much higher than the insertion frequency, and the frequency of deletion is highest after the 6 th site of 20bp targeted by CD7-sgRNA, followed by the 5 th site of 20bp and the 15 th site. The highest proportion of the number of the Reads with the deletion length of 12 to the total number of the deletion Reads reaches 62.6 percent. FIG. 14 shows the top 6 specific insertion or deletion sequences and the duty cycle, 12bp deletions, 1bp insertions, 15bp deletions, two 1bp deletions at different positions, and 4bp deletions, respectively, that occur most frequently.

Analysis of the results of the deep sequencing sequence of T cells transfected with nanoparticle/Cas 9/PD 1-sgrnas (RE-3D) revealed (fig. 15) that the highest frequency of insertions occurred at the 5 th site upstream of PAM, followed by the 4 th site upstream of PAM, which is consistent with the insertion case when targeting CD 7. Similarly, the probability of occurrence is greatest when the length of the insertion sequence is 1, accounting for 75.6% of the total number of insertion Reads. The frequency of deletion of gene editing is much higher than the insertion frequency, the frequency of deletion is highest after the 9 th site of 20bp targeted by PD1-sgRNA, and the sequence is next to the 4 th site of 20 bp. The number of Reads of the deletion length is relatively uniform, and the ratio of the number of Reads to the total number of the deletion Reads is 8% -20% when the deletion lengths are 8, 12, 16 and 1. From the first 6 specific insertion or deletion sequences and the duty cycle, which occur most frequently, it can be seen (fig. 16) that the specific preference of editing targeted to PD1 is reduced compared to gene editing targeted to CD 7. The above results help to learn more clearly the details of nanoparticle-mediated Cas9/sgRNA delivery for T cell editing.

Example 7: effect of nanoparticle delivery systems on T cell viability

The culture was continued for 7 days after nanoparticle/Cas 9/sgRNA transfection of primary T cells, cells were stained with acridine orange/propidium iodide dye (AO/PI, nexcelom Bioscience #cs2-0106) and cell viability assessed by an automated cell counter (Cellometer Auto 2000,Nexcelom Bioscience) (fig. 17). The ratio of living cells of the single activated cells after treatment of the delivery system was 85.3%, and the activity difference from untreated single activated cells was 6.2%; the ratio of the activated cells after the treatment of the delivery system was 80.5%, and the activity of the activated cells was only 6.3% worse than that of the untreated cells. These data indicate that nanoparticle delivery systems are less toxic to primary T cells, whether single-or re-activated, and are a potential method of T cell transfection.

The above examples show the use of the invention on T cell endogenous genesCD7 AndPD1the delivery system of the invention can also be used for knocking out other endogenous genes of T cells, so that the CAR T cells can be directed to various T-series antigens, thereby expanding the range of targetable tumors; or modifying a signal pathway in the T cell, enhancing an activation signal or weakening an inhibition signal of the cell, further enhancing the function of the CAR T cell; or by knocking out genes involved in immune monitoring in T cells, the immune rejection of the CAR T from heterogeneous sources is reduced, and the prepared universal CAR T cells can overcome the defects of quality and quantity of the T cells of patients and can also reduce the time and cost for manufacturing autologous T cell products. In conclusion, the invention has very wide application prospect in tumor immunotherapy.

Claims (12)

1. A method of gene editing of isolated T cells, the method comprising:

(1) Constructing degradable nano particles formed by proteins serving as inner cores and macromolecules serving as outer shells, wherein the macromolecules are formed by in-situ polymerization of primary amino groups of lysine in the proteins, electrically neutral monomers and cationic monomers in the presence of a free radical initiator after the primary amino groups of the lysine are modified and introduced into double bonds;

(2) Mixing the nanoparticle obtained in the step (1) with Cas9/sgRNA of a target T cell target gene to obtain a self-assembled complex formed by mixing the nanoparticle and the Cas9/sgRNA complex;

(3) Transferring the self-assembled complex obtained in step (2) into isolated T cells.

2. The method of claim 1, wherein the cationic monomer of step (1) is ethyl 2- (dimethylamino) methacrylate, the charge neutral monomer is acrylamide, the free radical initiator is ammonium persulfate and tetramethyl ethylenediamine, and the modification of the primary amine group of lysine in the protein is an acrylation modification.

3. The method according to claim 2, wherein the modification of the primary amine groups of lysine in the protein is performed using N-hydroxysuccinimide acrylate.

4. The method of claim 3, wherein the protein is any polypeptide having two or more lysine residues.

5. The method of claim 4, wherein the protein is bovine serum albumin.

6. The method of claim 5, wherein the bovine serum albumin: acrylamide: 2- (dimethylamino) ethyl methacrylate: ammonium persulfate: the molar ratio of the tetramethyl ethylenediamine is 1:3000:3000:250:1000.

7. the method of claim 1, wherein the sequence of sgRNA in Cas9/sgRNA in step (2) is shown in SEQ ID No.1, and the gene of interest of T cells is a gene encoding CD 7.

8. A CD7 deficient T cell prepared according to the method of claim 7.

9. The method of claim 1, wherein the sequence of sgRNA in Cas9/sgRNA in step (2) is shown in SEQ ID No.2, and the T cell gene of interest is a gene encoding PD 1.

10. A PD 1-deficient T cell prepared according to the method of claim 9.

11. Use of a T cell according to claim 8 or 10 for the preparation of a chimeric antigen receptor T cell.

12. Use of the T cell of claim 8 or 10 in the manufacture of a medicament for the treatment of a tumor or for the treatment of an autoimmune disease.

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