WO2024141754A1

WO2024141754A1 - Genetically manipulated cells

Info

Publication number: WO2024141754A1
Application number: PCT/GB2023/053374
Authority: WO
Inventors: Florian Hahn; Caitlin Mary DORAN; James SHELFORD; Lucy WILKINSON; Rowan RIMINGTON
Original assignee: Ivy Farm Technologies Limited
Priority date: 2022-12-29
Filing date: 2023-12-22
Publication date: 2024-07-04
Also published as: GB202219829D0

Abstract

The invention relates to a cultured animal cell having a genetic modification in the NF2 gene or a modification to the activity of the Merlin protein and wherein the animal is of an animal species suitable for human or animal consumption. Methods of producing cultivated meat or a cultured meat product 5 comprising culturing animal cells with such a mutation are also provided.

Description

Genetically manipulated cells

Field of invention

The invention relates to genetically manipulated cultured meat cells. More particularly, the invention relates to cultured meat cells which have been genetically manipulated to reduce cell doubling time.

Background

The world population is set to increase to almost 10 billion people within the next 50 years. As a result, there will be nearly two billion additional people to feed by 2050. This rising population will lead to an increase in global demand for meat by approximately 73% by the year 2050. The agricultural industry will have to scale, potentially doubling in size, to meet this demand. Of the earth’s habitable land, 39% is currently used to produce feed to rear livestock for the meat industry. It takes three years to rear a single cow for slaughter, or 6-12 months for pigs and poultry. Therefore, a large area of arable land is required to feed these animals to term. Currently, 80 billion animals are slaughtered each year for meat with 1 .2 billion slaughtered in the UK alone.

Cultivated meat has the potential to address the substantial global problems associated with livestock farming and the environmental impact of meat production along with animal welfare, food security and human health. Cultivated meat is a meat produced by in vitro cell cultures of animal cells. It is a form of cellular agriculture, with such agricultural methods being explored in the context of increased consumer demand for protein. Cellular agriculture relates to the production of animal-sourced foods from cell culture.

Cultivated meat is produced using tissue engineering techniques traditionally used in regenerative medicines and requires cell lines, usually stem cells. Stem cells are undifferentiated cells which have the potential to become many or all of the required kinds of specialized cell types. While pluripotent stem cells are often thought of as the ideal starting cell, the most prominent example of this subcategory of stem cell are embryonic stem cells which due to ethical issues are controversial for use in research. As a result, induced pluripotent stem cells (iPSCs) have been developed. iPSCs are multipotent blood and skin cells that are artificially regressed to a pluripotent state enabling them to differentiate into a greater range of cells. The alternative to iPSCs involves the use of multipotent adult stem cells which give rise to muscle cell lineages or unipotent progenitors which can differentiate into muscle cells. Favourable characteristics of stem cells which make them suitable for cultivated meat production include immortality, increased proliferative ability, lack of reliance on adherence, serum independence and easy differentiation into tissue.

Stem cells used to generate cell lines can be collected from a primary source, i.e., through a biopsy on an animal under local anaesthesia and can also be established from secondary sources such as cryopreserved cultures. However, somatic cells isolated from tissues/organs often used in food consumption (e.g. muscle, fat, and fibroblasts) from agriculturally relevant species (e.g. pigs, cows, chickens) have a limited lifespan when grown in vitro. Although it is possible to isolate primary cell lines from pigs (myoblasts, myofibroblasts, fibroblasts, adipose derived stem cells and epithelial cells) the ability to propagate these cell lines with efficient doubling times and for long term is not feasible.

Merlin ((Moesin-ezrin-radixin-like protein, also known as schwannomin) is a tumour suppressor protein encoded by the neurofibromatosis type 2 gene NF2. The NF2 gene and the Merlin protein have a central role in a multitude of important developmental signalling pathways. For example, NF2/Merlin is a known activator of the Hippo pathway, which restricts organ sizes (Hamaratoglu et al., 2006 (doi:10.1038/ncb1339)) and plays a role in anoikis (Zhao et al, 2012; doi: 10.1101/gad.173435.111). NF2/Merlin has also been shown to modulate Ras activity in mice cells (Cui et al., 2019 (doi:10.1038/s41388-019-0883-6)). Furthermore, it is involved in WNT/p-catenin signalling, receptor tyrosine kinase signalling and NOTCH signalling pathways amongst others (Mota & Shevde 2020 (doi. org/10.1186/s12964-020-00544-7)). NF2 also plays a driving role in allowing cancer cells to escape the primary tumour niche, through downregulating cell-to-cell adhesions and thus promoting metastasis (Lallemand et al, 2003; doi: 10.1 101/gad.1054603). NF2 knock-out models in various mice and human cell lines have shown increased cell proliferation and loss of contact inhibition (Wahiduzzaman et al., 2018 (doi:10.1111/cas.13871); Bosco et al 2010 (doi:10.1038/onc.2010.20); and Fomicheva & Macara, 2020 (doi:10.7554/eLife.636032).

There is a need to reduce cell doubling times (also in the context of suspension culture) and improve the economic viability of cultured meat. The invention addresses this need by providing manipulated primary animal cells that comprise modification of endogenous genes and do not require the expression of exogenous nucleic acid constructs. For this, the relative impact of loss of Hippo pathway members and regulators on proliferation in an anchorage-dependant and independent manner in various cell types and genetic backgrounds is compared.

Summary of the Invention

In a first aspect of the invention, there is provided a cultured animal cell wherein expression of the NF2 gene is modified or the activity of the Merlin protein is modified and wherein the animal is of an animal species suitable for human or animal consumption. It is described here for the first time that a functional knock-out of endogenous NF2 decreases doubling times in porcine and bovine myoblasts and Adipose- derived stem cells. Additionally, it is shown that alteration of NF2 supports the suspension adaptation process of adherent porcine and bovine cell cultures, which is essential to produce agriculturally relevant cell types for consumption. It is therefore advantageously demonstrated that inactivation of the endogenous NF2 gene is sufficient to speed up proliferation of porcine and bovine cell cultures and supports the suspension adaptation process. The commercial viability of cultured meat is greatly improved by the aforementioned advantages of increased proliferation, i.e. decreased doubling time, and supporting the suspension adaptation process.

In one embodiment, the modification decreases the doubling time of the cell by at least about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%.

In one embodiment, the animal is selected from a pig, bovine, poultry, sheep, goat, Equidae, Camelidae, fish, crustaceans or mollusc.

In one embodiment, the animal cell is a somatic cell.

In one embodiment, the animal cell is selected from one of the following cell types: myoblast, fibroblast, myofibroblast, adipose derived stem cell, epithelial cell, mesenchymal stem cell, satellite cell, iPSC, or hepatocyte.

In one embodiment, the expression of the NF2 gene or the activity of the Merlin protein is modified in the animal cell by any one or more of:

1) gene level modification by: a. knock-out or reduced activity/transcription/translation levels via editing in coding sequences, promoters, introns, regulatory regions; b. RNA-directed DNA methylation; or c. transcription activation or repression using CRISPRa or CRISPRi or similar target specific methods; d. knock-out or reduced activity/transcription/translation levels via undirected means, for example radiation or chemical mutagenesis;

2) post-transcription level (post-transcriptional gene silencing) modification by: a. RNAi or siRNA to reduce translation of mRNA into protein; or b. site specific nucleases to modify or cleave mRNA, such as CRISPR/Cas13a;

3) post-translational level (protein disruption) modification by: a. inclusion of activity blocking/reducing molecules, wherein the activity blocking/reducing molecules are small molecules, antibodies, or the like; or b. inclusion of protein degrading ingredients, wherein the protein degrading ingredients are specialised proteases, exoproteases, or endoproteases.

In one embodiment, the animal cell has a genetic modification in NF2 gene.

In one embodiment, the genetic modification in the NF2 gene is a loss of function modification or leads to reduction in function..

In one embodiment, the loss of function modification comprises a knock-out of the gene or loss of protein function.

In one embodiment, the modification is introduced using targeted genome modification or randomised mutagenesis or by spontaneous mutation.

In one embodiment, the modification is in the promoter region or coding region of the one of more genes. In one embodiment, the modification is introduced using targeted genome modification, optionally using a targeted endonuclease.

In one embodiment, the endonuclease is optionally selected from TALEN, ZFN or CRISPR, optionally CRISPR/Cas9.

In one embodiment, the cultured animal cell further comprises at least one additional genetic modification to manipulate the genome surveillance, cell cycle control and/or cell death control pathway. In one embodiment, the at least one additional genetic modification is in one or more of the following genes: RB1 , TP53, and/or a RAS gene. In one embodiment, the additional genetic modification may be a knock-out or reduced activity/transcription/translation levels via editing in coding sequences, promoters, introns, regulatory regions, for example in the RB1 or TP53 genes, or in another embodiment, the genetic mutation may be a knock-in or increased activity/transcription/translation levels via editing in coding sequences, promoters, introns, regulatory regions, for example for the RAS gene; In one embodiment, the animal cell has a genetic modification in RB1.

In one embodiment, the animal cell has a genetic modification in TP53.

In one embodiment, the animal cell has a genetic modification in a RAS gene.

In one embodiment, the animal cell has a genetic modification in RB1 and in TP53.

In one embodiment, the animal cell has a genetic modification in RB1 and in a RAS gene.

In one embodiment, the animal cell has a genetic modification in TP53 and in a RAS gene.

In one embodiment, the animal cell has a genetic modification in RB1, TP53 and in a RAS gene.

In one embodiment, the RAS gene is HRAS, NRAS, or KRAS.

In one embodiment, the RAS gene is HRAS.

According to a second aspect of the invention, there is provided a method of producing cultivated meat or a cultured meat product comprising culturing the animal cell as described herein.

According to a third aspect of the invention, there is provided a method of producing the modified animal cell as described herein.

In one embodiment, the animal cell is a somatic cell.

In one embodiment, the modification is introduced using targeted genome modification.

According to a fourth aspect of the invention, there is provided a cultivated or cultured animal tissue or a cultivated or cultured meat product comprising a modified cell as described herein.

In one embodiment, the culture is a suspension culture.

According to a fifth aspect of the invention, there is provided use of the modified animal cell as described herein for cellular agriculture. According to a sixth aspect of the invention, there is provided a method for producing an immortalised animal cell line comprising the method as described herein wherein the immortalised cell line comprises a NF2 gene modification.

In one embodiment, the modification is a loss of function modification or leads to reduction in function.. In one embodiment, the loss of function modification is a knock-out of the NF2 gene.

According to a seventh aspect of the invention, there is provided a guide RNA targeting the sequence of SEQ ID NO. 5, or SEQ ID NO. 8, or SEQ ID NO. 9, or SEQ ID NO. 10, or SEQ ID NO. 28, or SEQ ID NO. 29, or SEQ ID NO. 30 individually or in combination.

According to an eighth aspect of the invention, there is provided a kit comprising at least one of the guide RNA as described herein.

Figures and tables

The invention is further described in the following non-limiting figures.

Figure 1 is a graph that shows the doubling times in suspension conditions. Doubling time assessment of control cell pools (transfected with Cas9 only, no sgRNA) and NF2 knock-out cell pool after transfer from adherent into suspension growth conditions. Data points come from triplicate Erlenmeyer flasks and measured over 4 growth passages.

Figure 2 is a graph that shows the collective data from all 4 passages of the doubling time assessment from Figure 1

Figure 3 is a graph that shows the NF2 gene editing efficiencies. Assessment of NF2 knock-out efficiencies in porcine myoblast cell pools transfected with Cas9 protein and a sgRNA targeting the NF2 gene. At two time points post transfection and after a 4 passage suspension growth study in triplicate flasks, DNA was isolated from cell pools and knock-out efficiencies were determined by PCR amplification of the NF2 gene followed by Sanger Sequencing of the PCR amplicon and analysis of the sequencing results using the ICE analysis tool (ice.synthego.com).

Figure 4 shows functional knock-out of NF2 gene coding for the Merlin protein preserves mesenchymal cell phenotype and enhances adipogenic differentiation potential in immortalised myoblast cell lines, (a) Flow cytometry density plots for cell surface markers CD29 (mesenchymal), CD56 (myoblast), CD90 (mesenchymal), CD29 CD56+/+ (muscle stem cell), CD31 (endothelial) and CD45 (immune lineage) evidencing loss of CD56 and CD90 expression following adaptation of NF2 (+/+) cells to suspension from adherent culture conditions, which is retained following functional knockout of the NF2 gene, (b-g) Quantification of flow cytometry data for corresponding surface markers in NF2 (+/+, purple bars) and (-/-, green bars) suspension cell lines, (h) Fluorescence micrographs of NF2 (+/+) and NF2 (-/-) cell lines labelled for lipid marker BODIPY (green) and nuclear DNA (DAPI, blue) in suspension shows enhanced adipogenic potential of NF2 knock-out lines and corresponds with preserved mesenchymal cell phenotype. Light micrograph of NF2 (-/-) cells also demonstrates unilocular nuclear positioning indicative of mature adipocytes (indicated by white arrow), (i) Quantification of lipid accumulation in NF2 (+/+) and (-/-) cell lines.

Figure 5 shows NF2 knockout efficiencies across a variety of cell types, (a) Porcine primary myoblasts, (b) Procine CRISPR-immortalized (P53 ^/7RB1 ^/7HRAS^G12V/) myoblasts, (c) Porcine viral-immortalized myblasts. (d) Porcine viral-immortalized ADSCs (suspension), (e) Porcine CRISPR-immortalized (P53- '/RB /HRAS^{1312 7}) ADSCs. (f) Bovine var. Angus CRISPR-immortalized (PSS ^RBT⁷) ADSCs. (g) Bovine var. Angus CRISPR-immortalized (PSS '/RB /HRAS^{012 7}) ADSCs. (h) Bovine var. Angus CRISPR-immortalized (PSS '/RBI ⁷) myoblasts, (i) Bovine var. Angus CRISPR-immortalized (P53 ^z- /RB1 ^_/7HRAS^G12V/) myoblasts, (j) Bovine var. Wagyu CRISPR-immortalized (PSS '/RB ) ADSCs. (k) Bovine var. Wagyu CRISPR-immortalized (PSS '/RBP/HRAS^{012 7}) myoblasts.

Figure 6 shows doubling time assessments of NF2 knockout cell lines in comparison with control lines in adherent growth conditions, (a) Doubling time bovine var. Angus myoblasts (adherent), (b) Doubling time bovine var. Angus myoblasts (adherent), (c) Doubling time bovine var. Angus ADSCs (adherent), (d) Doubling time bovine var. Angus ADSCs (adherent), (e) Doubling time bovine var. Wagyu myoblasts (adherent), (f) Doubling time bovine var. Wagyu myoblasts (adherent).

Figure 7 shows doubling time assessments of NF2 knockout cell lines in comparison with control lines in suspension growth conditions, (a) Doubling time porcine myoblasts (suspension), (b) Doubling time porcine myoblasts (suspension), (c) Doubling time porcine ADSCs (suspension), (d) Doubling time porcine ADSCs (suspension), (e) Doubling times bovine var. Angus myoblasts (suspension), (f) Doubling times var. Angus myoblasts (suspension).

Figure 8 compares enrichment of cells mutated in different genes of the Hippo pathway in a growth competition assay.

Table 1 Sequences of nucleic acids. These sequences include target sequences according to the invention and illustrate genetic modifications.

Detailed description

The aspects of the invention will now be further described. In the following passages, different aspects are described. Each aspect so defined may be combined with any other aspect or aspects unless clearly indicated to the contrary. Generally, nomenclatures used in connection with, and techniques of, cell and tissue culture, pathology, oncology, molecular biology, immunology, microbiology, genetics and protein and nucleic acid chemistry and hybridization described herein are those well-known and commonly used in the art. The methods and techniques of the present disclosure are generally performed according to conventional methods well-known in the art and as described in various general and more specific references that are cited and discussed throughout the present specification unless otherwise indicated. See, e.g., Green and Sambrook etal., Molecular Cloning: A Laboratory Manual, 4^th ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (2012).

Enzymatic reactions and purification techniques are performed according to manufacturer’s specifications, as commonly accomplished in the art or as described herein. The nomenclatures used in connection with, and the laboratory procedures and techniques of, cell biology and cell culturing, analytical chemistry, synthetic organic chemistry, and medicinal and pharmaceutical chemistry described herein are those well-known and commonly used in the art. Standard techniques are used for any cell culturing, genetic targeting, chemical syntheses, chemical analyses, and delivery.

Low cell doubling times and growth in suspension conditions are essential for large scale cultured meat processes. Somatic cells isolated from tissues/organs often used in food consumption (e.g. muscle, fat, fibroblasts) from agriculturally relevant species (e.g. pigs, cows, chickens) have a limited proliferation capacity when grown in vitro. Also, cells from animal tissue isolations tend to grow only in adherent conditions and the transfer into suspension conditions can lead to very slow cell growth (if any).

Modified cells and methods

In a first aspect, the invention relates to a cultured animal cell wherein expression of the NF2 gene is modified or the activity of the Merlin protein is modified and wherein the animal is of an animal species suitable for human or animal consumption.

As used herein, the words “nucleic acid”, “nucleic acid sequence”, “nucleotide”, “nucleic acid molecule” or “polynucleotide” are intended to include DNA molecules (e.g., cDNA or genomic DNA), RNA molecules (e.g., mRNA), naturally occurring, mutated, synthetic DNA or RNA molecules, and analogs of the DNA or RNA generated using nucleotide analogs. It can be single -stranded or double -stranded. Such nucleic acids or polynucleotides include, but are not limited to, coding sequences of structural genes, anti-sense sequences, and non-coding regulatory sequences that do not encode mRNAs or protein products. These terms also encompass a gene. The term “gene”, “allele” or “gene sequence” is used broadly to refer to a DNA nucleic acid associated with a biological function. Thus, genes may include introns and exons as in the genomic sequence, or may comprise only a coding sequence as in cDNAs, and/or may include cDNAs in combination with regulatory sequences. Thus, according to the various aspects of the invention, genomic DNA, cDNA or coding DNA may be used. In one aspect, the nucleic acid is cDNA or coding DNA. The terms “peptide”, “polypeptide” and “protein” are used interchangeably herein and refer to amino acids in a polymeric form of any length, linked together by peptide bonds. The term “allele” designates any of one or more alternative forms of a gene at a particular locus. Heterozygous alleles are two different alleles at the same locus. Homozygous alleles are two identical alleles at a particular locus. A wild type (wt) allele is a naturally occurring allele without a modification at the target locus.

It is shown for the first time herein that disrupting the NF2 gene, which encodes the Merlin protein (a key regulator of multiple pathways involved in cell proliferation), speeds up the doubling time of porcine and bovine cells with different cell types or genetic backgrounds when transferred from adherent in suspension conditions. This allows for the cells to be used in cellular agriculture, where cells must proliferate at high speed in suspension conditions. We also show that disrupting the NF2 gene speeds up doubling times more than other genes of the Hippo pathway indicating that the impact of NF2 may be a result of its involvement in pathways beyond the Hippo pathway.

The expression of the NF2 gene or the activity of the Merlin protein can be targeted in a number of different ways, including at least one of:

In one embodiment, expression of the NF2 gene may be modified to knock out Merlin protein expression. In a related embodiment, CRISPR may be used to knock of the NF2 gene expression. In a further embodiment, single point mutation or multiple mutations may be used to knock out the NF2 gene expression. In a yet further embodiment, the CRISPR/Cas9 or CRISPR/Cas13a systems may be used to knock our NF2 gene expression.

According to one embodiment, the expression of the NF2 gene or the activity of the Merlin protein may be modified in an animal cell by at least one small molecule or at least one RNAi. In one embodiment, the RNAi may be shRNA or siRNA.

When double stranded RNAs are processed by an Rnase Ill-like protein known as Dicer mRNA can be silenced and protein activity lowered or abolished within a cell. Dicer typically contains an N-terminal RNA helicase domain, an RNA-binding so-called Piwi/Argonaute/Zwille (PAZ) domain, two Rnase III domains and a double-stranded RNA binding domain (dsRBD) (Collins et al 2005). Dicer processing of the long double stranded RNAs creates 21-24 nucleotide double stranded siRNAs with 2 base 3’ overhangs and a 5’ phosphate and 3’ hydroxyl group. The resulting siRNA duplexes are then incorporated into the effector complex known as RNA-induced silencing complex (RISC), where the antisense or guide strand of the siRNA guides RISC to recognize and cleave target mRNA sequences (Elbashir et al 2001) upon adenosine-triphosphate (ATP)-dependent unwinding of the double-stranded siRNA molecule through an RNA helicase activity (Nykanen et al 2001). The catalytic activity of RISC, which leads to mRNA degradation, is mediated by the endonuclease Argonaute 2 (AGO2) (Liu et al 2004; Song et al 2004). AGO2 belongs to the highly conserved Argonaute family of proteins. Argonaute proteins are GO Kda highly basic proteins that contain two common domains, namely PIWI and PAZ domains (Cerutti et al 2000). The PIWI domain is crucial for the interaction with Dicer and contains the nuclease activity responsible for the cleavage of mRNAs. AGO2 uses one strand of the siRNA duplex as a guide to find messenger RNAs containing complementary sequences and cleaves the phosphodiester backbone between bases 10 and 11 relative to the guide strand’s 5’ end (Elbashir et al 2001). An important step during the activation of RISC is the cleavage of the sense or passenger strand by AGO2, removing this strand from the complex (Rand et al 2005). Once the mRNA has been cleaved, due to the presence of unprotected RNA ends in the fragments the mRNA is further cleaved and degraded by intracellular nucleases and will no longer be translated into proteins. This leads to reduction of specific mRNA molecules and the corresponding proteins. It is possible to exploit this native mechanism for gene silencing with the purpose of regulating any gene(s) of choice.

Many studies have been published describing how to optimise siRNA, for example WO02/44321 , (Walton SP et al 2010, and Chang Cl et al 2011 the contents of which are incorporated herein by reference.

Godinho and Khvorova 2019 describes commonly used methods of delivering RNAi into cells. Examples of materials used as non-viral vectors, nanocarriers or in formulated nanosystems and ligands used for conjugation are described. Additional examples are provided in references included therein. Nano particles are often used to introduce RNAi into cells and cationic lipids (e.g. D-Lin-MC3- DMA), polymers (e.g. cyclodextrin-based polymers and biocollagen), polypeptides, and exosomes are all examples of biomaterials which can be used to transport RNAi into the cytoplasm of target cells.

The creation and delivery of RNAi are further described in US6,506,559 and W02007045930 the contents of which are incorporated herein by reference.

In some embodiments, post-translational Inactivation (protein disruption) can be used to inhibit the activity of the Merlin protein. In one embodiment, activity blocking/reducing molecules can inhibit Merlin protein activity. For example, small molecules can inhibit Merlin protein activity.

In some embodiments, the Merlin protein may be degraded using protein degrading ingredients. Examples include i) specialised proteases, e.g. a calcium-dependent cysteine protease, such as calpain, ii) exoproteases, or iii) endoproteases.

According to the various aspects of the invention, the modification can be in the promoter region or in the coding region of the one of more genes that is/are targeted. The cell is therefore genetically manipulated I engineered.

In one embodiment of the aspects of the invention, the modified cell is a primary cell. In another embodiment of the aspects of the invention, the modified cell is a somatic cell. Any somatic cell suitable for use in cellular agriculture, that is the production of animal-sourced foods from cell culture, is within the scope of the invention. For example, the cell may be a fat or muscle cell. For example, the cell may be selected from one or more of the following cell types: myoblast, fibroblast, myofibroblast, adipose derived stem cell, epithelial cell, mesenchymal stem cell, satellite cell, iPSC, or hepatocytes.

The terms “animal” and “non-human animal” with reference to animals and cells derived therefrom are used herein interchangeably and refer only to cells of non-human-animals. Cells for use in the invention may be of any other animal origin. However, the cells are not human cells. Cells suitable for use in cellular agriculture are preferably non-human animal cells that provide a source of any dietary protein, fat and/or carbohydrate.

The cells are cells of non-human animals that are suitable for human and animal consumption. These include animals such as non-human mammals, birds, fish, crustaceans, molluscs, reptiles, amphibians, or insects. Exemplary non-human mammals include those in the genera Bovinae, Camelidae, Canidae, Caprae, Cervidae, Felidae, Equidae, Lagomorphs, Macropodidae, Oves, Rodents, or Suidae. The cells may be cells of any livestock or poultry. The cells may be porcine, bovine (e.g. cattle), ovine, caprine, avine, or piscine. The cell may be shrimp, prawn, crab, crayfish, and/or lobster. In one embodiment, the animal is a pig or bovine (e.g. cattle). The animal used in various aspects of the invention may be of an animal species used in agriculture. An animal species used in is an animal farmed for human. Such animals are listed above. In a preferred embodiment, they include pig, bovine (e.g. cattle), poultry (e.g. chicken, turkey, duck, geese), sheep, goat, Equidae, Camelidae, fish, crustaceans or mollusc.

The doubling time of a cell line is the average time it takes for a population of the cells to double in size as a result of cell cycle progression and subsequent division. Therefore, removing cell cycle checkpoint inhibition of the cell cycle decreases the time required for one cell to undergo mitosis and form two new daughter cells. When applied to a whole population of cells of the cell line, this modification reduces the doubling time of said cell line and means the cells are quick to expand and better suited for use in cellular agriculture.

The term “genetic modification” relates to a modification that alters expression of the gene that is targeted or functional activity of the gene product, i.e. the NF2 gene which encodes the Merlin protein. The genetic modification may result in a loss of function, for example by creating a knock-out. To create a loss of function/knock-out, a mutation may be introduced in the coding sequence which renders the expressed protein non-functional (e.g. an amino acid substitution, deletion or addition/insertion) or creates a premature stop codon/ prevents expression of a functional protein.

Examples of loss of function mutations are described herein. However, any mutation that results in a dominant loss of function as described herein is encompassed within the scope of the invention. As used herein, “dominant” also encompasses “semi-dominant” or “partially dominant”. Therefore, the mutant allele may be fully dominant, partially dominant or semi-dominant. Preferably, the mutant allele is fully dominant. A loss of function mutation includes a knock-out modification or any other modification that causes an amino acid substitution or change wherein the substitution or change causes the resulting protein to lack a specific function or causes a reduction in the activity of said protein or prevents expression of the protein. Preferably, both alleles of NF2 are knocked out.

A knock-out modification or mutation may eliminate at least partially the specific endogenous nucleic acid sequence from the genomic DNA of the cell that codes for the protein of interest. By eliminating the corresponding nucleic acid sequence, the protein can no longer be synthesised by the cellular machinery. In some embodiment, a knock-out modification occurs from the introduction of an indel (insertion and/or deletion event) that results in a change of the native amino acid composition of the resulting protein, often this takes the form of a frameshifting mutation.

Examples of gain of function are also described herein. In some embodiment, a change in the gene sequence might lead to a change to the native amino acid composition of the resulting protein, which increases the activity of said protein. In a further embodiment, changes in the amino acid sequence of a protein might add or remove regulatory regions of a protein, such as, but not limiting to, phosphorylation, acetylation and ubiquitination sites. In a further embodiment, changes in the amino acid sequence of a protein might stabilize or destabilize intermediate states of its enzymatic reaction substrates and products. In a further embodiment, changes in the amino acid sequence of a protein might lock it in a permanent “on”-state. In a further embodiment, changes in regulatory gene sequences might increase transcription of a gene and thereby protein amount and the total activity of that protein per cell. In a further embodiment, changes in the amino acid sequence of a protein might influence its’ interactions with other proteins. In a further embodiment, gain of function changes are introduced in a targeted manner by knock-in of specific nucleotides which lead to desired amino acid changes on protein level or desired nucleotide exchanges in regulatory gene regions. In a further embodiment, gain of function mutations are introduced into cells by addition of exogeneous nucleotide sequences encoding for the desired protein.

An amino acid substitution is affected by alterations in a nucleic acid sequence that results in the production of a different amino acid at a given site. This modification may affect the functional properties and/or activity of the encoded polypeptide or it may not affect the functional properties of the encoded polypeptide (conservative substitution). Conservative substitutions are well known in the art. For example, a codon for the amino acid alanine, a hydrophobic amino acid, may be substituted by a codon encoding another less hydrophobic residue, such as glycine, or a more hydrophobic residue, such as valine, leucine, or isoleucine. Similarly, changes which result in substitution of one negatively charged residue for another, such as aspartic acid for glutamic acid, or one positively charged residue for another, such as lysine for arginine, can also be expected to produce a functionally equivalent product. Nucleotide changes which result in alteration of the N-terminal and C-terminal portions of the polypeptide molecule would also not be expected to alter the activity of the polypeptide. Each of the proposed modifications is well within the routine skill in the art, as is determination of retention of biological activity of the encoded products. Non-conservative substitution leads to an encoded protein which does not retain the same functional properties and/or activity of the non-modified protein.

Sequence identity is commonly defined with reference to the algorithm GAP (Wisconsin GCG package, Accelerys Inc, San Diego USA). GAP uses the Needleman and Wunsch algorithm to align two complete sequences, maximising the number of matches and minimising the number of gaps. Generally, default parameters are used, with a gap creation penalty typically equalling 12 and a gap extension penalty equalling 4. Use of GAP may be preferred but other algorithms may be used, e.g. BLAST, or the Smith- Waterman algorithm, or the TBLASTN program, of, generally employing default parameters. In particular, the psi-Blast algorithm may be used. Sequence identity may be defined using the Bioedit, ClustalW algorithm. Alignments can be performed using Snapgene and based on MUSCLE (Multiple Sequence Comparison by Log-Expectation) algorithms. Sanger Sequencing of PCR amplicons and analysis of the sequencing results using the ICE analysis tool (ice.synthego.com) were also used to confirm sequence identity. In one embodiment, the modification is introduced using targeted genome modification and/or a rare- cutting endonuclease, for example a TALEN, ZFN or CRISPR/Cas9.

Genome editing techniques have emerged as alternative methods to conventional mutagenesis methods (such as physical and chemical mutagenesis) or methods using the expression of transgenes in animal cells to produce mutant animal cells with improved phenotypes that are important in cellular research and cellular agriculture. These techniques employ sequence -specific nucleases (SSNs) including zinc finger nucleases (ZFNs), transcription activator -like effector nucleases (TALENs), and the RNA -guided nuclease Cas9 (CRISPR/Cas9), which generate targeted DNA double -strand breaks (DSBs), which are then repaired mainly by either error -prone non-homologous end joining (NHEJ) or high- fidelity homologous recombination (HR).

As explained in detail below, mutations according to the various aspects of the invention can be introduced into animal cells using targeted genome modification based on such editing techniques.

In another aspect, the invention also relates to a method for modifying the expression or function of one or more genes in a non-human animal wherein the gene is associated with genome surveillance, cell cycle control and/or cell death control. In a preferred embodiment, the animal is an animal suitable for human or animal consumption, for example used in agriculture. In an embodiment, the method comprises introducing a mutation into the one or more genes in the animal cell.

In another aspect, the invention relates to a method of producing a modified non-human animal cell described herein, wherein the method comprises introducing a genetic modification in one or more genes associated with genome surveillance, cell cycle control and/or cell death control. In a preferred embodiment, the animal is an animal used in agriculture. The method is performed in vitro or ex vivo.

In yet another aspect the invention provides a modified animal cell having a genetic modification in the NF2 gene. In one embodiment, the modified animal cell may be an immortalised animal cell. In a further embodiment, the immortalised animal cell may have been immortalised using targeted genome modification. In other embodiments, the immortalised animal cell may have been immortalised using randomised mutagenesis. In yet further embodiments, the immortalised animal cell may have been immortalised using radiation or chemical mutagenesis. In yet further embodiments, the immortalised animal cell may have been spontaneously immortalised.

In some embodiments, the genetic modification in the NF2 gene may be created using targeted genome modification. In other embodiments, the genetic modification in the NF2 gene may be created using randomised mutagenesis. In yet further embodiments, the genetic modification in the NF2 gene may have occurred spontaneously. In all aspects of the invention the animal is not human. Animals that can be used, in particular agriculturally relevant animals, are listed herein.

modification of animal cells

Targeted genome modification or targeted genome editing is a genome engineering technique that uses targeted DNA double-strand breaks (DSBs) to stimulate genome editing through homologous recombination (HR)-mediated recombination events. To achieve effective genome editing via introduction of site-specific DNA DSBs, four major classes of customizable DNA binding proteins can be used: meganucleases derived from microbial mobile genetic elements, ZF nucleases based on eukaryotic transcription factors, rare-cutting endonucleases/sequence specific endonucleases (SSN), for example TALENs, transcription activator-like effectors (TALEs) from Xanthomonas bacteria, and the RNA-guided DNA endonuclease Cas9 from the type II bacterial adaptive immune system CRISPR (clustered regularly interspaced short palindromic repeats). Other CRISPR/Cas systems using different Cas proteins would be well known to the skilled person in the art. Meganuclease, ZF, and TALE proteins all recognize specific DNA sequences through protein-DNA interactions. Although meganucleases integrate their nuclease and DNA-binding domains, ZF and TALE proteins consist of individual modules targeting 3 or 1 nucleotides (nt) of DNA, respectively. ZFs and TALEs can be assembled in desired combinations and attached to the nuclease domain of Fokl to direct nucleolytic activity toward specific genomic loci.

Upon delivery into host cells via the bacterial type III secretion system, TAL effectors enter the nucleus, bind to effector-specific sequences in host gene promoters and activate transcription. Their targeting specificity is determined by a central domain of tandem, 33-35 amino acid repeats. This is followed by a single truncated repeat of 20 amino acids. The majority of naturally occurring TAL effectors examined have between 12 and 27 full repeats.

These repeats only differ from each other by two adjacent amino acids, their repeat- variable di-residue (RVD). The RVD determines which single nucleotide the TAL effector will recognize: one RVD corresponds to one nucleotide, with the four most common RVDs each preferentially associating with one of the four bases. Naturally occurring recognition sites are uniformly preceded by a T that is required for TAL effector activity. TAL effectors can be fused to the catalytic domain of the Fokl nuclease to create a TAL effector nuclease (TALEN) which makes targeted DNA double-strand breaks (DSBs) in vivo for genome editing. The use of this technology in genome editing is well described in the art, for example in US 8,440,431 , US 8,440, 432 and US 8,450,471 . Customized plasmids can be used with the Golden Gate cloning method to assemble multiple DNA fragments. The Golden Gate method uses Type IIS restriction endonucleases, which cleave outside their recognition sites to create unique 4 bp overhangs. Cloning is expedited by digesting and ligating in the same reaction mixture because correct assembly eliminates the enzyme recognition site. Assembly of a custom TALEN or TAL effector construct and involves two steps: (i) assembly of repeat modules into intermediary arrays of 1-10 repeats and (ii) joining of the intermediary arrays into a backbone to make the final construct.

Another genome editing method that can be used according to the various aspects of the invention is CRISPR. The use of this technology in genome editing is well described in the art, for example in US 8,697,359. In short, CRISPR is a microbial nuclease system involved in defence against invading phages and plasmids. CRISPR loci in microbial hosts contain a combination of CRISPR-associated (Cas) genes as well as non-coding RNA elements capable of programming the specificity of the CRISPR-mediated nucleic acid cleavage. Three types (l-lll) of CRISPR systems have been identified across a wide range of bacterial hosts. One key feature of each CRISPR locus is the presence of an array of repetitive sequences (direct repeats) interspaced by short stretches of non-repetitive sequences (spacers). The non-coding CRISPR array is transcribed and cleaved within direct repeats into short crRNAs containing individual spacer sequences, which direct Cas nucleases to the target site (protospacer).

By “crRNA” or CRISPR RNA is meant the sequence of RNA that contains the protospacer element and additional nucleotides that are complementary to the tracrRNA. By “tracrRNA” (transactivating RNA) is meant the sequence of RNA that hybridises to the crRNA and binds a CRISPR enzyme, such as Cas9 thereby activating the nuclease complex to introduce double-stranded breaks at specific sites within the genomic sequence of at least one nucleic acid or promoter sequence of the one or more genes. By “protospacer element” is meant the portion of crRNA (or sgRNA) that is complementary to the genomic DNA target sequence, usually around 20 nucleotides in length. This may also be known as a spacer or targeting sequence.

By “sgRNA” (single-guide RNA) is meant the combination of tracrRNA and crRNA in a single RNA molecule, preferably also including a linker loop (that links the tracrRNA and crRNA into a single molecule). “sgRNA” may also be referred to as “gRNA” and in the present context, the terms are interchangeable. The sgRNA or gRNA provide both targeting specificity and scaffolding/binding ability for a Cas nuclease. A gRNA may refer to a dual RNA molecule comprising a crRNA molecule and a tracrRNA molecule.

The Type II CRISPR is one of the most well characterized systems and carries out targeted DNA double-strand breaks in four sequential steps. First, two non-coding RNA, the pre-crRNA array and tracrRNA, are transcribed from the CRISPR locus. Second, tracrRNA hybridizes to the repeat regions of the pre-crRNA and mediates the processing of pre-crRNA into mature crRNAs containing individual spacer sequences. Third, the mature crRNA: tracrRNA complex directs Cas9 to the target DNA via Watson-Crick base-pairing between the spacer on the crRNA and the protospacer on the target DNA next to the protospacer adjacent motif (PAM), an additional requirement for target recognition. Finally, Cas9 mediates cleavage of target DNA to create a double-stranded break within the protospacer. Cas9 is thus the hallmark protein of the type I CRISPR-Cas system, and a large monomeric DNa nuclease guided to a DNA target sequence adjacent to the PAM sequence motif by a complex of two noncoding RNAs: CRISPR RNA (crRNA) and trans-activating crRNA (tracrRNA). The Cas9 protein contains two nuclease domains homologous to RuvC and HNH nucleases. The HNH nuclease domain cleaves the complementary DNA strand whereas the RuvC-like domain cleaves the non-complementary strand and, as a result, a blunt cut is introduced in the target DNA. Heterologous expression of Cas9 together with a guide RNA (gRNA) also called single guide RNA (sgRNA) can introduce site-specific double strand breaks (DSBs) into genomic DNA of live cells from various organisms. For applications in eukaryotic organisms, codon optimized versions of Cas9, which is originally from the bacterium Streptococcus pyogenes, have been used.

Synthetic CRISPR systems typically consist of two components, the gRNA and a non-specific CRISPR-associated endonuclease and can be used to generate knock-out cells or animals by co-expressing a gRNA specific to the gene to be targeted and capable of association with the endonuclease Cas9. Notably, the gRNA is an artificial molecule comprising one domain interacting with the Cas or any other CRISPR effector protein or a variant or catalytically active fragment thereof and another domain interacting with the target nucleic acid of interest and thus representing a synthetic fusion of crRNA and tracrRNA. The genomic target can be any 20 nucleotide DNA sequence, provided that the target is present immediately upstream of a PAM sequence. The PAM sequence is of outstanding importance for target binding and the exact sequence is dependent upon the species of Cas9.

The PAM sequence for the Cas9 from Streptococcus pyogenes has been described to be “NGG” or “NAG” (Standard IUPAC nucleotide code) (Jinek et al, “A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity”, Science 2012, 337: 816-821). The PAM sequence for Cas9 from Staphylococcus aureus is “NNGRRT” or “NNGRR(N)”. Further variant CRISPR/Cas9 systems are known. Thus, a Neisseria meningitidis Cas9 cleaves at the PAM sequence NNNNGATT. A Streptococcus thermophilus Cas9 cleaves at the PAM sequence NNAGAAW. Recently, a further PAM motif NNNNRYAC has been described for a CRISPR system of Campylobacter (WO 2016/021973). For Cpf1 nucleases, e.g. Cas12a, it has been described that the Cpf1 -crRNA complex, without a tracrRNA, efficiently recognize and cleave target DNA proceeded by a short T-rich PAM in contrast to the commonly G-rich PAMs recognized by Cas9 systems. Furthermore, by using modified CRISPR polypeptides, specific single-stranded breaks can be obtained. The combined use of Cas nickases with various recombinant gRNAs can also induce highly specific DNA double-stranded breaks by means of double DNA nicking. By using two gRNAs, moreover, the specificity of the DNA binding and thus the DNA cleavage can be optimized. Further CRISPR effectors like CasX and CasY effectors originally described for bacteria, are meanwhile available and represent further effectors, which can be used for genome engineering purposes (Burstein et al., “New CRISPR-Cas systems from uncultivated microbes”, Nature, 2017, 542, 237-241). Once expressed, the Cas9 protein and the gRNA form a ribonucleoprotein complex through interactions between the gRNA “scaffold” domain and surface-exposed positively-charged grooves on Cas9. Cas9 undergoes a conformational change upon gRNA binding that shifts the molecule from an inactive, non-DNA binding conformation, into an active DNA-binding conformation. Importantly, the “spacer” sequence of the gRNA remains free to interact with target DNA. The Cas9-gRNA complex will bind any genomic sequence with a PAM, but the extent to which the gRNA spacer matches the target DNA determines whether Cas9 will cut. Once the Cas9-gRNA complex binds a putative DNA target, a “seed” sequence at the 3' end of the gRNA targeting sequence begins to anneal to the target DNA. If the seed and target DNA sequences match, the gRNA will continue to anneal to the target DNA in a 3' to 5' direction (relative to the polarity of the gRNA).

CRISPR/Cas9 and likewise CRISPR/Cpf1 and other CRISPR systems are highly specific when gRNAs are designed correctly, but especially specificity is still a major concern, particularly for clinical uses based on the CRISPR technology. The specificity of the CRISPR system is determined in large part by how specific the gRNA targeting sequence is for the genomic target compared to the rest of the genome. The sgRNA is a synthetic RNA chimera created by fusing crRNA with tracrRNA. The sgRNA guide sequence located at its " end confers DNA target specificity. Therefore, by modifying the guide sequence, it is possible to create sgRNAs with different target specificities. The canonical length of the guide sequence is 20 bp.

Thus, as used herein, the term “guide RNA” relates to a synthetic fusion of two RNA molecules, a crRNA (CRISPR RNA) comprising a variable targeting domain, and a tracrRNA. In one embodiment, the guide RNA comprises a variable targeting domain of 12 to 30 nucleotide sequences and a RNA fragment that can interact with a Cas endonuclease. sgRNAs suitable for use in the methods of the invention are described below. As used herein, the term “guide polynucleotide”, relates to a polynucleotide sequence that can form a complex with a Cas endonuclease and enables the Cas endonuclease to recognize and optionally cleave a DNA target site. The guide polynucleotide can be a single molecule or a double molecule. The guide polynucleotide sequence can be an RNA sequence, a DNA sequence, or a combination thereof (a RNA-DNA combination sequence). Optionally, the guide polynucleotide can comprise at least one nucleotide, phosphodiester bond or linkage modification such as, but not limited, to Locked Nucleic Acid (LNA), 5-methyl dC, 2,6-Diaminopurine, 2'-Fluoro A, 2'-Fluoro U, 2'-O-Methyl RNA, phosphorothioate bond, linkage to a cholesterol molecule, linkage to a polyethylene glycol molecule, linkage to a spacer 18 (hexaethylene glycol chain) molecule, or 5' to 3' covalent linkage resulting in circularization. A guide polynucleotide that solely comprises ribonucleic acids is also contemplated. The terms “target site”, “target sequence”, “target DNA”, “target locus”, “genomic target site”, “genomic target sequence”, and “genomic target locus” are used interchangeably herein and refer to a polynucleotide sequence in the genome (including choloroplastic and mitochondrial DNA) of a cell at which a double-strand break is induced in the cell genome by a Cas endonuclease. The target site can be an endogenous site in the genome, or alternatively, the target site can be heterologous to the plant and thereby not be naturally occurring in the genome, or the target site can be found in a heterologous genomic location compared to where it occurs in nature. As used herein, terms “endogenous target sequence” and “native target sequence” are used interchangeably herein to refer to a target sequence that is endogenous or native to the genome and is at the endogenous or native position of that target sequence in the genome.

The length of the target site can vary, and includes, for example, target sites that are at least 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30 or more nucleotides in length. It is further possible that the target site can be palindromic, that is, the sequence on one strand reads the same in the opposite direction on the complementary strand. The nick/cleavage site can be within the target sequence or the nick/cleavage site could be outside of the target sequence. In another variation, the cleavage could occur at nucleotide positions immediately opposite each other to produce a blunt end cut or, in other cases, the incisions could be staggered to produce single stranded overhangs, also called “sticky ends”, which can be either 5' overhangs, or 3' overhangs.

In one embodiment, the Cas endonuclease gene is a Cas9 endonuclease, such as but not limited to, Cas9 genes listed in W02007/025097 incorporated herein by reference. In another embodiment, the Cas endonuclease gene is animal optimized Cas9 endonuclease.

In one embodiment, the Cas endonuclease gene is an animal codon optimized streptococcus pyogenes Cas9 gene that can recognize any genomic sequence of the form N(12--30)NGG can in principle be targeted.

In one embodiment, the Cas endonuclease is introduced directly into a cell by any method known in the art, for example, but not limited to transient introduction methods, transfection and/or topical application.

Cas9 expression plasmids for use in the methods of the invention can be constructed as described in the art.

In one embodiment, targeted genome modification according to the various aspects of the invention comprises the use of a rare-cutting endonuclease, for example a TALEN, ZFN or CRISPR/Cas; e.g. CRISPR/Cas9. Rare-cutting endonucleases/ sequence specific endonucleases are naturally or engineered proteins having endonuclease activity and are target specific. These bind to nucleic acid target sequences which have a recognition sequence typically 12-40 bp in length. In one embodiment, the SSN is selected from a TALEN. In another embodiment, the SSN is selected from CRISPR/Cas9. This is described in more detail below.

In one embodiment, the step of introducing a mutation comprises contacting a population of animal cells with DNA binding protein targeted to the NF2 gene. In one embodiment, the method comprises contacting a population of cells with one or more rare-cutting endonucleases; e.g. ZFN, TALEN, or CRISPR/Cas9, targeted to the NF2 gene.

The method may further comprise the steps of selecting, from said population, a cell in which NF2 gene sequence has been modified and regenerating said selected animal cell.

In an embodiment, the method comprises the use of CRISPR/Cas9. In this embodiment, the method therefore comprises introducing and co-expressing in an animal cell Cas9 and sgRNA targeted to the NF2 gene sequences and screening for induced targeted mutations in the NF2 gene.

Cas9 and sgRNA may be comprised in a single or two expression vectors. The target sequence is the NF2 nucleic acid sequence as shown herein.

In one embodiment, screening for CRISPR-induced targeted mutations in the NF2 gene comprises obtaining a DNA sample from a transfected/transduced animal cell and carrying out DNA amplification and optionally restriction enzyme digestion to detect a mutation in NF2 gene.

In one embodiment, the restriction enzyme is mismatch-sensitive T7 endonuclease. T7E1 is an enzyme that is specific to heteroduplex DNA caused by genome editing.

PCR fragments amplified from the transfected/transduced animal cells are then assessed using a gel electrophoresis based assay. In a further step, the presence of the mutation may be confirmed by sequencing the NF2 gene. Genomic DNA (i.e. wt and mutant) can be prepared from each sample, and DNA fragments encompassing each target site are amplified by PCR. The PCR products are digested by restriction enzymes as the target locus includes a restriction enzyme site. The restriction enzyme site is destroyed by CRISPR- or TALEN-induced mutations by NHEJ or HR, thus the mutant amplicons are resistant to restriction enzyme digestion, and result in uncleaved bands. Alternatively, the PCR products are digested by T7E1 (cleaved DNA produced by T7E1 enzyme that is specific to heteroduplex DNA caused by genome editing) and visualized by agarose gel electrophoresis. In a further step, they are sequenced.

In one embodiment, the method uses the sgRNA (and template, synthetic single-strand DNA oligonucleotides (ssDNA oligos) or donor DNA) constructs defined in detail below to introduce a targeted SNP or mutation, in particular one of the substitutions described herein into a NF2 gene and/or promoter. The introduction of a template DNA strand, following a sgRNA-mediated SNP in the double-stranded DNA, can be used to produce a specific targeted mutation (i.e. a SNP) in the gene using homology directed repair. Synthetic single-strand DNA oligonucleotides (ssDNA oligos) or DNA plasmid donor templates can be used for precise genomic modification with the homology-directed repair (HDR) pathway. Homologous recombination is the exchange of DNA sequence information through the use of sequence homology. Homology-directed repair (HDR) is a process of homologous recombination where a DNA template is used to provide the homology necessary for precise repair of a double-strand break (DSB). CRISPR guide RNAs program the Cas9 nuclease to cut genomic DNA at a specific location. Once the double-strand break (DSB) occurs, the mammalian cell utilizes endogenous mechanisms to repair the DSB. In the presence of a donor DNA, either a ssDNA oligo or a plasmid donor, the DSB can be repaired precisely using HDR resulting in a desired genomic alteration (insertion, removal, or replacement).

Single-strand DNA donor oligos are delivered into a cell to insert or change short sequences (SNPs, amino acid substitutions, epitope tags, etc.) of DNA in the endogenous genomic target region

A “donor sequence” is a nucleic acid sequence that contains all the necessary elements to introduce the specific substitution into a target sequence, preferably using homology-directed repair (HDR). In one embodiment, the donor sequence comprises a repair template sequence for introduction of at least one SNP. Preferably the repair template sequence is flanked by at least one, preferably a left and right arm, more preferably around 100bp each that are identical to the target sequence. More preferably the arm or arms are further flanked by two gRNA target sequences that comprise PAM motifs so that the donor sequence can be released by Cas9/gRNAs.

The methods above use animal cell in which an expression vector has been introduced comprising a sequence-specific nucleases into an animal cell to target a NF2 nucleic acid sequence. The term“"introduction”" or“"transfected/transduced”" as referred to herein encompasses the transfer of an exogenous polynucleotide into a host cell, irrespective of the method used for transfer.

Advantageously, any of several transfection/transduction methods may be used to introduce the gene of interest into a suitable cell. The methods described for the transfection/transduction of animal cells may be utilized for transient or for stable transfection/transduction. transfection/transduction methods include the use of liposomes, electroporation, chemicals that increase free DNA uptake, injection of the DNA directly into the animal cell, particle bombardment as described in the examples, transfection/transduction using viruses or microinjection. Methods may be selected from , microinjection into animal material, DNA or RNA-coated particle bombardment, infection with (non-integrative or integrative) viruses and the like. Following DNA transfer and regeneration, putatively transformed animal cells may also be evaluated, for instance using Southern analysis, for the presence of the gene of interest, copy number and/or genomic organisation. Alternatively or additionally, expression levels of the newly introduced DNA may be monitored using Northern and/or Western analysis, both techniques being well known to persons having ordinary skill in the art.

The sequence-specific nucleases may also be introduced into an animal cell as part of an expression vector. The vector may contain one or more replication systems which allow it to replicate in host cells. Self-replicating vectors include plasmids, cosmids and virus vectors. Alternatively, the vector may be an integrating vector which allows the integration into the host cef's chromosome of the DNA sequence. The vector desirably also has unique restriction sites for the insertion of DNA sequences. If a vector does not have unique restriction sites it may be modified to introduce or eliminate restriction sites to make it more suitable for further manipulation. Vectors suitable for use in expressing the nucleic acids, are known to the skilled person and a non-limiting example is pcDNA3.1. The nucleic acid is inserted into the vector such that it is operably linked to a suitable animal active promoter. Suitable animal active promoters for use with the nucleic acids include, but are not limited to PGK, CMV, EF1 a, CAG, SV40 and Ubc.

In an embodiment of the invention the modification is made to the promoter region or coding region of the one or more genes.

In one embodiment, the cultured animal cell further comprises at least one additional genetic modification to manipulate the genome surveillance, cell cycle control and/or cell death control pathway. The genetic modification in the NF2 gene or a modification to the activity of the Merlin protein may be used in combination with other genetic modifications in order to further assist in reducing the doubling time. For example, see Applicant’s own Patent Application PCT/GB2023/052528, which is hereby incorporated by reference. Thus, in one embodiment, the at least one additional genetic modification may be in one or more of the following genes: RB1, TP53, and/or a RAS gene.

The genetic modification to the RB1, TP53, and/or a RAS genes may be made in combination with the genetic modification in the NF2 gene individually or in any combination. In one embodiment, the genetic modification may be a single point mutation or multiple mutations to knock out gene expression, e.g. for the RB1 and TP53 genes, or the genetic modification may be a single point mutation or multiple mutations to knock in gene expression, e.g. for the RAS gene.

In one embodiment, the animal cell has an additional genetic modification in RB1. In one embodiment, the animal cell has an additional genetic modification in TP53. In one embodiment, the animal cell has an additional genetic modification in a RAS gene. In one embodiment, the animal cell has an additional genetic modification in RB1 and in TP53. In one embodiment, the animal cell has additional genetic modifications in RB1 and in a RAS gene. In one embodiment, the animal cell has additional genetic modifications in TP53 and in a RAS gene. In one embodiment, the animal cell has additional genetic modifications in RB1, TP53 and in a RAS gene. In one embodiment, the RAS gene is HRAS, NRAS, or KRAS. In one embodiment, the RAS gene is HRAS.

Suitable sequence from genes in pig (Sus scrota) are described as follows (see also table 1). Thus, the modified cell may be a pig cell and the targeted gene is selected from RB1, TP53, and/or HRAS, NRAS, or KRAS.

For example, in one embodiment, exon 2 of porcine HRAS (wild type sequence shown in SEQ ID No: 31) and a modified cell may comprise a modification in porcine HRAS exon 2 as shown in SEQ ID No: 32, 33, and/or 40. The mutation in HRAS may comprise Gly > Vai (aa12) [GGA > GTA] and optionally a PAM-blocking mutation Gly > Vai (aa15) [GGG > GtG],

In a further embodiment, exon 8 of porcine RB1 (wild type sequence SEQ ID NO: 34) may be targeted and modified porcine RB1 exon 8 sequences may be as shown in SEQ ID No: 35 and/or 36.

In a further still embodiment, exon 5 of porcine TP53 (Wild type sequence SEQ ID No: 37) may be targeted and a modified cell may comprise a modification in porcine TP53 as shown in SEQ ID No: 38 and/or 39.

Alternatives sequences for porcine HRAS (SEQ ID NO. 41), KRAS (SEQ ID NO. 42 (isoform A) and 43 (isoform B)), and NRAS (SEQ ID NO. 44) are provided in Table 1 and may also be targeted.

The skilled person would be aware of other suitable genetic modifications to these genes and others as well as suitable genetic modifications for these genes and others in other species, e.g. bovine species. For example, see Applicant’s own Patent Application PCT/GB2023/052528.

The invention is not limited to modified pig cells. A skilled person would know that for the manipulation of other animal cells from animal species suitable for human or animal consumption, e.g. suitable for human consumption, e.g. suitable for animal consumption, e.g. used in agriculture, e.g. as listed herein, the equivalent orthologue, i.e. the endogenous RB1, TP53, and/or HRAS gene specific to the nonhuman animal species targeted is to be genetically modified. Suitable gene sequences can be identified from public databases. A skilled person would also be able to identify suitable sequences using standard methods in the art to identify homologs and orthologs, for example based on sequence identity with the pig sequences.

In a further embodiment of the invention, the gene is RAS and the modification is a hyperactivation modification. In one embodiment, the resulting modifications in the RAS protein keep it in a constantly active state. In one embodiment, activating modifications reduce GTP hydrolysis. The RAS gene may be selected from any one of HRAS, NRAS, or KRAS (isoform A or isoform B). In a related embodiment of the invention, the hyperactivation modification comprises one or more amino acid substitutions in the protein. The RAS gene may be a porcine RAS gene. The RAS gene may be a bovine RAS gene. For example, in one embodiment, the one or more amino acid substitution comprises substituting the glycine at position 12 of SEQ ID NO: 41 , 42, 43, or 44. In one embodiment, the one or more amino acid substitutions comprises substituting the glycine at position 12 of SEQ ID NO: 41 , 42, 43, or 44, wherein the one or more amino acid is selected from a list comprising alanine, cysteine, aspartic acid, arginine, serine, and valine. In one embodiment, the one or more amino acid substitutions comprises substituting the glycine at position 12 of SEQ ID NO: 41 , 42, 43, or 44, wherein the one or more amino acid is selected from a list consisting of alanine, cysteine, aspartic acid, arginine, serine, and valine. In one embodiment, the one or more amino acid substitutions comprises substituting the glycine at position 12 of SEQ ID NO: 41 , 42, 43, or 44 with valine. In one embodiment, the one or more amino acid substitutions comprises substituting the glycine at position 13 of SEQ ID NO: 41 , 42, 43, or 44. In one embodiment, the one or more amino acid substitutions comprises substituting the glycine at position 13 of SEQ ID NO: 41 , 42, 43, or 44, wherein the one or more amino acid is selected from a list comprising alanine, cysteine, aspartic acid, arginine, serine, and valine. In one embodiment, the one or more amino acid substitutions comprises substituting the glycine at position 13 of SEQ ID NO: 41 , 42, 43, or 44, wherein the one or more amino acid is selected from a list consisting of alanine, cysteine, aspartic acid, arginine, serine, and valine. In one embodiment, the one or more amino acid substitutions comprises substituting the glycine at position 13 of SEQ ID NO: 41 , 42, 43, or 44 with valine. In one embodiment, the one or more amino acid substitutions comprises substituting the glutamine at position 61 of SEQ ID NO: 41 , 42, 43, or 44. In one embodiment, the one or more amino acid substitutions comprises substituting the glycine at position 61 of SEQ ID NO: 41 , 42, 43, or 44, wherein the one or more amino acid is selected from a list comprising glutamic acid, histidine, lysine, proline, leucine and arginine. In one embodiment, the one or more amino acid substitutions comprises substituting the glycine at position 61 of SEQ ID NO: 41 , 42, 43, or 44, wherein the one or more amino acid is selected from a list consisting of glutamic acid, histidine, lysine, proline, and arginine. In a yet further related embodiment, the one or more amino acid substitution comprises substituting the glycine at position 12 of SEQ ID NO: 31 with Valine. In one embodiment, gain of function mutations are introduced into the RAS genes using targeted nucleases or derivations thereof. In another embodiment, gain of function versions of the RAS proteins are introduced as exogenous nucleotides into the cells. In one embodiment, the gain of function mutations are introduced via random mutagenesis, including but not limited to chemical mutagenesis. In one embodiment, the gain of function mutations are introduced by spontaneous mutations. In another embodiment, RAS activity is increased by perturbing other regulators of RAS activity. Cultivated meat

and methods

In another aspect, the invention provides a method of producing cultivated meat / a cultivated meat product I food product comprising culturing a modified cell according to any previous embodiments of the invention. In a related embodiment, the method comprises carrying out continuous or batch culture of the modified cell.

The term“"cultivated meat” is used herein to describe meat grown from in vitro animal cell culture distinguished from meat of slaughtered animals. Additional terms that may be used in the Art to describe meat grown from in vitro animal cell culture include cultured meat, cell-grown meat, clean meat, lab- grown meat, test tube meat, in vitro meat, tube steak, synthetic meat, cell-cultured meat, cell grown meat, tissue engineered meat, engineered meat, artificial meat, and manmade meat. The phrases “cellbased meat”, “slaughter-free cell- based meat”, “in vitro produced meat”, “in vitro cell-based meat”, “cultured meat”, “slaughter- free cultured meat”, “ in vitro produced cultured meat”, “in vitro meat”, “in vitro cultured meat” and other similar such phrases are interchangeably used herein, and refer to the meat that is generated in vitro, starting with cells in culture, and that method which does not involve the slaughter of an animal in order to directly obtain meat from that animal for dietary consumption. The modified cells of the invention may be suitable for human and/or non-human consumption. In some embodiments, the cell-based meat is suitable for consumption by animals, such as domesticated animals. Accordingly, the cellular biomass herein support the growth of “pet food”, e.g. dog food, cat food, and the like.

In one embodiment, the invention is a cultured animal cell wherein expression of the NF2 gene is modified or the activity of the Merlin protein is modified and wherein the animal is of an animal species suitable for human or animal consumption. In a further embodiment, the cultured animal cell is a cultured or cultivated meat cell suitable for human or animal consumption. In a further embodiment the cultured animal cell is an animal cell cultured in vitro animal cell. In a yet further embodiment, the cultured animal cell is not a treatment for cancer. In a still further embodiment, the invention does not relate to treatments for cancer or to products or genetic modifications for use in the treatment of cancer.

Batch culture refers to culturing cells in a closed system whereby the culture of cells is carried out for a defined period of time or until a defined criteria is met. Once this criteria or time is met the culture is stopped, the cells harvested and the system emptied and cleaned ready for a new culture. The nutrients and/or culture additives may be added at the beginning of culture or during the culture. Continuous culture refers to culturing cells in a system whereby cells are continuously removed after a period of growth, or removed at specific points in time, while a population of cells remain in the system which are able to continue to grow and divide. This process is repeated for a set period of time or indefinitely. The nutrients and/or culture additives are added periodically or continuously so that the cells present in the system always have optimum conditions in which to grow and divide. In another embodiment the invention provides cultivated animal tissue comprising the modified cell according to any previous embodiments of the invention.

In another aspect, the invention provides the use of the modified animal cell according to any previous embodiments for cellular agriculture.

In another aspect, the invention provides a method for producing an immortalised cell line comprising a method according to any previous aspects of the invention, wherein the immortalised cell line comprises a modification to the NF2 gene. The modification may be a loss of function modification. The loss of function modification may be a knock-out of the NF2 gene. This cell line can be used in cellular agriculture.

In a further aspect, the invention provides a method of producing a cultured meat product comprising culturing the one or more modified animal non-human cells or cell line according to any previous embodiments and optionally forming the cells into a tissue like structure. In a related embodiment, the method comprises forming the cells into a muscle tissue like structure. In a further aspect, the invention provides a cultured meat product for human or non-human consumption comprising a modified cell or cell line of the invention.

In a particular embodiment, a cultured meat product refers to a product in which cells according to the invention are formed into a product that is acceptable and/or suitable and/or appropriate for human consumption. The product may be of a structure that mimics or is intended to mimic the tissue of animal species which are used for human consumption. The cultured meat product may have a tissue like structure. The tissue may be selected from one or more of the following: muscle, fat, heart, liver, kidney and/or any tissue that is used for human consumption.

A tissue like structure according to the invention is a structure that resembles the specific tissue of an animal in terms of texture, taste, mouthfeel, visual structure, visual texture and colour. The tissue like structure does not have to be able to carry out the bodily functions that the tissue would carry out in vivo. Tissue like structure is intended to mean that the tissue like structure appears similar or the same as tissue taken from the animal to a consumer of the cultured meat product.

The cultured meat product comprises modified cells according to the invention but may additionally comprise other components such as colourant, flavourings and/or flavour enhancing compositions and dietary supplements such as vitamins and/or minerals.

Also provided is a packaged cultivated meat product comprising or derived from a cell or cell line of the invention. Guide RNA and kits

In another aspect, the invention provides a guide RNA targeting the sequence of SEQ ID NO. 5, or SEQ ID NO. 8, or SEQ ID NO. 9, or SEQ ID NO. 10, or SEQ ID NO. 28, or SEQ ID NO. 29, or SEQ ID NO. 30 individually or in combination. In a further embodiment the invention provides a guide RNA according to any previous embodiment of the invention for use in a method of producing a modified cell according to any previous embodiment of the invention. In a related embodiment the invention provides a guide RNA according to the previous embodiment of the invention wherein the modified cell is a modified cell according to any previous embodiment of the invention.

In a further embodiment the invention provides a kit of parts comprising at least one of the guide RNA according as described above. In one embodiment, the guide RNA may be a chemically synthesized sgRNA. In a related embodiment, the chemically synthesized sgRNA may be used to perform CRISPR in conjunction with a Cas9 recombinant purified protein.

As explained above, in some embodiments, the methods of the invention use gene editing using sequence specific endonucleases that target one or more genes in an animal cell of interest. As also explained, Cas9 and gRNA may be comprised in a single or two expression vectors. The sgRNA targets the one or more gene nucleic acid sequence.

Thus, in another aspect of the invention, there is provided a nucleic acid construct comprising a nucleic acid sequence encoding at least one DNA-binding domain that can bind to the one or more genes. In one embodiment, the porcine NF2 gene comprises the sequence of SEQ ID NO. 1 (Sus scrofa) or SEQ ID NO. 3 (Sus scrofa— Largewhite variety) or a functional variant, homolog or orthologue thereof as explained herein. In this embodiment, the porcine Merlin protein comprises the sequence of SEQ ID NO. 2 (Sus scrofa) or SEQ ID NO. 4 (Sus scrofa— Largewhite variety) or a functional variant, homolog or orthologue thereof as explained herein. In one embodiment, the bovine NF2 gene comprises the sequence of SEQ ID NO. 6 (Bos taurus) or a functional variant, homolog or orthologue thereof as explained herein. In this embodiment, the bovine Merlin protein comprises the sequence of SEQ ID NO. 7 (Bos taurus) or a functional variant, homolog or orthologue thereof as explained herein.

In one embodiment, the nucleic acid sequence encodes at least one protospacer element.

In one embodiment, the construct further comprises a nucleic acid sequence encoding a CRISPR RNA (crRNA) sequence, wherein said crRNA sequence comprises the protospacer element sequence and additional nucleotides. In one embodiment, the construct further comprises a nucleic acid sequence encoding a transactivating RNA (tracrRNA). In a further embodiment, the construct encodes at least one single-guide RNA (sgRNA), wherein said sgRNA comprises the tracrRNA sequence and the crRNA sequence, wherein the sgRNA targets the sequence of SEQ ID NO. 5 listed herein. PAM sequences are also shown in the in the section entitled sequences listing. The sgRNA can be used for manipulation of animal cells. In another aspect of the invention, there is provided a nucleic acid construct comprising a DNA donor nucleic acid wherein said DNA donor nucleic acid is operably linked to a regulatory sequence. The regulatory sequence may be one or more of the following: intron, promoter and/or terminator.

Cas9 and sgRNA may be combined or in separate expression vectors (or nucleic acid constructs, such terms are used interchangeably). Similarly, Cas9, sgRNA and the donor DNA sequence may be combined or in separate expression vectors. In other words, in one embodiment, an isolated animal cell is transfected with a single nucleic acid construct comprising both sgRNA and Cas9 or sgRNA, Cas9 and the donor DNA sequence as described in detail above. In an alternative embodiment, an isolated animal cell is transfected with two or three nucleic acid constructs, a first nucleic acid construct comprising at least one sgRNA as defined above, a second nucleic acid construct comprising Cas9 or a functional variant or homolog thereof and optionally a third nucleic acid construct comprising the donor DNA sequence as defined above. The second and/or third nucleic acid construct may be transfected before, after or concurrently with the first and/or second nucleic acid construct. The advantage of a separate, second construct comprising a Cas protein is that the nucleic acid construct encoding at least one sgRNA can be paired with any type of Cas protein, as described herein, and therefore is not limited to a single Cas function (as would be the case when both Cas and sgRNA are encoded on the same nucleic acid construct).

In one embodiment, a construct as described above is operably linked to a promoter, for example a constitutive promoter.

In another embodiment, the nucleic acid construct further comprises a nucleic acid sequence encoding a CRISPR enzyme. Preferably, the CRISPR enzyme is a Cas protein. More preferably, the Cas protein is Cas9 or a functional variant thereof.

In an alternative embodiment, the nucleic acid construct encodes a TAL effector. Preferably, the nucleic acid construct further comprises a sequence encoding an endonuclease or DNA-cleavage domain thereof. More preferably, the endonuclease is Fokl.

In another aspect of the invention there is provided a single guide (sg) RNA molecule wherein said sgRNA comprises a crRNA sequence and a tracrRNA sequence. In one embodiment, the sgRNA molecule may comprise at least one chemical modification, for example that enhances its stability and/or binding affinity to the target sequence or the crRNA sequence to the tracrRNA sequence. For example, the crRNA may comprise a phosphorothioate backbone modification, such as "-fluoro (”-F), "-0-methyl ("-0-Me) and S-constrained ethyl (cET) substitutions.

In a further embodiment, the nucleic acid construct may further comprise at least one nucleic acid sequence encoding an endoribonuclease cleavage site. Preferably the endoribonuclease is Csy4 (also known as Cas6f). Where the nucleic acid construct comprises multiple sgRNA nucleic acid sequences the construct may comprise the same number of endoribonuclease cleavage sites. In another embodiment, the cleavage site is " of the sgRNA nucleic acid sequence. Accordingly, each sgRNA nucleic acid sequence is flanked by an endoribonuclease cleavage site. The ternT'varian" refers to a nucleotide sequence where the nucleotides are substantially identical to one of the above sequences. The variant may be achieved by mo’ifications such as insertion, substitution or deletion of one or more nucleotides. In a preferred embodiment, the variant has at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% identity to any one of the above described sequences. In one embodiment, sequence identity is at least 90%. In another embodiment, sequence identity is 100%. Sequence identity can be determined by any one known sequence alignment program in the art.

The invention also relates to a nucleic acid construct comprising a nucleic acid sequence operably linked to a suitable animal promoter. A suitable animal promoter may be a constitutive or strong promoter or may be a tissue-specific promoter. In one embodiment, suitable animal promoters are selected from, but not limited to, PGK, CMV, EF1 a, CAG, SV40 and Ubc.

The nucleic acid construct of the present invention may also further comprise a nucleic acid sequence that encodes a CRISPR enzyme. In a specific embodiment Cas9 is codon-optimised Cas9. In another embodiment, the CRISPR enzyme is a protein from the family of Class 2 candidate proteins, such as C2c1 , C2C2 and/or C2c3. In one embodiment, the Cas protein is from Streptococcus pyogenes. In an alternative embodiment, the Cas protein may be from any one of Staphylococcus aureus, Neisseria meningitides or Streptococcus thermophiles.

The term "functional variant" as used herein with reference to Cas9 refers to a variant Cas9 gene sequence or part of the gene sequence which retains the biological function of the full non-variant sequence, for example, acts as a DNA endonuclease, or recognition or/and binding to DNA. A functional variant also comprises a variant of the gene of interest which has sequence alterations that do not affect function, for example non-conserved residues. Also encompassed is a variant that is substantially identical, i.e. has only some sequence variations, for example in non-conserved residues, compared to the wild type sequences as shown herein and is biologically active. In a further embodiment, the Cas9 protein has been modified to improve activity. For example, in one embodiment, the Cas9 protein may comprise the D10A amino acid substitution, this nickase cleaves only the DNA strand that is complementary to and recognized by the gRNA. In an alternative embodiment, the Cas9 protein may alternatively or additionally comprise the H840A amino acid substitution, this nickase cleaves only the DNA strand that does not interact with the sRNA. In this embodiment, Cas9 may be used with a pair (i.e. two) sgRNA molecules (or a construct expressing such a pair) and as a result can cleave the target region on the opposite DNA strand, with the possibility of improving specificity by 100-1500 fold. In a further embodiment, the Cas9 protein may comprise a D1135E substitution. The Cas 9 protein may also be the VQR variant. Alternatively, the Cas protein may comprise a mutation in both nuclease domains, HNH and RuvC-like and therefore is catalytically inactive. Rather than cleaving the target strand, this catalytically inactive Cas protein can be used to prevent the transcription elongation process, leading to a loss of function of incompletely translated proteins when co-expressed with a sgRNA molecule. An example of a catalytically inactive protein is dead Cas9 (dCas9) caused by a point mutation in RuvC and/or the HNH nuclease domains.

In a further embodiment, a Cas protein, such as Cas9 may be further fused with a repression effector, such as a histone-modifying/DNA methylation enzyme or a Cytidine deaminase to effect site-directed mutagenesis. In the latter, the cytidine deaminase enzyme does not induce dsDNA breaks, but mediates the conversion of cytidine to uridine, thereby effecting a C to T (or G to A) substitution.

In a further embodiment, the nucleic acid construct comprises an endoribonuclease. Preferably the endoribonuclease is Csy4 (also known as Cas6f) and more preferably a codon optimised csy4. In one embodiment, where the nucleic acid construct comprises a Cas protein, the nucleic acid construct may comprise sequences for the expression of an endoribonuclease, such as Csy4 expressed as a " terminal P2A fusion (used as a self-cleaving peptide) to a Cas protein, such as Cas9.

In one embodiment, the Cas protein, the endoribonuclease and/or the endoribonuclease-Cas fusion sequence may be operably linked to a suitable animal promoter. Suitable animal promoters are already described above, but in one embodiment, may be PGK, CMV, EF1 a, CAG, SV40 and Ubc.

Suitable methods for producing the CRISPR nucleic acids and vectors system are known, and for example are published in Ran et al 2013, Nat Protoc 8, 2281-2308 (2013).

In a further aspect of the invention, there is provided an isolated animal cell transfected with at least one nucleic acid construct as described herein. In one embodiment, the isolated animal cell is transfected with at least one nucleic acid construct as described herein and a second nucleic acid construct, wherein said second nucleic acid construct comprises a nucleic acid sequence encoding a Cas protein, preferably a Cas9 protein or a functional variant thereof. Preferably, the second nucleic acid construct is transfected before, after or concurrently with the first nucleic acid construct described herein. In an alternative aspect of the invention, the nucleic acid construct comprises at least one nucleic acid sequence that encodes a TAL effector. Targeted nucleases, e.g. Meganucleases, ZNF, TALEN, CRISPR nucleases and derivations thereof, such as (but not exclusively) PRIME editors, base editors, CRISPRi, amongst others may form part of the invention.

Preferably, the nucleic acid encoding the sgRNA and/or the nucleic acid encoding a Cas protein is integrated in a stable form.

Also included in the scope of the invention, is the use of the nucleic acid constructs (CRISPR constructs) described above or the sgRNA molecules in any of the above described methods. For example, there is provided the use of the above CRISPR constructs or sgRNA molecules to modulate the activity of one or more gene as described herein. In particular, as described herein, the CRISPR constructs may be used to create loss of function or hyperactivation alleles.

Unless otherwise defined herein, scientific and technical terms used in connection with the present disclosure shall have the meanings that are commonly understood by those of ordinary skill in the art. While the foregoing disclosure provides a general description of the subject matter encompassed within the scope of the present disclosure, including methods, as well as the best mode thereof, of making and using this disclosure, the following examples are provided to further enable those skilled in the art to practice this disclosure. However, those skilled in the art will appreciate that the specifics of these examples should not be read as limiting on the invention, the scope of which should be apprehended from the claims and equivalents thereof appended to this disclosure. Various further aspects and embodiments of the present disclosure will be apparent to those skilled in the art in view of the present disclosure.

All documents mentioned in this specification are incorporated herein by reference in their entirety, including references to gene accession numbers, scientific publications and references to patent publications.

“and/or” where used herein is to be taken as specific disclosure of each of the two specified features or components with or without the other. For example, “A and/or B” is to be taken as specific disclosure of each of (i) A, (ii) B and (iii) A and B, just as if each is set out individually herein. Unless context dictates otherwise, the descriptions and definitions of the features set out above are not limited to any particular aspect or embodiment of the invention and apply equally to all aspects and embodiments which are described.

The invention is further illustrated in the following non-limiting examples. EXAMPLES

Example 1 : Determining the doubling time of NF2 gene knock-out cells

Figures 1 and 2 show the doubling times of NF2 gene knock-out cells in suspension conditions.

Method

Doubling time assessment of control cell pools (transfected with Cas9 only, no sgRNA) and NF2 knockout cell pool after transfer from adherent into suspension growth conditions. Data points come from triplicate Erlenmeyer flasks and measured over 4 growth passages.

Results

The average doubling time is shown to be reduced by 42% (Cas only control: 46h, NF2 knock-out cell pool: 27h). Figure 1 shows the difference between control cell pools (transfected with Cas9 only, no sgRNA) and NF2 knock-out cell pool between each of the 4 passages and Figure 2 shows a collective grouping of data points for both the control cell and the N2 knock-out cells.

Example 2: NF2 gene editing efficiencies

Method

Assessment of NF2 knock-out efficiencies in porcine myoblast cell pools transfected with Cas9 protein and a sgRNA targeting the NF2 gene. At two time points post transfection and after a 4 passage suspension growth study in triplicate flasks, DNA was isolated from cell pools and knock-out efficiencies were determined by PCR amplification of the NF2 gene followed by Sanger Sequencing of the PCR amplicon and analysis of the sequencing results using the ICE analysis tool (ice.synthego.com).

Results

As shown in Figure 3, Assessment of NF2 knock-out efficiencies in porcine myoblast cell pools showed high efficiencies were retained over time. This demonstrates that the NF2 gene knock-out was stable over the course of 4 passages. Example 3: Functional knock-out of NF2 gene coding for the Merlin protein preserves mesenchymal cell phenotype and enhances adipogenic differentiation potential in immortalised porcine myoblast cell lines.

A significant challenge facing the cultivated meat industry is the development of cell lines that rapidly and continuously expand in number to generate high volumes of nutritious cellular protein for meat production. While retaining the ability of skeletal muscle derived precursor cells to either fuse into fibres to provide higher-order structured meat or produce intra-muscular fat content that is associated with traditional meat products. This dynamic represents a crucial interface between innate biological capacity and business viability that is one of the critical blocks in the cultivated meat product pipeline. In agriculturally relevant species skeletal muscle tissue comprises a heterogenous mixture of cell types (muscle, mesenchymal stem cells (MSCs), nerves, immune cells, vasculature etc.,) that act synergistically in response to environmental stimuli to tailor to content of the tissue and maintain physiological homeostasis. Regarding cultivated meat specifically, protein content and fat accumulation are pertinent. Retaining this ability in cultivated meat cell lines as different nutritional and physiological demands are placed on the cells requires the preservation of this innate heterogeneity. Here, by introducing a functional knock-out of the NF2 gene, coding for the merlin protein and relieving its inhibitory effects on cell growth and survival pathways, we have successfully preserved a heterogeneous cell population, inclusive of MSCs that are key to fat production in muscle, throughout adaptation to and growth in suspension cell culture; a key process of cultivated meat cell line development.

MSCs in skeletal muscle tissue are diverse in both their own individual heterogeneity and developmental potential to undergo cell and tissue lineage specification. MSCs in muscle are typically identified via flow cytometry using cell surface markers CD29 and CD90, and preserving this population enables muscle derived cells to retain a plastic element to their phenotype. One sub population of MSCs in skeletal muscle are described as fibro-adipogenic progenitors (FAPs) that are responsible for intramuscular fat deposition. FAPs are also CD90+ and PDGFRa+ in flow cytometry and readily undergo adipogenic differentiation upon nutritional and physiological cues in vivo or chemical induction in vitro. Here, we show that adapting our adherent immortalised muscle derived cells to suspension culture ameliorates this mesenchymal CD90+ cell population (Fig.4a, d) and that this change in cell culture environment limits the functional capacity of these cells to then undergo adipogenic differentiation and accumulate intracellular fat (Fig.4h,i), limiting the nutritional value potential of these cells. However, by introducing a functional knock-out of the NF2 gene in the same immortalised cell line and adaptation to suspension protocol, we are able to retain this CD90+ population. Further, we are then able to evidence the preservation of cell plasticity associated with muscle tissue in our NF2 knock-out cells via enhanced lipid accumulation and adipogenic differentiation following chemical induction in vitro (Fig.4h,i), compared to non-edited NF2 (+/+) parents. In the context of cultivated meat, functional NF2 gene deletion permits both the rapid growth of muscle derived cells in suspension culture while also maintaining the cell phenotype and plastic state required for intramuscular fat accumulation as it is achieved in vivo. This will enable the development of cultivated meat products with enhanced nutritional value and fat content, without additional complexity to manufacturing processes, hereby providing a suitable alternative to traditional meat that is nutritionally comparable and environmentally conscious.

Example 4: Functional knock-out of NF2 gene coding for the Merlin protein is possible across of range of cell types with different genetic backgrounds in different species.

Figure 5 shows the editing efficiencies in a variety of cell types and shows that the edit is retained over time.

Method:

Cells were edited using nucleofection with synthetic single guide RNAs and Strep. Pyogenes Cas9 protein. Note that the same guide RNAs were used between varieties of a given species (e.g. bovine var. Wagyu and var. Angus) as well as cell types (e.g. porcine myoblasts and porcine ADSC).

Editing efficiencies in cell pools were verified at 2-3 time points post editing to screen for enrichment or depletion of desired mutations. Enrichment of a mutation of interest suggest a positive impact of a given mutation on cell growth, while depletion suggests a detrimental effect on cell health or growth. Editing efficiencies were measured by PCR amplification of target region, Sanger Sequencing and ICE analysis of the Sanger Sequencing file (Synthego).

In some cases, cells were pre edited with sgRNAs against the P53, RB1 and/or HRAS gene (Seq ID No. 11 , 12,13,14,15,16,17,18,19) before addition of the NF2 edit or cell were edited in those genes at the same time as in the NF2 gene to immortalize the cell lines (see Patent Application PCT/GB2023/052528). For porcine and bovine HRAS, a G12V mutation was created by addition of a ssODN homology template (Seq ID No. 20, 21 , 32, 33). In some cases, cells were immortalised by stably transfecting them with a lentiviral construct containing a hyperactive HRAS variant and the Simian Virus 40 large T antigen before NF2 editing (compare Hahn et al, 1999; https; /doLo^/13,1038 22783 and Patent Application PCT/GB2023/052528).

Also note that Fig. 3 is equivalent to Fig. 5B.

Results:

The NF2 gene can be edited efficiently in different cell backgrounds and the edit is retained in mixed cell populations. Cells were edited using indicated sgRNAs against NF2 and editing efficiencies were measured at two to three time points post editing as well as after functional assays if applicable. Cells were edited in adherent state if not indicated otherwise. The edited cell types were (a) porcine primary myoblasts (two independent editing reactions); (b) porcine CRISPR-immortalized myoblasts (one editing reaction, results from triplicate flasks during growth assay); (c) porcine viral-immortalized myoblasts; (d) porcine viral-immortalized ADSCs grown in suspension;(e) porcine CRISPR immortalized ADSCs (data point from one editing reaction, two data points taken from independent flasks during growth assay); (f) Bovine var. Angus CRISPR immortalized ADSCs. Note that the cells were co-edited with P53 and RB1 sgRNAs in this experiment to ensure concurrent immortalisation. Data point from one editing reaction, three data points taken from independent flasks during growth assay; (g) Bovine var. Angus CRISPR immortalized ADSCs. Note that the cells were co-edited with P53 and RB1 and HRAS sgRNAs (plus an HRAS G12V repair template) in this experiment to ensure concurrent immortalisation; (h) Bovine var. Angus CRISPR immortalized (P53 ^/_, RB1 ^Z) myoblasts. Data point from one editing reaction, three data points taken from independent flasks during growth assay; (i) Bovine var. Angus CRISPR immortalized (P53 ^/_, RB1 ^A, HRAS^G12V/) myoblasts; (j) Bovine var. Wagyu CRISPR immortalized ADSCs. Note that the cells were co-edited with P53 and RB1 sgRNAs in this experiment to ensure concurrent immortalisation. Data point from two independent editing reactions, one data point taken from one replicate flask at the end of growth assays, (k) Bovine var. Wagyu CRISPR immortalized myoblasts. Note that the cells were co-edited with P53 and RB1 sgRNAs in this experiment to ensure concurrent immortalisation. Data point from two independent editing reactions, one data point taken from one replicate flask at the end of growth assays.

Example 5: The NF2 knockout can provide a growth advantage in adherence

Figure 6 shows doubling time assessments of NF2 knockout cell lines in comparison with control lines in adherent growth conditions.

Method:

Cells were grown in adherence for multiple passages to obtain doubling time data and/or cumulative generation numbers. Cells were seeded at 2000-4000 cells/cm2 into flasks coated with Matrigel or without coating (as annotated in graphs). Cells were counted and passaged every 3-4 days. Media for myoblasts was DMEM 4.5 g/L glucose, 20% FBS, 2 mM L-glutamine, 5 ng/pL FGF2. Media for ADSC was DMEM 1 g/L glucose, 10% FBS, 2 mM L-glutamine, 5 ng/pL FGF

Results:

For a growth assay, cells were seeded into triplicate flasks and grown on Matrigel coated flasks or without coating for 5-8 passages as indicated. Doubling times were compared to one or two control lines (Ctrl). Unpaired two-tailed T-Test was used to determine significance levels between groups with *p<0.05, ** p<0.01 , *** p<0.001 and **** p<0.0001. (a) Doubling times of bovine var. Angus myoblast cell pools over 8 passages, (b) Combined doubling time data of all 8 passages from (a). The average doubling time for the Ctrl is 29.3 h vs. 27.1 h for the NF2 ^Z- cells, (c) Doubling times of bovine var. Angus ADSC pools over 8 passages, (d) Combined doubling time data of all 8 passages from (c). The average doubling time for the Ctrl is 25.2 h vs. 23.1 h for the NF2 ^/_ cells (e) Doubling times of bovine var. Wagyu myoblast cell pools over 5 passages, (f) Combined doubling time data of all 5 passages from (e). The average doubling time for the plastic grown non edited control, the PSS ^/RBT⁷’, and the PSS^/RBr⁷’ /NF2 ^A cells are 37, 24.9 and 21 .4 h respectively. The average doubling time for the matrigel grown non edited control, the PSS '/RBT⁷-, and the P53 ^/7RBT^/7NF2 ^/- cells are 34.6, 24.3 and 24.3 h respectively.

Example 6: The NF2 knockout can provide a growth advantage during suspension adaptation

Figure 7 shows doubling time assessments of NF2 knockout cell lines in comparison with control lines in suspension growth conditions.

Method:

For suspension growth assays, cells were transferred from adherent flasks into Erlenmeyer flasks and grown in suspension media at 100 rpm using a seeding density of 100000 cells/mL. Cells were counted and passaged every 3-4 days.

Results:

For suspension adaptation, cells were seeded into triplicate Erlenmeyer flasks and grown in suspension media for 4-5 passages as indicated. Doubling times were compared to a control line (Ctrl). Unpaired two-tailed T-Test was used to determine significance levels between groups with *p<0.05, ** p<0.01 , *** p<0.001 and **** p<0.0001. (a) Doubling times porcine myoblast cell pools over 4 passages, (b) Combined doubling time data of all 4 passages from (a). The average doubling time for the Ctrl is 45.8 h vs. 27 h for the NF2 ^Z- cells, (c) Doubling times of porcine ADSC pools over 5 passages, (d) Combined doubling time data of all 5 passages from (c). The average doubling time for the Ctrl is 118.2 h vs. 25.1 h for the NF2 ^/_ cells, (e) Doubling times of bovine var. Angus myoblast cell pools over 5 passages, (f) Combined doubling time data of all 5 passages from (e). The average doubling time for the Ctrl is 72.2 h vs. 62.9 h for the NF2 ^/_ cells, (g) Doubling times of bovine var. Angus ADSC pools over 5 passages, (h) Combined doubling time data of all 5 passages from (g). The average doubling time for the Ctrl is 36.7 h vs. 25.3 h for the NF2 ^Z- cells.

Example 7: The NF2 knockout provides a stronger growth advantage in suspension than other Hippo pathway genes

Method:

Porcine CRISPR immortalized suspension cells (P53⁷-, RBT⁷-, HRAS^G12V/) were edited in separate editing reactions in one out of three Hippo pathway genes (NF2/LATS1/LATS2) using three sgRNAs per gene (Seq ID No. 22, 23, 24, 25, 26, 27, 28, 29, 30). After editing, edited cell pools were combined in an Erlenmeyer flask together with other mutant cell pools (data not shown) and grown in suspension at 100 rpm for ten days. Samples were taken on day 1 after combining the cell pools and on day 6 (day of peak cell density) for DNA extraction and amplification of target genes in a multiplex PCR reaction. Frameshift mutation frequencies for each gene of interest in the cell pools were analysed by next generation sequencing. The % change of frameshift mutations in the NGS reads (as an approximation for functional gene knockouts) between both time points was compared to screen for mutations providing a stronger growth advantage.

Results:

When combined in one flask, cells with a NF2 knockout enrich faster than cells with other mutations in the Hippo pathway as shown by a higher increase in frameshifted next generation sequencing reads over the analysed time period.

Table 1 Sequences

Claims

1. A cultured animal cell having a genetic modification in the NF2 gene or a modification to the activity of the Merlin protein and wherein the animal is of an animal species suitable for human or animal consumption.

2. The cultured animal cell according to claim 1 , wherein the modification decreases the doubling time of the cell by at least about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%.

3. The cultured animal cell according to claim 1 or claim 2, wherein the animal is selected from a pig, bovine, poultry, sheep, goat, Equidae, Camelidae, fish, crustaceans or mollusc.

4. The cultured animal cell according to any preceding claim, wherein the animal cell is a somatic cell.

5. The cultured animal cell according to claim 4, wherein the animal cell is selected from one of the following cell types: myoblast, fibroblast, myofibroblast, adipose derived stem cell, epithelial cell, mesenchymal stem cell, satellite cell, iPSC, or hepatocyte.

6. The cultured animal cell according to any preceding claim, wherein the expression of the NF2 gene or the activity of the Merlin protein is modified in the animal cell by any one or more of:

7. The cultured animal cell according to any one of claims 1 to 6, wherein the animal cell has a genetic modification in NF2 gene.

8. The cultured animal cell according to claim 7, wherein the genetic modification in the NF2 gene is a loss of function modification or leads to reduction in function.

9. The cultured animal cell according to claim 8, wherein the loss of function modification comprises a knock-out of the gene or loss of protein function.

10. The cultured animal cell according to any preceding claim, wherein the modification is introduced using targeted genome modification or randomised mutagenesis or by spontaneous mutation.

11. The cultured animal cell according to any preceding embodiment, wherein the modification is in the promoter region or coding region of one or more genes.

12. The cultured animal cell according to any preceding embodiment, wherein the modification is introduced using targeted genome modification, optionally using a targeted endonuclease.

13. The cultured animal cell according to claim 12 using an endonuclease, wherein the endonuclease is optionally selected from TALEN, ZFN or CRISPR, optionally CRISPR/Cas9.

14. The cultured animal cell according to any one of the preceding claims, wherein the cultured animal cell further comprises at least one additional genetic modification to manipulate the genome surveillance, cell cycle control and/or cell death control pathway.

15. The cultured animal cell according to claim 14, wherein the at least one additional genetic modification is in one or more of the following genes: RB1, TP53, and/or a RAS gene.

16. The cultured animal cell according to claim 15, wherein the animal cell has a genetic modification in RB1.

17. The cultured animal cell according to claim 15, wherein the animal cell has a genetic modification in TP53.

18. The cultured animal cell according to claim 15, wherein the animal cell has a genetic modification in a RAS gene.

19. The cultured animal cell according to claim 15, wherein the animal cell has a genetic modification in RB1 and in TP53.

20. The cultured animal cell according to claim 15, wherein the animal cell has a genetic modification in RB1 and in a RAS gene.

21. The cultured animal cell according to claim 15, wherein the animal cell has a genetic modification in TP53 and in a RAS gene.

22. The cultured animal cell according to claim 15, wherein the animal cell has a genetic modification in RB1, TP53 and in a RAS gene.

23. The cultured animal cell according to any one of claims 15 to 22, wherein the RAS gene is HRAS, NRAS, or KRAS.

24. The cultured animal cell according to claim 23, wherein the RAS gene is HRAS.

25. A method of producing cultivated meat or a cultured meat product comprising culturing the animal cell according to any of claims 1 to 24.

26. A method of producing the cultured animal cell according to any of claims 1 to 24.

27. The method according to claim 26, wherein the animal is selected from a pig, bovine, poultry, sheep, goat, fish, Equidae, Camelidae, crustaceans or mollusc.

28. The method according to any of claims 26 to 27, wherein the animal cell is a somatic cell.

29. The animal cell according to claim 28, wherein the animal cell is selected from one of the following cell types: myoblast, fibroblast, myofibroblast, adipose derived stem cell, epithelial cell, mesenchymal stem cell, satellite cell, iPSC, or hepatocyte.

30. The method according to claims 26 to 29, wherein the modification is introduced using targeted genome modification or randomised mutagenesis or by spontaneous mutation.

31 . Cultivated or cultured animal tissue or a cultivated or cultured meat product comprising a modified cell according to any of claims 1 to 24.

32. Use of the modified cultured animal cell according to any of claims 1 to 24 for cellular agriculture.

33. A method for producing an immortalised animal cell line comprising the method according to any of claims 26 to 28, wherein the immortalised cell line comprises a NF2 gene modification.

34. A guide RNA targeting the sequence of SEQ ID NO. 5, or SEQ ID NO. 8, or SEQ ID NO. 9, or SEQ ID NO. 10, or SEQ ID NO. 28, or SEQ ID NO. 29, or SEQ ID NO. 30 individually or in combination 35. A kit comprising at least one the guide RNA of claim 34.