Crispr/cas screening system materials and methods
AssigneeUniversity of Copenhagen
InventorsMorten Frödin, Yiyuan Niu, Catarina Ferreira A. Azevedo, Claus Storgaard Sørensen
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Abstract
The present disclosure relates to methods for assessing the effects of a mutation of interest in a cell. Herein are also disclosed systems for assessing the effects of a mutation of interest in a cell. The disclosure also provides host cells and host cell populations comprising the system.
Claims81
A method for assessing the effects of a mutation of interest in a cell, said method comprising the steps of:
- i) providing a cell population comprising a target nucleic acid sequence;
- ii) introducing in at least some of the cells of the cell population:
- a) a nuclease or a polynucleotide encoding said nuclease, wherein the nuclease is capable of generating one or more single-strand breaks (SSBs) or double-strand breaks (DSBs) in a target nucleic acid sequence, and targeting means directing the nuclease to the target nucleic acid sequence, whereby the nuclease is capable of binding to a binding region of the target nucleic acid sequence, and whereby the nuclease is capable of generating one or more single-stranded breaks (SSBs) or double-strand breaks (DSBs) in the target nucleic acid sequence;
- b) a first oligonucleotide comprising a mutation of interest, preferably a non-silent mutation, preferably a non-synonymous mutation, wherein said non-synonymous mutation introduces a change in the encoded amino acid sequence compared to the amino acid sequence encoded by the target nucleic acid sequence, and otherwise identical to or complementary to said target nucleic acid sequence, wherein said mutation of interest preferably lies within the binding region of said nuclease;
- and
- c) a second oligonucleotide comprising a synonymous mutation, wherein said synonymous mutation preferably lies within the binding region of said nuclease, and wherein said synonymous mutation introduces no change in the encoded amino acid sequence compared to the amino acid sequence encoded by the target nucleic acid sequence;
- whereby said first oligonucleotide or said second oligonucleotide is integrated in, or copied into, the target nucleic acid sequence of at least some of the cells, thereby obtaining a mixed population of cells comprising cells in which the mutation of the first or the second oligonucleotides has not been introduced, cells in which only the mutation of the first oligonucleotide has been introduced, and cells in which only the mutation of the second oligonucleotide has been introduced;
- iii) incubating the mixed population of cells in a medium for a determined duration, under conditions allowing a parameter of interest to be monitored, wherein the parameter of interest is a temporal parameter and/or a spatial parameter;
- iv) determining the effect of the mutation of interest on the parameter of interest, wherein:
- A. if the parameter of interest is a temporal parameter, determining the effect of the mutation of interest on the parameter of interest comprises the steps of:
- v) determining an initial ratio of cells in which the mutation of interest has been introduced in the target nucleic acid sequence to cells in which the synonymous mutation has been introduced in the target nucleic acid sequence, wherein the initial ratio of cells is determined at an initial time point;
- determining a subsequent ratio of cells in which the mutation of interest has been introduced in the target nucleic acid sequence to cells in which the synonymous mutation has been introduced in the target nucleic acid sequence, wherein the subsequent ratio of cells is determined at a subsequent time point;
- and determining a change in ratio between the initial ratio and the subsequent ratio;
- and
- vi) correlating said change in ratio to the parameter of interest,
- and/or
- B. if the parameter of interest is a spatial parameter, determining the effect of the mutation of interest on the parameter of interest comprises the steps of:
- v) defining and/or spatially separating subpopulations of cells on the basis of said spatial parameter of interest in each subpopulation, preferably wherein the spatial parameter of interest is different in each subpopulation;
- vi) determining, for each subpopulation, a ratio of cells in which the mutation of interest has been introduced in the target nucleic acid sequence to cells in which the synonymous mutation has been introduced in the target nucleic acid sequence;
- and
- vii) correlating said ratio to the measured spatial parameter of interest for each subpopulation;
- thereby assessing the effect of the mutation on the parameter of interest.
The method according to any one of the preceding claims, wherein step B.vi) further comprises a step of, for each subpopulation, determining a frequency of cells with an indel in the target nucleic acid sequence which is different from the mutation of the first and the second oligonucleotides.
The method according to any one of the preceding claims, wherein the mixed population also comprises cells in which the mutation of the first or the second oligonucleotides has been introduced, and/or wherein one or more indel mutations have been introduced in the target nucleic acid sequence.
The method according to any one of the preceding claims, wherein said first oligonucleotide consists of or comprises a stretch of nucleotides identical to said second oligonucleotide except for said mutation of interest or wherein said second oligonucleotide consists of or comprises a stretch of nucleotides identical to said first oligonucleotide except for said synonymous mutation.
The method according to any one of the preceding claims, wherein the synonymous mutation of said second oligonucleotide is located in the same genomic position as the mutation of interest in said first oligonucleotide.
The method according to any one of the preceding claims, wherein the first and the second oligonucleotides are of different lengths.
The method according to any one of the preceding claims, wherein the first and the second oligonucleotides are of the same length.
The method according to any one of the preceding claims, wherein the parameter of interest is a temporal parameter of interest, and wherein:
- A. If the initial ratio of cells is lower than the subsequent ratio of cells, the mutation is characterised as a mutation having a positive effect on the temporal parameter;
- B. If the initial ratio of cells is greater than the subsequent ratio of cells, the mutation is characterised as a mutation having a negative effect on the temporal parameter;
- C. If the initial and the subsequent ratio of the cells are substantially the same, the mutation is characterised as a mutation having no effect on the temporal parameter.
The method according to any one of the preceding claims, wherein the temporal parameter is selected from the group consisting of cell proliferation, cell growth, anchorage-independent cell growth, contribution to tumor growth, fitness, cell motility, cell invasiveness, cellular metabolism, DNA damage, expression levels of pre-defined genes and/or proteins, resistance to a compound, sensitivity to a compound, production of a compound, anoikis, senescence, contact inhibition and apoptosis.
The method according to any one of the preceding claims, wherein step B.v) comprises defining at least one subpopulation of cells and a reference subpopulation of cells from the mixed population on the basis of the spatial parameter of interest and wherein:
- A. If the ratio of cells in said subpopulation is greater than in said reference subpopulation, the mutation is characterised as a mutation having a positive effect on the spatial parameter;
- B. If the ratio of cells in said subpopulation is lower than the ratio of said reference subpopulation, the mutation is characterised as a mutation having a negative effect on the spatial parameter;
- C. If the ratio of cells in said subpopulation is substantially the same as the ratio of cells in said reference subpopulation, the mutation is characterised as a mutation having no effect on the spatial parameter.
The method according to any one of the preceding claims, wherein the spatial parameter is selected from the group consisting of:
- cell proliferation, cell growth, fitness, cell motility, cell invasiveness, cellular metabolism, cell differentiation, DNA damage, expression levels of pre-defined genes and/or proteins, resistance to a compound, sensitivity to a compound, production of a compound, anoikis, senescence, apoptosis, DNA methylation, and protein post-translational modification.
The method according to any one of the preceding claims, wherein steps iii) and iv), and optionally steps A.v) to A.vi) and/or steps B.v) to B.vii), are performed more than once for further predetermined duration(s).
The method according to any one of the preceding claims, wherein step ii) further comprises selecting the cells in which one of the first oligonucleotide or the second oligonucleotide has been introduced, thereby obtaining a subpopulation of cells comprising cells in which the mutation of interest has been introduced in the target nucleic acid sequence, and cells in which the synonymous mutation has been introduced in the target nucleic acid sequence.
The method according to any one of the preceding claims, wherein step ii) further comprises selecting the cells in which the nuclease or the polynucleotide encoding said nuclease has been introduced, thereby obtaining a subpopulation of cells enriched in cells in which the mutation of interest and/or the synonymous mutation has been introduced in the target nucleic acid sequence.
The method according to any one of the preceding claims, wherein the first oligonucleotide comprises at least one mutation of interest within the binding region of the nuclease, and wherein the second oligonucleotide comprises at least one synonymous mutation within the same binding region of the nuclease.
The method according to any one of the preceding claims, wherein the first oligonucleotide comprises at least one first mutation, which is a synonymous mutation lying inside the binding region of the nuclease, and further comprises at least one second mutation, which is a non-synonymous mutation of interest lying outside the binding region of the nuclease, and wherein the second oligonucleotide comprises at least one synonymous mutation lying within the same region as the first mutation and further comprises at least one further synonymous mutation lying inside the same region as the second mutation, wherein the first mutation and the synonymous mutation when introduced in the target nucleic acid sequence prevent the nuclease and the targeting means from binding to and/or generating a further SSB or a further DSB in the resulting nucleic acid sequence, preferably wherein the first mutation and the synonymous mutation are identical.
The method according to any one of the preceding claims, wherein the first oligonucleotide and the second oligonucleotide differ only in the location of the mutation of interest.
The method according to any one of the preceding claims, wherein the method is performed in vivo or in vitro.
The method according to any one of the preceding claims, wherein the first oligonucleotide is a plurality of first oligonucleotides each comprising a pre-determined mutation of interest and wherein the second oligonucleotide is a plurality of second oligonucleotides each comprising a pre-determined synonymous mutation.
The method according to any one of the preceding claims, wherein the cell is a vertebrate cell, an invertebrate cell, a plant cell, a yeast cell, a fungal cell or a bacterial cell.
The method according to any one of the preceding claims, wherein the cell is a human cell.
The method according to any one of the preceding claims, wherein the target nucleic acid sequence is within a gene, a promoter or an enhancer of a gene, wherein the gene is or is suspected to be an oncogene, a proto-oncogene, a tumour suppressor gene, a gene encoding an enzyme such as an enzyme involved in the production of a compound such as a metabolite, a resistance gene, such as a gene involved in resistance to a compound, a pharmaceutical compound or a pathogen such as a virus, a gene encoding a protein involved in cellular fitness and/or growth, a gene encoding a protein for any cell function, a microRNA or a long non-coding RNA.
The method according to any one of the preceding claims, wherein the nuclease comprises or consists of a CRISPR/Cas nuclease and the targeting means comprise or consist of a guide RNA capable of hybridizing to the genomic target region.
The method according to any one of the preceding claims, wherein the synonymous mutation is a single base change compared to the genomic target region.
The method according to any one of the preceding claims, wherein the mutation of interest is a single base change compared to the genomic target region.
The method according to any one of the preceding claims wherein the step of determining the ratio of cells of step A.v) and/or step B.vi) is performed for only a fraction of the cell population and/or only a fraction of each subpopulation.
The method according to any one of the preceding claims, wherein step A.v) and/or step B.vi) comprises amplifying a region comprising the target nucleic acid sequence, such as by PCR, to produce an amplicon comprising the target nucleic acid sequence, optionally followed by sequencing, such as next-generation sequencing, of said amplicon.
The method according any one of the preceding claims, wherein the determined duration is at least 2 hours, such as at least 4 hours, such as at least 8 hours, such as at least 12 hours, such as at least 18 hours, such as at least 24 hours, such as at least 48 hours, such as at least 72 hours.
The method according any one of the preceding claims, wherein the determined duration is at least such as at least 1 week, such as at least 2 weeks, such as at least 3 weeks, such as at least 4 weeks, such as at least 2 months, such as at least 4 months, such as at least 6 months, such as at least 8 months, such as at least 10 months, such as at least 12 months, such as at least 1½ year, such as at least 2 years.
The method according any one of the preceding claims, wherein the time between the initial time point and the subsequent time point is at least 4 hours, such as at least 8 hours, such as at least 12 hours, such as at least 18 hours, such as at least 24 hours, such as at least 48 hours, such as at least 72 hours.
The method according any one of the preceding claims, wherein the time between the initial time point and the subsequent time point is at least 1 week, such as at least 2 weeks, such as at least 3 weeks, such as at least 4 weeks, such as at least 2 months, such as at least 4 months, such as at least 6 months, such as at least 8 months, such as at least 10 months, such as at least 12 months, such as at least 1½ years, such as at least 2 years.
The method according to any one of the preceding claims, wherein step B.v) comprises a step of spatially separating the cells to separate the mixed cell population into subpopulations on the basis of a cell marker, such as the presence or absence or a graded level of a cell marker, for example a cell marker for cell proliferation, cell growth, fitness, cell motility, cell invasiveness, cellular metabolism, cell differentiation, DNA damage, expression levels of pre-defined genes or proteins, resistance to a compound, sensitivity to a compound, production of a compound, anoikis, senescence, apoptosis, DNA methylation or protein post-translational modification, optionally wherein the cell marker is the spatial parameter of interest.
The method according to any one of the preceding claims, wherein step B.v) comprises defining the subpopulations on the basis of a cell property, such as the ability of the cells to migrate or invade, optionally wherein the cell property is the spatial parameter of interest.
The method according to any one of the preceding claims, wherein each subpopulation of step B.v) comprises one or more cells, such as a single cell or a plurality of cells.
The method according to any one of the preceding claims, wherein the parameter of interest is a cellular response to a compound or an external stimulus, such as temperature, drought or pressure, and wherein the medium of step iii) comprises said compound or step iii) additionally comprises subjecting the cell population to the external stimulus, wherein the cellular response is a temporal parameter or a spatial parameter.
The method according to any one of the preceding claims, wherein one or more of the first oligonucleotide, the second oligonucleotide, the targeting means and the polynucleotide encoding the nuclease are comprised within one or more vectors or within a virus.
The method according to any one of the preceding claims wherein the first oligonucleotide and/or the second oligonucleotide is single-stranded.
The method according to any one of the preceding claims wherein the first oligonucleotide and/or the second oligonucleotide is double-stranded.
The method according to any one of the preceding claims wherein the first oligonucleotide and/or the second oligonucleotide is modified, such as by introduction of one or more phosphorothioate bonds to inhibit oligonucleotide degradation by nucleases.
A system comprising:
- i. a nuclease or a polynucleotide encoding said nuclease, wherein the nuclease is capable of generating one or more single-strand breaks (SSBs) or double-strand breaks (DSBs) in a target nucleic acid sequence, and targeting means directing the nuclease to the target nucleic acid sequence, whereby the nuclease is capable of binding to a binding region of the target nucleic acid sequence, and whereby the nuclease is capable of generating one or more single-stranded breaks (SSBs) or double-strand breaks (DSBs) in the target nucleic acid sequence;
- ii. a first oligonucleotide comprising a mutation of interest, preferably a non-silent mutation, preferably a non-synonymous mutation, wherein said non-synonymous mutation introduces a change in the encoded amino acid sequence compared to the amino acid sequence encoded by the target nucleic acid sequence, and otherwise identical to or complementary to said target nucleic acid sequence, wherein said mutation of interest preferably lies within the binding region of said nuclease;
- and
- iii. a second oligonucleotide comprising a synonymous mutation, wherein said synonymous mutation preferably lies within the binding region of said nuclease, and wherein said synonymous mutation introduces no change in the encoded amino acid sequence compared to the amino acid sequence encoded by the target nucleic acid sequence,
- wherein i., ii., and iii. are comprised within the same cell population.
Dependencies are inferred from the claim text.