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Definitions

• отодетс ⁇ ество мо ⁇ ет ⁇ тункт ⁇ или или то ⁇ ет о ⁇ оловани ⁇ о ⁇ оловани ⁇ о ⁇ олованн ⁇ е о ⁇ оло ⁇ омасул ⁇ носте о ⁇ оло ⁇ етс ⁇ о ⁇ олованн ⁇ е о ⁇ оло ⁇ овани ⁇ о ⁇ оловани ⁇ о ⁇ олованн ⁇ ел ⁇ ел ⁇ ел ⁇ ел ⁇ ированн ⁇ о ⁇ ентавл ⁇ ированн ⁇ о ⁇ ентавл ⁇ ированн ⁇ ел ⁇ ност ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о ⁇ о
• Engineered (synthetic/artificial) genetic (gene) circuits generally are useful, for example, for ex vivo differentiation and manufacturing of cell therapies.
• Cells harboring engineered genetic circuits (heterologous genetic circuits) that enable the dynamic control of cell function may be used in patients as therapeutics for treating/preventing many different conditions. Once the desired cell types are created and deployed into patients, however, the engineered circuits may not be necessary for the therapeutic application and may even have adverse effects.
• the ability to effectively remove these genetic circuits e.g., heterologous DNA cassettes after they are deployed into patients is useful for patient safety.
• the differentiation of stem cells into pancreatic beta-islet cells can be enhanced through genetic circuits , but once the beta-islet cells are introduced into patients, removal of the genetic circuits would reduce regulatory and safety concerns.
• the multilayer platform as provided herein which in some embodiments combines several genetic excision and/or degradation technologies, is engineered for efficient removal ("erasing") of heterologous nucleic acid (e.g., DNA).
• erasing of heterologous nucleic acid
• the engineered genetic constructs of the present disclosure may be referred to as "genetic erasers.”
• aspects of the present disclosure provide engineered genetic constructs (genetic erasers) comprising an expression cassette (a cassette) that comprises (a) a nucleotide sequence encoding a first product of interest (e.g., a recombinase or nuclease), and (b) a nucleotide sequence encoding a second product of interest (e.g., a therapeutic molecule) and a counterselectable marker (e.g., a prodrug), wherein expression or activity of the first product of interest is activatable, and wherein the first product of interest modulates excision or degradation of the cassette.
• component (a) is upstream from component (b).
• the engineered genetic constructs comprise an expression cassette (a cassette) that comprises (a) a nucleotide sequence encoding a recombinase, (b) a nucleotide sequence encoding a nuclease, and (b) a nucleotide sequence encoding a product of interest (e.g., a therapeutic molecule) and a counterselectable marker (e.g., a prodrug), wherein the recombinase and nuclease are activatable and modulates excision and/or degradation of the cassette.
• a cassette that comprises (a) a nucleotide sequence encoding a recombinase, (b) a nucleotide sequence encoding a nuclease, and (b) a nucleotide sequence encoding a product of interest (e.g., a therapeutic molecule) and a counterselectable marker (e.g., a prodrug),
• the engineered genetic constructs comprise a cassette that comprises (a) an inducible promoter operably linked to a nucleotide sequence encoding a recombinase, and (b) a promoter operably linked to a nucleotide sequence encoding a product of interest and a counterselectable marker, wherein the cassette is flanked by cognate recombinase recognition sites.
• the engineered genetic constructs comprise a cassette that comprises (a) an inducible promoter operably linked to a nucleotide sequence encoding a nuclease, and (b) a promoter operably linked to a nucleotide sequence encoding a product of interest and a counterselectable marker, wherein the cassette is flanked by nuclease recognition sites.
• the engineered genetic constructs comprise a cassette that comprises (a) an inducible promoter operably linked to a nucleotide sequence encoding a recombinase, (b) an inducible promoter operably linked to a nucleotide sequence encoding a nuclease, and (c) a promoter operably linked to a nucleotide sequence encoding a product of interest and a counterselectable marker, wherein the cassette is flanked by cognate recombinase recognition sites and includes cognate nuclease recognition sites.
• Some aspects of the present disclosure provide methods comprising introducing into a cell of any one of the engineered genetic constructs as described herein, wherein the product of interest aids in differentiation, expansion or phenotypic maintenance of the cell.
• inventions comprising introducing into a cell of any one of the engineered genetic constructs as described herein, wherein the product of interest is a therapeutic molecule and/or prophylactic molecule.
• the present disclosure also provides vectors, cells, compositions and kits comprising any of the engineered genetic constructs as described herein.
• FIG. 1 shows an example of how multiple redundant and orthogonal recombinase proteins are utilized to excise heterologous DNA constructs from target cells. These recombinases are controlled through inducible transcription, reconstitution of split protein activity, or translocation of protein to the nuclease.
• FIGS. 2A-2B show an example of how nucleases are used to target DNA for (FIG. 2A) destruction and/or (FIG. 2B) trigger recombination to excise large DNA fragments located in between nuclease target sites (NTS).
• NTS nuclease target sites
• These nucleases can include meganucleases, CRISPR-Cas nucleases, zinc-finger nucleases, and TALE nucleases. Double-stranded breaks induced by nucleases can result in recombination that inactivates targeted protein-coding sequences or catalyzes large deletions, which can be further enhanced through the presence of donor DNA.
• FIG. 3 shows an example of counterselectable markers (CSMs) encoded in heterologous DNA constructs so that cells that do not undergo efficient DNA excision with the recombinase-based or nuclease-based approaches are killed upon addition of a prodrug that is converted into a toxic drug.
• CSMs counterselectable markers
• inducible kill switches are encoded that trigger cell death upon addition of a small-molecule inducer that expresses toxins or dimerizes split toxins.
• FIG. 4 shows an example of a recombinase-based excision construct for stable integration. This modular construct enables easy exchange of genetic parts by simply digesting the vector with difference combinations of restriction enzymes.
• FIG. 5 shows an example of a system to assay for recombinase excision efficiency.
• the reporter vector encodes recombination sequences flanking a counter- selection marker (e.g., HSV thymidine kinase).
• DNA assembly may be performed with multi-step approaches including, for example, restriction enzyme cloning, Gibson assembly and Golden Gate assembly.
• the recombinase vector encodes a recombinase (e.g., Bxbl).
• FIG. 6 shows data from a transient 293FT cell transfection assay to test recombinase activity of various tyrosine recombinases.
• 293FT cells were transiently transfected with an equal ratio of reporter plasmid, recombinase plasmid, and a transfection marker plasmid (e.g., a plasmid encoding BFP). The cells were assayed for GFP fluorescence 24 hours post transfection and gated for BFP expression.
• the top graph represents % GFP+ cells, and the bottom graph represents the median of the GFP mean fluorescence intensity of the GFP+ cells.
• Each group of bars shows, left to right, data for: reporter, recombinase, and reporter + recombinase.
• FIG. 7 shows data from a transient 293FT cell transfection assay to test recombinase activity of various tyrosine recombinases.
• 293FT cells were transiently transfected with an equal ratio of reporter plasmid, recombinase plasmid, and a transfection marker plasmid (e.g., a plasmid encoding BFP). The cells were assayed for GFP fluorescence 24 hours post transfection and gated for BFP expression. The histograms represent transfected cell populations with and without recombinase.
• FIG. 8 shows an example of a system used to assay for recombinase excision efficiency.
• a BpiI(x2)-HSVtk-SV40pA-EGFP-Esp3I(x2) cassette was inserted into the pcDNA3.1(+) mammalian expression vector (Life Tech). Recombination sequences were inserted into the Bpil and Esp3I sites via Golden Gate digestion/ligation.
• FIG. 9 shows data from a transient 293FT cell transfection assay to test recombinase activity of various serine integrases.
• 293FT cells were transiently transfected with an equal ratio of reporter plasmid, recombinase plasmid, and a transfection marker plasmid (e.g., a plasmid encoding BFP). The cells were assayed for GFP fluorescence 24 hours post transfection and gated for BFP expression.
• the top graph represents % GFP+ cells, and the bottom graph represents the median of the GFP mean fluorescence intensity of the GFP+ cells.
• Each group of bars shows, left to right, data for: reporter, recombinase, and reporter + recombinase.
• FIG. 10 shows data from a transient 293FT cell transfection assay to test expression of various serine integrases.
• 293FT cells were transiently transfected with an equal ratio of reporter plasmid, recombinase plasmid, and a transfection marker plasmid (e.g., a plasmid encoding BFP). The cells were assayed for GFP fluorescence 24 hours post transfection and gated for BFP expression. The histograms represent transfected cell populations with and without recombinase.
• FIG. 11 shows an example of a recombinase-based excision construct for site-specific integration.
• An entry vector encoding a recombinase-based excision construct is integrated into a pre-engineered 293FT landing pad cell line that expresses YFP and hygromycin.
• FIG. 12 shows successful integration of a GFP reporter into a 293FT landing pad cell line. Upon integration, cells express GFP and simultaneously lose expression of YFP.
• FIG. 13 shows an example of a method for excising genomically-integrated constructs.
• An entry vector encoding a recombinase-based excision construct is integrated into a pre-engineered 293FT landing pad cell line.
• Integrated cell lines are transiently transfected with a recombinase-expressing plasmid and a reporter plasmid (e.g., expressing BFP) and assayed for GFP expression over time.
• a counter-selection marker CSM is used to kill off cells that retain the integrated construct.
• FIG. 14 shows example data obtained using the experimental method described in FIG. 13.
• Cell lines expressing 3 different recombinase-based excision constructs were transiently transfected with the cognate recombinase, and GFP expression was assayed over time.
• the % of GFP+ cells were plotted for cell populations that were either ungated or gated for BFP expression. Each group of bars shows, left to right, data for: day 2, day 4, and day 7.
• FIG. 15 shows example data obtained using the experimental method described in FIG. 13.
• a prodrug was applied to kill off cells that retained the pENTR_B3RT excision construct.
• the counter selection marker CSM
• CSM counter selection marker
• the CSM was HSVtk and the prodrug was ganciclovir (GCV).
• GCV ganciclovir
• the cells were treated with 0.5, 1, 2, and 5 ⁇ GCV for 7 days, and GFP expression was assayed over time.
• the histograms represent the % of GFP- and % of GFP+ cells.
• FIG. 16 shows example data obtained using the experimental method described in FIG. 13. Following transient transfection of the Flp recombinase in FIG. 14, a prodrug was applied to kill off cells that retained the pENTR_FRT excision construct.
• the counter selection marker (CSM) converts the prodrug into a toxic drug.
• the CSM was HSVtk and the prodrug was ganciclovir (GCV).
• the cells were treated with 0.5, 1, 2, and 5 ⁇ GCV for 7 days, and GFP expression was assayed over time. The histograms represent the % of GFP- and % of GFP+ cells.
• FIG. 13 shows example data obtained using the experimental method described in FIG. 13. Following transient transfection of the Flp recombinase in FIG. 14, a prodrug was applied to kill off cells that retained the pENTR_FRT excision construct.
• the counter selection marker (CSM) converts the prodrug into a toxic drug.
• the CSM
• FIG. 17 shows an example of a system in which guide RNAs (gRNAs) cleave and remove a genomically-integrated circuit.
• gRNAs guide RNAs
• the gRNAs target the 5'-UTR and 3'- UTR if a YFP reporter that has been stably integrated into cells.
• FIG. 18 shows data from a transient transfection assay to test the removal of a genomically-integrated circuit using CRISPR/Cas9.
• Vectors encoding a single gRNA and Cas9 were co-transfected along with a reporter plasmid (e.g., expressing BFP) into a cell line that expresses YFP.
• a reporter plasmid e.g., expressing BFP
• two vectors encoding different gRNAs were transfected along with a reporter plasmid.
• the cell populations were gated for BFP expression, and the % of YFP+ cells were plotted over time. Different combinations of gRNAs may be used to remove YFP.
• the histograms represent the % of YFP- and % of YFP+ cells. Each group of bars shows, left to right, data for: day 2, day 5, and day 7.
• FIG. 19 shows example data obtained using the experimental method described in FIG. 13.
• Cell lines expressing the pENTR_B3RT_FRT recombinase-based excision construct were sequentially transfected with B3 or Flp according to the indicated timeline.
• GFP expression was assayed over time, and the histograms represent the % of GFP+ cells on day 15.
• the pENTR_B3RT_FRT recombinase-based excision construct encodes the construct B 3 RT_FRT_iC asp9_S V40p A_FRT_B 3 RT_EGFP_B GHp A, in which B3RT and FRT are recombination sequences for B3 and Flp, respectively; and iCasp9 is a counter selection marker (CSM).
• CSM counter selection marker
• FIG. 20 shows example data obtained using the experimental method described in FIG. 13.
• Cell lines expressing the pENTR_B3RT_FRT recombinase-based excision construct were sequentially transfected with B3 or Flp according to the indicated timeline.
• GFP expression was assayed over time, and the % of GFP+ cells on day 15 were plotted. Bars show, left to right, data for: no rec; B3; B3, Flp; Flp,; and Flp, B3.
• Described herein is a powerful technology that enables next-generation cell therapies, in part, by enabling highly efficient removal of heterologous nucleic acid from engineered cells.
• the engineered genetic constructs herein may be referred to as "genetic erasers.”
• the genetic eraser technologies described herein are useful for at least two major applications. First, they are useful for creating genetic circuits that aid in the differentiation, expansion, or phenotypic maintenance of cells ex vivo, which can then be removed prior to being introduced into patients. Second, they are used as safety switches that can be triggered after cell therapies are delivered in vivo by removing heterologous DNA from engineered cells so that the cell therapies lose their function.
• these genetic erasers enable the implementation of genetic circuits that enhance the differentiation, expansion, or persistence of specific phenotypes ex vivo and subsequent removal the genetic circuits before introduction into the body.
• Existing strategies for regulating cell phenotypes include the use of small molecules, growth factors, RNA constructs, or DNA circuits. Small molecules can be useful for enhancing
• RNA constructs encoding transcription factors and other intracellular regulators of cell function have been utilized for cell programming, but have not been used to encode complex dynamics into cell programs that are necessary for improved efficiency due to the lack of programmable RNA regulators (albeit, this is beginning to change with recent advancements (25)).
• DNA circuits have been used to program complex transcriptional programs, such as the differentiation of progenitor cells derived from iPS cells into beta-isletlike cells (3), as discussed above.
• circuits can be used to express intracellular regulators, such as transcription factors and microRNAs, as well as secrete paracrine factors such as growth factors and cytokines, and thus have the potential to increase the scale and reduce the cost of ex vivo cellular programming.
• intracellular regulators such as transcription factors and microRNAs
• secrete paracrine factors such as growth factors and cytokines
• the genetic erasers of the present disclosure integrate multiple mechanisms to achieve significant levels of genetic erasure (deletion/degradation), which can restore cells to a baseline state without heterologous activities and can restore the genome to a baseline state with almost no trace of foreign DNA (recombinases may leave small DNA scars with minimal effects).
• Using multiple redundant layers of genetic erasers enables significantly improved efficiencies of genetic deletion and is important for enabling clinical applications (achieving clinical-grade activity) of this technology.
• efficiencies of removing heterologous DNA or killing cells that contain heterologous DNA are measured.
• fluorescence or qPCR-based assays are used.
• cell survival is monitored using live-dead assays.
• This is prototyped in cell lines and extended into therapeutically relevant cell types (e.g., mesenchymal stem cells, T cells, NK cells).
• Such technologies are useful for programming efficient cell differentiation and then removing these circuits prior to therapy.
• Such technologies also are useful as kill switches or OFF switches for in vivo applications of genetically engineered cell therapies.
• a key technical challenge for genetic erasers is to minimize the number of cells that escape from the genetic erasing process.
• Doses of CAR T cells in trials range from 2* 10 5 - 2* 10 CD19 CAR T cells/kg, whereas mesenchymal stem cells (MSCs) being used in the clinic are in the range of 1-3* 10 6 MSCs/kg (27).
• MSCs mesenchymal stem cells
• maximal doses of cell therapies being used in the clinic appear to be less than 10 9 cells on the high end.
• genetic erasers that can achieve efficiencies of greater than 10 9 are preferred.
• multiple genetic erasure mechanisms can be layered together, as provided herein.
• Combinations of genetic eraser components lead to enhanced efficiencies. For example, if greater than 97% excision efficiency is achieved with four different recombinases and greater than 97% killing efficiency is achieved with two counterselectable markers, then only one cell in -7.3 10 cells would remain after application of genetic eraser technology.
• conditionally replicating plasmids are used instead of encoding genetic circuits into the genome to improve the efficiency of removing heterologous DNA or RNA circuits with new dynamic regulators (25).
• engineered genetic constructs comprising a cassette that comprises (a) an inducible promoter operably linked to a nucleotide sequence encoding a recombinase, and (b) a promoter operably linked to a nucleotide sequence encoding a product of interest and a counterselectable marker, wherein the cassette is flanked by cognate recombinase recognition sites.
• the recombinase functions to self-excise the cassette, and the counterselectable marker functions to kill off any cells in which the cassette remains following an excision event.
• the inducible promoter operably linked to a nucleotide sequence encoding a recombinase is upstream from (5' from) the promoter operably linked to a nucleotide sequence encoding a product of interest. See, e.g., FIGS. 1 and 3.
• engineered genetic constructs comprising a cassette that comprises (a) an inducible promoter operably linked to a nucleotide sequence encoding a nuclease, and (b) a promoter operably linked to a nucleotide sequence encoding a product of interest and a counterselectable marker, wherein the cassette comprises cognate nuclease recognition sites.
• the nuclease functions to cut up/degrade the cassette, and the
• the inducible promoter operably linked to a nucleotide sequence encoding a nuclease is upstream from (5' from) the promoter operably linked to a nucleotide sequence encoding a product of interest. See, e.g., FIG. 2 and 3.
• a single genetic construct encoding a product of interest may encode multiple (e.g., at least 2, 3, 4, or 5) different recombinases, nucleases and/or counterselectable markers.
• the same genetic construct may include multiple pairs of recombinase recognition sites and/or multiple nuclease recognitions sites to enable highly efficient excision and/or degradation of the nucleic acid encoding the different recombinases and/or nucleases and the product of interest.
• a single construct encodes a recombinase, a nuclease and a counterselectable marker. In some embodiments, a single construct encodes at least one (e.g.,
• recombinase at least one (e.g., 1, 2, 3, 4 or 5) nuclease and at least one (e.g., 1,
• a single construct encodes at least one recombinase and at least one nuclease. In some embodiments, a single construct encodes at least one recombinase and at least one counterselectable marker. In some embodiments, a single construct encodes at least one nuclease and at least one
• a single construct encodes at least two recombinases and at least one nuclease. In some embodiments, a single construct encodes at least two recombinases and at least one counterselectable marker. In some embodiments, a single construct encodes at least two nucleases and at least one recombinase. In some embodiments, a single construct encodes at least two nucleases and at least one
• a single construct encodes at least two recombinases, at least two nucleases and at least one counterselectable marker. In some embodiments, a single construct encodes at least two recombinases, at least two nucleases and at least two counterselectable markers.
• a cassette of a single construct may be flanked by multiple pairs of cognate recombinase recognition site and/or may contain multiple nuclease recognition sites.
• an engineered genetic construct comprising a cassette that comprises at least two inducible promoters, each linked to a nucleotide sequence encoding a different recombinase and/or nuclease, wherein the cassette is flanked by recombinase recognition sites cognate to the different recombinases and/or comprises nuclease recognition sites cognate to the different nucleases.
• the inducible promoter is linked to at least two nucleotide sequences, each encoding a different recombinase and/or nuclease, and wherein the cassette is flanked by recombinase recognition sites cognate to the different recombinases and/or comprises nuclease recognition sites cognate to the different nucleases.
• the construct comprises at least three inducible promoters, each linked to a nucleotide sequence encoding a different recombinase and/or nuclease, wherein the cassette is flanked by recombinase recognition sites cognate to the different recombinases and/or comprises nuclease recognition sites cognate to the different nucleases.
• the inducible promoter is linked to at least three nucleotide sequences, each encoding a different recombinase and/or nuclease, wherein the cassette is flanked by recombinase recognition sites cognate to the different recombinases and/or comprises nuclease recognition sites cognate to the different nucleases.
• the different combinations of genetic eraser components lead to enhanced efficiencies in removal of heterologous nucleic acid.
• degradation and/or counterselection reactions which include exposing the cells to all inducing agents and/or counterselective agents necessary to express each component of the expression cassette, in some embodiments, less than 20% (e.g., 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1% or 0%) of the cells that initially received the engineered genetic constructs retain the expression cassettes.
• 80% e.g., 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%
• 80-100%, 80-95%, 80-90%, 80-85%, 85-100%, 85-95%, 85-90%, 90-100% or 95-100% of the cells that initially received the engineered genetic constructs no longer contain the expression cassette following a series of excision, degradation and/or counterselection reactions.
• methods of the present disclosure may include introducing into a population of cells an engineered genetic construct as provided herein, culturing the cells to produce the product of interest, culturing the cells in the presence of at least one (one or more) inducer agent to express the recombinase and/or nuclease to excise and/or degrade the cassette from the engineered genetic construct, culturing cells of the population in the presence of a counterselective agent to kill cells that still retain and express the counterselectable marker.
• An inducer agent is any agent that activates a cognate inducible promoter (the activity of which is activated in the presence of the inducer).
• a counterselective agent is any agent that kills a cell that expresses/contains the
• counterselectable marker (which is toxic to the cells, e.g., is converted to a toxic agent, in the presence of the counterselective agent).
• an engineered genetic construct comprises an expression cassette (a cassette) that comprises (a) an inducible promoter operably linked to a nucleotide sequence encoding a recombinase, and (b) a promoter operably linked to a nucleotide sequence encoding a product of interest and a counterselectable marker, wherein the cassette is flanked by cognate recombinase recognition sites.
• component (a) is upstream from component (b).
• a terminator sequence is located between component (a) and component (b). See, e.g., FIG. 1.
• component (a) comprises at least two (or at least three) inducible promoters, each linked to a different recombinase, and the cassette is flanked by recombinase recognition sites cognate to the different recombinases.
• the nucleotide sequence of component (a) encodes at least two (or at least three) different recombinases, and the cassette is flanked by recombinase recognition sites cognate to the different recombinases.
• the nucleotide sequence of component (b) encodes at least two (or at least three) counterselectable markers.
• the recombinase(s) is selected from tyrosine recombinases and tyrosine integrases.
• the recombinase(s) may be selected from Cre, Dre, Flp, KD, B2, B3, ⁇ , HK022 and HP1 recombinases.
• the recombinase(s) is selected from serine recombinases or serine integrases.
• the recombinase(s) may be selected from ⁇ , ParA, Tn3, Gin, OC31, Bxbl and R4 recombinases.
• a recombinase is a site-specific enzyme that recognizes short DNA sequence(s), typically between about 30 base pairs (bp) and 40 bp, that mediates the recombination between these recombinase recognition sequences, which results in the excision, integration, inversion, or exchange of DNA fragments between the recombinase recognition sequences.
• Recombinases can be classified into two distinct families: serine recombinases (e.g. , resolvases and invertases) and tyrosine recombinases (e.g. , integrases), based on distinct biochemical properties. Serine recombinases and tyrosine recombinases are further divided into bidirectional recombinases and unidirectional recombinases.
• bidirectional serine recombinases include, without limitation, ⁇ -six, CinH, ParA and ⁇ ; and examples of unidirectional serine recombinases include, without limitation, Bxbl, (
• bidirectional tyrosine recombinases include, without limitation, Cre, FLP, and R; and unidirectional tyrosine recombinases include, without limitation, Lambda, HKlOl, HK022 and pSAM2.
• the serine and tyrosine recombinase names stem from the conserved nucleophilic amino acid residue that the recombinase uses to attack the DNA and which becomes covalently linked to the DNA during strand exchange. Recombinases have been used for numerous standard biological applications, including the creation of gene knockouts and the solving of sorting problems.
• recombinases bind to these repeated sequences, which are specific to each recombinase, and are herein referred to as recombinase recognition sequences or recombinase recognition sites.
• a recombinase is specific for a recombinase recognition site when the recombinase can mediate inversion or excision between the repeat DNA sequences.
• a recombinase may also be said to recognize its cognate recombinase recognition sites, which flank an intervening genetic element (e.g., promoter, terminator, or output nucleic acid sequence).
• a nucleic acid or fragment of a nucleic acid is said to be flanked by recombinase recognition sites when the element is located between and immediately adjacent to two repeated DNA sequences.
• the recombinase recognition sites do not overlap each other. However, in other embodiments, recombinase recognition sites do overlap each other, which permits greatly increased combinatorial complexity.
• Inversion recombination happens between two short, inverted, repeated DNA sequences.
• a DNA loop formation assisted by DNA bending proteins, brings the two repeat sequences together, at which point DNA cleavage and ligation occur.
• This reaction is ATP independent and requires supercoiled DNA. The end result of such an inversion
• the recombination event is that the stretch of DNA between the repeated site inverts (i.e., the stretch of DNA reverses orientation) such that what was the coding strand is now the non- coding strand and vice versa. In such reactions, the DNA is conserved with no net gain or no loss of DNA.
• integration occurs between two short, repeated DNA sequences that are oriented in the same direction.
• the intervening DNA is excised/removed.
• Recombinases can also be classified as irreversible or reversible.
• An irreversible recombinase is a recombinase that can catalyze recombination between two complementary recombination sites, but cannot catalyze recombination between the hybrid sites that are formed by this recombination without the assistance of an additional factor.
• an irreversible recognition site refers to a recombinase recognition site that can serve as the first of two DNA recognition sequences for an irreversible recombinase and that is modified to a hybrid recognition site following recombination at that site.
• a complementary irreversible recognition site refers to a recombinase recognition site that can serve as the second of two DNA recognition sequences for an irreversible recombinase and that is modified to a hybrid recombination site following homologous recombination at that site.
• attB and attP are the irreversible recombination sites for Bxbl and phiC31 recombinases— attB is the complementary irreversible recombination site of attP, and vice versa.
• AttB/attP sites can be mutated to create orthogonal B/P pairs that only interact with each other but not the other mutants. This allows a single recombinase to control the excision or integration or inversion of multiple orthogonal B/P pairs.
• the phiC31 (cpC31) integrase for example, catalyzes only the attB x attP reaction in the absence of an additional factor not found in eukaryotic cells.
• the recombinase cannot mediate recombination between the attL and attR hybrid recombination sites that are formed upon recombination between attB and attP. Because recombinases such as the phiC31 integrase cannot alone catalyze the reverse reaction, the phiC31 attB x attP recombination is stable.
• irreversible recombinases are described in the art and can be obtained using routine methods.
• irreversible recombinases include, without limitation, phiC31 (cpC31) recombinase (SEQ ID NO: 11), coliphage P4 recombinase, coliphage lambda integrase, Listeria A118 phage recombinase, and actinophage R4 Sre recombinase, HKlOl, HK022, pSAM2, Bxbl, TP901, TGI, ⁇ , (pRVl, cpFCl, MRU, U153 and gp29.
• a reversible recombinase is a recombinase that can catalyze
• recombination between two complementary recombinase recognition sites can catalyze recombination between the sites that are formed by the initial recombination event, thereby reversing it.
• the product-sites generated by recombination are themselves substrates for subsequent recombination.
• reversible recombinase systems include, without limitation, the Cre-lox and the Flp-frt systems, R, ⁇ -six, CinH, Par A and ⁇ .
• an engineered genetic construct encodes a recombinase selected from tyrosine recombinases or tyrosine integrases.
• the recombinase is selected from Cre, Dre, Flp, KD, B2, B3, ⁇ , HK022 and HP1 recombinases.
• an engineered genetic construct encodes a recombinase selected from serine recombinases or serine integrases.
• the recombinase is selected from ⁇ , ParA, Tn3, Gin, OC31, Bxbl and R4 recombinases.
• recombinases provided herein are not meant to be exclusive examples of recombinases that can be used in embodiments of the present disclosure.
• the complexity of genetic erasers of the present disclosure can be expanded by mining databases for new orthogonal recombinases or designing synthetic recombinases with defined DNA
• control of recombinase expression and/or activation can be achieved many difference ways, using, for example, the ABA system (Liang, F.S., et al. Sci. Signal., 2011, 4, rs2 LP-rs2), the GIB system (Miyamota, T. et al. Nat Chem Biol, 2012, 8, 465-470), the FKBP-FRB based dimerization system ( Komatsu, T. et al. Nat Meth, 2010, 7, 206-208), the tamoxifen system (Matsuda, T. et al. Proc. Natl. Acad. Sci.
• an engineered genetic construct comprising a cassette that comprises (a) a nucleotide sequence encoding at least one ligand-dependent chimeric recombinase, and (b) a nucleotide sequence encoding a product of interest and a
• an engineered genetic construct comprising a cassette that comprises (a) a nucleotide sequence encoding a first fragment of a recombinase, (b) a nucleotide sequence encoding a second fragment of a recombinase, wherein the first fragment and the second fragment when combined (dimerize) form a full-length functional
• an engineered genetic construct comprises an expression cassette (a cassette) that comprises (a) an inducible promoter operably linked to a nucleotide sequence encoding a nuclease, and (b) a promoter operably linked to a nucleotide sequence encoding a product of interest and a counterselectable marker, wherein the cassette comprises cognate nuclease recognition sites.
• nuclease recognition sites flank the cassette.
• component (a) is upstream from component (b).
• a terminator sequence is located between component (a) and component (b). See, e.g., FIG. 2.
• component (a) comprises at least two inducible promoters, each linked to a different nuclease, and the cassette comprises nuclease recognition sites cognate to the different nucleases.
• the nucleotide sequence of component (a) encodes at least two different nucleases, and the cassette comprises nuclease recognition sites cognate to the different nucleases.
• the nucleotide sequence of component (b) encodes at least two counterselectable markers.
• the nuclease(s) is selected from meganucleases and RNA- guided nucleases.
• the nuclease(s) may be a meganuclease selected from intron endonucleases and intein endonucleases.
• the nuclease(s) is a RNA- guided nuclease selected from Cas9 nucleases and Cpf 1 nucleases.
• the cassette may further comprise nucleotide sequences encoding guide RNAs (gRNAs) complementary to the nuclease recognitions sites.
• a nuclease is an enzyme that cleaves the phosphodiester bonds between monomers of nucleic acids.
• Many nucleases such as restriction endonuclease, cleaves DNA at specific sites along the molecule. These sites at which a nuclease cleaves are referred to as nuclease recognition sites.
• restriction nucleases such as meganucleases, RNA- guided nucleases, zinc-finger nucleases, and transcription activator-like effector nucleases.
• endodeoxyribonucleases that have a long recognition site (e.g., double-stranded DNA sequences of 12 to 40 base pairs). Thus, this site generally occurs only once in any given genome.
• Meganucleases are mainly represented by two main enzyme families collectively known as homing endonucleases: intron endonucleases and intein endonucleases.
• the meganuclease is a LAGLIDADG family endonuclease. The name of this family corresponds to an amino acid sequence (or motif) that is found, generally conserved, in all the proteins of this family.
• RNA-guided nucleases are endonucleases that are selectively guided to their target sites by associating with a guide RNA (gRNA) strand that includes a sequence
• the RNA-guided nuclease is a member of the clustered, regularly interspaced, short palindromic repeats (CRISPR)- CRISPR-associated (Cas) system.
• CRISPR regularly interspaced, short palindromic repeats
• Cas CRISPR-associated
• the RNA-guided nuclease is a member of the Type II CRISPR-Cas system.
• CRISPR-Cas systems are used by various bacteria and archaea to mediate defense against viruses and other foreign nucleic acid. Short segments of foreign DNA, called spacers, are incorporated into the genome between CRISPR repeats and serve as a 'memory' of past exposures.
• RNA-guided nucleases typically include two components: a short -100 nucleotide single guide RNA (gRNA), containing 20 variable nucleotides at the 5' end involved in base pairing with a target DNA sequence, and the Cas9 nuclease, which cleaves the target DNA (Jinek, M., et al. Science 337, 816-821 (2012)).
• CRISPR-Cas The specificity of CRISPR-Cas is dictated by the identity of spacer sequences flanked by direct repeats encoded in the CRISPR locus, which are transcribed and processed into mature guide RNAs (gRNA) (Jinek, M. et al. (2012)). With the aid of a trans-activating small RNA (tracrRNA), gRNAs license the Cas9 endonuclease to introduce double-stranded breaks in target DNA sequences (protospacers) (Jinek, M. et al. (2012); Bikard, D., et al. (2012)).
• gRNAs trans-activating small RNA
• an RNA-guided nuclease can direct cleavage of almost any DNA sequence with the only design restriction being a NGG motif immediately 3' of the protospacer (Jinek, M. et al. (2012)).
• Non-limiting examples of RNA-guided nucleases that may be used herein include Cas9 and Cpfl.
• programmable nucleases and systems
• ZFNs zinc- finger nucleases
• TALENs transcription activator-like effector nucleases
• the engineered genetic constructs further comprise a nucleotide sequence encoding a counterselectable marker.
• a counterselectable marker is a molecule that promotes death of the cell harboring it (see, e.g., Reyrat, J. et al., Infect Immun. 66(9): 4011-4017, 1998). Cells that have integrated an engineered genetic construct that includes counterselectable marker, for example, are eliminated in the presence of a counter- selective compound.
• counterselectable markers can be used, as provided herein, for the positive selection of cells that have undergone an excision/degradation (eraser) event leading to the loss of the counterselectable marker.
• the cassette of an engineered genetic construct includes a (at least one) counterselectable marker, thus the counterselectable marker may be located between cognate recombinase recognition sites and/or may include nuclease recognition sites.
• a counterselectable marker is downstream from a nucleic acid encoding a product of interest.
• the promoter operably linked to the nucleotide sequence encoding a product of interest is also operably linked to the nucleotide sequence encoding the counterselectable marker.
• the counterselectable marker is a prodrug.
• a prodrug is a medication or compound that, after administration, is metabolized into a pharmacologically active drug.
• the counterselectable marker is a cytosine deaminase. Cytosine deaminase converts 5-fluorocytosine (5-FC) into 5-fluorouracil (5-FU), which can result in cell toxicity.
• the counterselectable marker is a thymidine kinases (e.g., HSV thymidine kinase).
• HSV thymidine kinase converts ganciclovir into a toxic product and can be used to trigger cell killing.
• Other counterselectable markers e.g., kill switches
• kill switches are known and may be used as provided herein.
• counterselectable markers are encompassed by the present disclosure including, for example, those described by the following: Deans, T.L. et al. Cell 130, 363-372, 2007; Ramos, C. A et al. Stem Cells, 28(6): 1107-1115, 2010; and Chung, H.K. et al. Nature Chemical Biology, 11: 713-720, each of which is incorporated herein by reference).
• an engineered nucleic acid is a nucleic acid that does not occur in nature. It should be understood, however, that while an engineered nucleic acid as a whole is not naturally-occurring, it may include nucleotide sequences that occur in nature.
• an engineered nucleic acid comprises nucleotide sequences from different organisms ⁇ e.g., from different species).
• an engineered nucleic acid includes a murine nucleotide sequence, a bacterial nucleotide sequence, a human nucleotide sequence, and/or a viral nucleotide sequence.
• engineered nucleic acids includes recombinant nucleic acids and synthetic nucleic acids.
• a “recombinant nucleic acid” refers to a molecule that is constructed by joining nucleic acid molecules and, in some embodiments, can replicate in a live cell.
• a “synthetic nucleic acid” refers to a molecule that is amplified or chemically, or by other means, synthesized. Synthetic nucleic acids include those that are chemically modified, or otherwise modified, but can base pair with naturally-occurring nucleic acid molecules. Recombinant nucleic acids and synthetic nucleic acids also include those molecules that result from the replication of either of the foregoing.
• Engineered nucleic acid of the present disclosure may be encoded by a single molecule (e.g. , included in the same plasmid or other vector) or by multiple different molecules (e.g. , multiple different independently-replicating molecules).
• Engineered nucleic acid of the present disclosure may be produced using standard molecular biology methods (see, e.g. , Green and Sambrook, Molecular Cloning, A
• engineered nucleic acid constructs are produced using GIBSON ASSEMBLY® Cloning (see, e.g. , Gibson, D.G. et al. Nature Methods, 343-345, 2009; and Gibson, D.G. et al. Nature Methods, 901-903, 2010, each of which is incorporated by reference herein).
• GIBSON ASSEMBLY® typically uses three enzymatic activities in a single-tube reaction: 5' exonuclease, the ' Y extension activity of a DNA polymerase and DNA ligase activity.
• engineered nucleic acid constructs are produced using IN-FUSION® cloning (Clontech).
• a promoter refers to a control region of a nucleic acid sequence at which initiation and rate of transcription of the remainder of a nucleic acid sequence are controlled.
• a promoter may also contain sub-regions at which regulatory proteins and molecules may bind, such as RNA polymerase and other transcription factors. Promoters may be constitutive, inducible, activatable, repressible, tissue-specific or any combination thereof.
• a promoter drives expression or drives transcription of the nucleic acid sequence that it regulates.
• a promoter is considered to be operably linked when it is in a correct functional location and orientation in relation to a nucleic acid sequence it regulates to control ("drive") transcriptional initiation and/or expression of that sequence.
• Constitutive promoters are unregulated promoters that continually activate
• constitutive promoters include the cytomegalovirus (CMV) promoter, the elongation factor 1-alpha (EFla) promoter, the elongation factor (EFS) promoter, the MND promoter (a synthetic promoter that contains the U3 region of a modified MoMuLV LTR with myeloproliferative sarcoma virus enhancer), the phosphoglycerate kinase (PGK) promoter, the spleen focus-forming virus (SFFV) promoter, the simian virus 40 (SV40) promoter, and the ubiquitin C (UbC) promoter.
• CMV cytomegalovirus
• EFla elongation factor 1-alpha
• EFS elongation factor
• MND promoter a synthetic promoter that contains the U3 region of a modified MoMuLV LTR with myeloproliferative sarcoma virus enhancer
• PGK phosphoglycerate kinase
• SFFV
• Inducible promoters are promoters that are characterized by regulating (e.g., initiating or activating) transcriptional activity when in the presence of, influenced by or contacted by a signal.
• the signal may be endogenous or a normally exogenous condition (e.g., light), compound (e.g., chemical or non-chemical compound) or protein (e.g., cytokine) that contacts an inducible promoter in such a way as to be active in regulating transcriptional activity from the inducible promoter.
• Activation of transcription may involve directly acting on a promoter to drive transcription or indirectly acting on a promoter by inactivation a repressor that is preventing the promoter from driving transcription.
• deactivation of transcription may involve directly acting on a promoter to prevent transcription or indirectly acting on a promoter by activating a repressor that then acts on the promoter.
• a promoter is considered responsive to a signal if in the presence of that signal transcription from the promoter is activated, deactivated, increased or decreased.
• a terminator sequence separates nucleotide sequences encoding recombinases and/or nucleases from downstream nucleotide sequences encoding products of interest.
• a terminator sequence is a nucleic acid sequence that causes transcription to stop.
• a terminator may be unidirectional or bidirectional. It is comprised of a DNA sequence involved in specific termination of an RNA transcript by an RNA polymerase.
• a terminator sequence prevents transcriptional activation of downstream nucleic acid sequences by upstream promoters.
• the most commonly used type of terminator is a forward terminator. When placed downstream of a nucleic acid sequence that is usually transcribed, a forward transcriptional terminator will cause transcription to abort.
• bidirectional transcriptional terminators are provided, which usually cause transcription to terminate on both the forward and reverse strand.
• the terminator region may comprise specific DNA sequences that permit site-specific cleavage of the new transcript so as to expose a polyadenylation site. This signals a specialized endogenous polymerase to add a stretch of about 200 A residues (polyA) to the 3' end of the transcript. RNA molecules modified with this polyA tail appear to more stable and are translated more efficiently.
• a terminator may comprise a signal for the cleavage of the RNA.
• the terminator signal promotes polyadenylation of the message.
• the terminator and/or polyadenylation site elements may serve to enhance output nucleic acid levels and/or to minimize read through between nucleic acids.
• the vector is an episomal vector, such as a plasmid or viral vector (e.g., adenoviral vector, retroviral vector, herpes simplex virus vectors, and/or chimeric viral vectors).
• a plasmid or viral vector e.g., adenoviral vector, retroviral vector, herpes simplex virus vectors, and/or chimeric viral vectors.
• Products encoded by the engineered genetic constructs of the present disclosure may be, for example, therapeutic molecules and/or prophylactic molecules.
• the product of interest is protein or peptide (e.g., a therapeutic protein or peptide).
• the product of interest is a nucleic acid (e.g., a therapeutic nucleic acid).
• nucleic acids include RNA, DNA or a combination of RNA and DNA.
• the product interest is DNA (e.g., single-stranded DNA or double-stranded DNA).
• the product of interest is RNA.
• the product of interest may be selected form RNA interference (RNAi) molecules, such as short-hairpin RNAs, short interfering RNAs and micro RNAs.
• RNAi RNA interference
• therapeutic and/or prophylactic molecules such as antibodies, enzymes, hormones, inflammatory agents, anti-inflammatory agents, immunomodulatory agents, and anti-cancer agents.
• the present disclosure provides, in some embodiments, cells comprising the engineered genetic constructs described herein and/or vectors containing the engineered genetic constructs described herein.
• the cell is a stem cell.
• the stem cell may be a mesenchymal stem cell, a hematopoietic stem cell, an embryonic stem cell, or a pluripotent stem cell (e.g., induced pluripotent stem cell).
• a “stem cell” refers to a cell with the ability to divide for indefinite periods in culture and to give rise to specialized cells.
• a “pluripotent stem cell” refers to a type of stem cell that is capable of differentiating into all tissues of an organism, but not alone capable of sustaining full organismal development.
• a "human induced pluripotent stem cell” refers to a somatic (e.g., mature or adult) cell that has been reprogrammed to an embryonic stem cell-like state by being forced to express genes and factors important for maintaining the defining properties of embryonic stem cells (see, e.g., Takahashi and Yamanaka, Cell 126 (4): 663-76, 2006, incorporated by reference herein).
• Human induced pluripotent stem cell cells express stem cell markers and are capable of generating cells characteristic of all three germ layers (ectoderm, endoderm, mesoderm).
• the cell is an immune cell.
• immune cells that may be used as provided herein include natural killer (NK) cells, NKT cells, mast cells, eosinophils, basophils, macrophages, neutrophils, dendritic cells, T cells and B cells.
• T cells include, but are not limited to, CD8+ T cells, CD4+ T cells, gamma-delta T cells, and T regulatory cells (e.g., (CD4+, FOXP3+, CD25+ cells).
• the T cell is a chimeric antigen receptor (CAR) T cells (e.g., fusions of single-chain variable fragments (scFv) derived from monoclonal antibodies, fused to CD3-zeta transmembrane- and endodomain).
• CAR chimeric antigen receptor
• compositions comprising at least one of the engineered genetic constructs of the present disclosure, a vector comprising at least one of the engineered genetic constructs of the present disclosure, or a cell comprising at least one of the engineered genetic constructs of the present disclosure.
• kits comprising at least one of the engineered genetic constructs of the present disclosure or at least one vector comprising at least one of the engineered genetic constructs of the present disclosure.
• the kits in some embodiments, further comprise at least one inducer agent that modulates activity of the inducible promoter(s) of the expression cassette.
• the kits further comprise a counterselective agent.
• aspects of the present disclosure provide methods that include introducing into a population of cells at least one engineered genetic construct (e.g., encoding (a) at least one recombinase and/or at least one nuclease and (b) a product of interest and at least one counterselectable marker), wherein the product of interest aids in differentiation, expansion or phenotypic maintenance (persistence) of the cells (e.g., transcription factors, growth factors, etc.).
• the methods further comprise culturing cells of the population and producing the product of interest.
• the methods further comprise culturing cells of the population in the presence of an inducer agent, activating the inducible promoter operably linked to a recombinase(s), and excising the cassette from the engineered genetic construct (and/or excising heterologous nucleic acid in the cell).
• the methods further comprise culturing cells of the population in the presence of a counterselective agent and killing cells that express the counterselectable marker.
• the methods further comprise delivering cells of the population to a subject (e.g., a human subject).
• less than 20% of the cells of the population comprise the cassette following the step of culturing cells of the population in the presence of a
• the cells of the population comprise the cassette following the step of culturing cells of the population in the presence of a counterselective agent. In some embodiments, less than 10% of the cells of the population comprise the cassette following the step of culturing cells of the population in the presence of a counterselective agent. In some embodiments, less than 5% of the cells of the population comprise the cassette following the step of culturing cells of the population in the presence of a counterselective agent.
• a population of cells may include 10 5 - 10 11 cells.
• a population of cells may include 10 5 , 10 6 , 10 7 , 10 8 , 10 9 , 10 10 , or 10 11 cells.
• a population of cells in some embodiments, is a homogeneous population of cells (all the same cell type), while in other embodiments, the population of cells is a heterogeneous population of cells (a mixture of different cell types).
• aspects of the present disclosure provide introducing into a population of cells at least one engineered genetic construct (e.g., encoding (a) at least one recombinase and/or at least one nuclease and (b) a product of interest and at least one counterselectable marker), wherein the product of interest is a therapeutic molecule and/or a prophylactic molecule.
• the methods further comprise delivering cells of the population to a subject.
• the methods further comprise exposing the subject to an inducer agent to activate the inducible promoter and express the recombinase(s) and excising the cassette from the engineered genetic construct (and/or excising heterologous nucleic acid in the cell).
• the methods further comprise exposing the subject to a counterselective agent and killing cells that express the counterselectable marker.
• less than 20% of the cells of the population comprise the cassette following the step of exposing the subject to a counterselective agent. In some embodiments, less than 15% of the cells of the population comprise the cassette following the step of exposing the subject to a counterselective agent. In some embodiments, less than 10% of the cells of the population comprise the cassette following the step of exposing the subject to a counterselective agent. In some embodiments, less than 5% (e.g., 4%, 3%, 2% or 1%) of the cells of the population comprise the cassette following the step of exposing the subject to a counterselective agent.
• methods may include delivering to a cell any of the engineered constructs of the present disclosure.
• any of the cells, as provided herein may be delivered to a subject, such as a human subject.
• Engineered genetic constucts may be delivered to cells using a viral delivery system (e.g., retroviral, adenoviral, adeno-association, helper-dependent adenoviral systems, hybrid adenoviral systems, herpes simplex, pox virus, lentivirus, Epstein-Barr virus) or a non-viral delivery system (e.g., physical: naked DNA, DNA bombardment, electroporation, hydrodynamic, ultrasound or magnetofection; or chemical: cationic lipids, different cationic polymers or lipid polymer) (Nayerossadat N et al. Adv Biomed Res. 2012; 1: 27,
• a viral delivery system e.g., retroviral, adenoviral, adeno-association, helper-dependent adenoviral systems, hybrid adenoviral systems, herpes simplex, pox virus, lentivirus, Epstein-Barr virus
• a non-viral delivery system e
• the non-viral based deliver system is a hydrogel-based delivery system (see, e.g., Brandl F, et al. Journal of Controlled Release, 2010, 142(2): 221-228, incorporated herein by reference).
• Engineered genetic constructs and/or cells may be delivered to a subject (e.g., a mammalian subject, such as a human subject) by any in vivo delivery method known in the art.
• a subject e.g., a mammalian subject, such as a human subject
• engineered genetic constructs and/or cells may be delivered intravenously.
• engineered genetic constructs and/or cells are delivered in a delivery vehicle (e.g., non-liposomal nanoparticle or liposome).
• engineered genetic constructs and/or cells are delivered systemically to a subject having a cancer or other disease and activated (transcription is activated) specifically in cancer cells or diseased cells of the subject.
• An engineered genetic construct comprising a cassette that comprises:
• cassette is flanked by cognate recombinase recognition sites.
• nucleic acid comprises RNA, DNA or a combination of RNA and DNA.
• RNA is selected from short-hairpin RNAs, short interfering RNAs and micro RNAs.
• An engineered genetic construct comprising a cassette that comprises:
• cassette is flanked by recombinase recognition sites cognate to the different recombinases.
• a vector comprising the engineered genetic construct of any one of paragraphs 1-22.
• a cell comprising the engineered genetic construct of any one of paragraphs 1-22.
• a cell comprising the vector of paragraph 23 or 24.
• stem cell selected from mesenchymal stem cells, hematopoietic stem cells, embryonic stem cells, and pluripotent stem cells.
• the immune cell is selected from natural killer (NK) cells, NKT cells, mast cells, eosinophils, basophils, macrophages, neutrophils, dendritic cells, T cells and B cells.
• NK natural killer
• NKT cells NKT cells
• mast cells eosinophils, basophils, macrophages, neutrophils, dendritic cells, T cells and B cells.
• T cell is selected from CD8+ T cells, CD4+ T cells, gamma-delta T cells, and T regulatory cells.
• T cell is a chimeric antigen receptor (CAR) T cell or an engineered T cell receptor (TCR) cell.
• CAR chimeric antigen receptor
• TCR engineered T cell receptor
• composition comprising the engineered genetic construct of any one of paragraphs 1-22.
• composition comprising the vector of paragraph 23 or 24.
• composition comprising the cell of any one of paragraphs 25-32.
• kit comprising the engineered genetic construct of any one of paragraphs 1-22 and at least one inducer agent that modulates activity of the inducible promoter(s) of (a).
• kits comprising the vector of paragraph 23 or 24 and at least one inducer agent that modulates activity of the inducible promoter(s) of (a).
• a method comprising introducing into a cell the engineered genetic construct of any one of paragraphs 1-24, wherein the product of interest aids in differentiation, expansion or phenotypic maintenance (persistence) of the cell.
• a method comprising introducing into a cell the engineered genetic construct of any one of paragraphs 1-24, wherein the product of interest is a therapeutic or prophylactic molecule.
• a method comprising delivering to a subject the cell of any one of paragraphs 25-32.
• An engineered genetic construct comprising a cassette that comprises:
• engineered genetic construct comprises cognate nuclease recognition sites, optionally flanking the cassette.
• RNA-guided nucleases are selected from Cas9 nucleases and Cpf 1 nucleases.
• nucleic acid comprises RNA, DNA or a combination of RNA and DNA.
• RNA is selected from short-hairpin RNAs, short interfering RNAs and micro RNAs.
• An engineered genetic construct comprising a cassette that comprises:
• cassette is flanked by nuclease recognition sites cognate to the different nucleases.
• a vector comprising the engineered genetic construct of any one of paragraphs 48-69.
• a cell comprising the engineered genetic construct of any one of paragraphs 48-69.
• a cell comprising the vector of paragraph 70 or 71.
• stem cell is selected from mesenchymal stem cells, embryonic stem cells, and pluripotent stem cells.
• the immune cell is selected from natural killer (NK) cells, NKT cells, mast cells, eosinophils, basophils, macrophages, neutrophils, dendritic cells, T cells and B cells.
• NK natural killer
• NKT cells NKT cells
• mast cells eosinophils
• macrophages neutrophils
• dendritic cells T cells and B cells.
• T cell is selected from CD8+ T cells, CD4+ T cells, gamma-delta T cells, and T regulatory cells.
• T cell is a chimeric antigen receptor (CAR) T cell or an engineered T cell receptor (TCR) cell.
• CAR chimeric antigen receptor
• TCR engineered T cell receptor
• composition comprising the engineered genetic construct of any one of paragraphs D1-D22.
• composition comprising the vector of paragraph 70 or 71.
• composition comprising the cell of any one of paragraphs 72-79.
• a kit comprising the engineered genetic construct of any one of paragraphs 48-69 and at least one inducer agent that modulates activity of the inducible promoter(s) of (a).
• kits comprising the vector of paragraph 70 or 71 and at least one inducer agent that modulates activity of the inducible promoter(s) of (a).
• a method comprising introducing into a cell the engineered genetic construct of any one of paragraphs 48-71, wherein the product of interest aids in differentiation, expansion or phenotypic maintenance (persistence) of the cell.
• a method comprising introducing into a cell the engineered genetic construct of any one of paragraphs 48-71, wherein the product of interest is a therapeutic or prophylactic molecule.
• a method comprising delivering to a subject the cell of any one of paragraphs 72-79.
• An engineered cell comprising: (a) a nucleic acid comprising a promoter operably linked to a nucleotide sequence encoding a ligand-dependent chimeric recombinase; and
• nucleic acid of (b) a nucleic acid comprising a promoter operably linked to a nucleotide sequence encoding a product of interest, wherein the nucleic acid of (b) is flanked by cognate recombinase recognition sites.
• nucleic acid comprises RNA, DNA or a combination of RNA and DNA.
• RNA is selected from short-hairpin RNAs, short interfering RNAs and micro RNAs.
• nucleic acid of (b) further comprises a nucleotide sequence encoding counterselectable marker.
• the engineered cell of paragraph 108, wherein the stem cell is selected from mesenchymal stem cells, embryonic stem cells, and pluripotent stem cells.
• the engineered cell of paragraph 110, wherein the immune cell is selected from natural killer (NK) cells, NKT cells, mast cells, eosinophils, basophils, macrophages, neutrophils, dendritic cells, T cells and B cells.
• NK natural killer
• T cell is selected from CD8+ T cells, CD4+ T cells, gamma-delta T cells, and T regulatory cells.
• T cell is a chimeric antigen receptor (CAR) T cell or an engineered T cell receptor (TCR) cell.
• CAR chimeric antigen receptor
• TCR engineered T cell receptor
• composition comprising the engineered cell of any one of paragraphs 95-113.
• a kit comprising:
• nucleic acid comprising a promoter operably linked to a nucleotide sequence encoding a ligand-dependent chimeric recombinase
• nucleic acid of (b) a nucleic acid comprising a promoter operably linked to a nucleotide sequence encoding a product of interest, wherein the nucleic acid of (b) is flanked by cognate recombinase recognition sites.
• a method comprising culturing the engineered cell of any one of paragraphs 95-113 and producing the product of interest.
• An engineered cell comprising:
• nucleic acid comprising a promoter operably linked to a nucleotide sequence encoding a first fragment of a recombinase
• nucleic acid of (b) a nucleic acid comprising a promoter operably linked to a nucleotide sequence encoding a second fragment of a recombinase, wherein the first fragment and the second fragment when combined form a full-length functional recombinase; and (c) a nucleic acid comprising a promoter operably linked to a nucleotide sequence encoding a product of interest, wherein the nucleic acid of (c) is flanked by cognate recombinase recognition sites.
• nucleic acid comprises RNA, DNA or a combination of RNA and DNA.
• RNA is selected from short-hairpin RNAs, short interfering RNAs and micro RNAs.
• the engineered cell of paragraph 133, wherein the stem cell is selected from mesenchymal stem cells, embryonic stem cells, and pluripotent stem cells.
• the immune cell is selected from natural killer (NK) cells, NKT cells, mast cells, eosinophils, basophils, macrophages, neutrophils, dendritic cells, T cells and B cells.
• T cell is a chimeric antigen receptor (CAR) T cell or an engineered T cell receptor (TCR) cell.
• CAR chimeric antigen receptor
• TCR engineered T cell receptor
• composition comprising the engineered cell of any one of paragraphs 121-138.
• a kit comprising:
• nucleic acid comprising a promoter operably linked to a nucleotide sequence encoding a first fragment of a recombinase
• nucleic acid comprising a promoter operably linked to a nucleotide sequence encoding a second fragment of a recombinase, wherein the first fragment and the second fragment when combined form a full-length functional recombinase;
• nucleic acid of (c) a nucleic acid comprising a promoter operably linked to a nucleotide sequence encoding a product of interest, wherein the nucleic acid of (c) is flanked by cognate recombinase recognition sites.
• a method comprising culturing the engineered cell of any one of paragraphs 121- 138 and producing the product of interest.
• a cassette comprising (a) a promoter operably linked to a nucleotide sequence encoding a first product of interest upstream from (b) a promoter operably linked to a nucleotide sequence encoding a second product of interest and optionally a counterselectable marker, wherein expression or activity of the first product of interest is activatable (inducible), and wherein the first product of interest modulates excision or degradation of the cassette.
• a cell comprising the engineered genetic construct of any one of paragraphs 146-152.
• composition or kit comprising the engineered genetic construct of any one of paragraphs 146-152or the cell of paragraph K8
• An engineered genetic circuit comprising:
• recombinase proteins are used to excise heterologous genetic cassettes (FIG. 1). Control of recombinase activity is achieved through inducible
• recombinase expression is controlled through the use of doxycycline, phloretin (9), vanillic acid (13), macrolides (12), or other inducers.
• a recombinase can be fused to a nuclear receptor so the recombinase does not catalyze recombination in the absence of an inducer agent.
• recombinase Upon addition of an inducer agent, such as 40HT, the recombinase translocates into the nucleus and catalyzes recombination (14, 15).
• an inducer agent such as 40HT
• the recombinase translocates into the nucleus and catalyzes recombination (14, 15).
• Cre, Flp, and PhiC31 This approach has been validated for Cre, Flp, and PhiC31 and is extensible to additional integrases (15-17).
• a recombinase protein can be split into two fragments that are inactive on their own, but can be dimerized by the addition of a small-molecule (e.g., rapamycin analogs) due to interactions with two protein domains, each fused to one of the fragments (e.g., FKBP and FRB) (18).
• This approach has been demonstrated for Cre and is extensible to other recombinases.
• nuclease proteins such as meganucleases or CRISPR-Cas nucleases
• FGS. 2 targeted double-stranded breaks
• These nucleases are programmed to cut at specific sites that surround our heterologous DNA constructs, which has been shown to significantly enhance the efficiency of genetic deletion (20).
• the addition of donor DNA that is homologous to the flanking ends of region to be deleted can be used to enhance deletion efficiencies.
• effectors are placed under the control of inducible promoters, in some embodiments.
• counterselectable markers such as cytosine deaminase or thymidine kinase
• cytosine deaminase or thymidine kinase are used to kill cells that still contain heterologous DNA following an excision or degradation reaction (see FIG. 3).
• yeast or bacterial cytosine deaminase converts 5-fluorocytosine (5-FC) into 5-fluorouracil (5-FU), which can result in cell toxicity (21, 22).
• HSV thymidine kinase HSV thymidine kinase (HSV-tk) converts ganciclovir into a toxic product and can be used to trigger cell killing, although toxicity can be variable depending on cell background (23).
• An inducible kill switch may be used, which expresses the alpha chain of diphtheria toxin under the control of IPTG to trigger cell death (24).
• the inducible activation of toxins through dimerization via small molecules can be used to enhance cell killing.
• transient 293FT cell transfection assays were performed to test recombinase activity of various tyrosine recombinases.
• 293FT cells were transiently transfected with an equal ratio of reporter plasmid, recombinase plasmid, and a transfection marker plasmid (e.g., a plasmid encoding BFP). The cells were assayed for GFP fluorescence 24 hours post transfection and gated for BFP expression.
• FIGS. 6 and 7 show data from the transient 293FT cell transfection assays. The top graph represents % GFP+ cells, and the bottom graph represents the median of the GFP mean fluorescence intensity of the GFP+ cells.
• transient 293FT cell transfection assays were performed to test recombinase activity of various serine integrases.
• 293FT cells were transiently transfected with an equal ratio of reporter plasmid, recombinase plasmid, and a transfection marker plasmid (e.g., a plasmid encoding BFP). The cells were assayed for GFP fluorescence 24 hours post transfection and gated for BFP expression.
• FIGS. 9 and 10 show data from the transient 293FT cell transfection assays. The top graph represents % GFP+ cells, and the bottom graph represents the median of the GFP mean fluorescence intensity of the GFP+ cells.
• an entry vector encoding a recombinase-based excision construct is integrated into a pre-engineered 293FT landing pad cell line that expresses YFP and hygromycin. See FIG. 11.
• FIG. 12 shows successful integration of a GFP reporter into the 293FT landing pad cell line. Upon integration, cells express GFP and simultaneously lose expression of YFP. Selection pressure with puromycin removes unintegrated cells.
• Example 8
• This Examples outlines a method for excising genomically-integrated constructs.
• An entry vector encoding a recombinase-based excision construct is integrated into a pre- engineered 293FT landing pad cell line.
• Integrated cell lines are transiently transfected with a recombinase-expressing plasmid and a reporter plasmid (e.g., expressing BFP) and assayed for GFP expression over time.
• a counter-selection marker CSM is used to kill off cells that retain the integrated construct. See FIG. 13.
• a prodrug was applied to kill off cells that retained the pENTR_B3RT excision construct.
• the counter selection marker CSM
• CMV counter selection marker
• the cells were treated with 0.5, 1, 2, and 5 ⁇ GCV for 7 days, and GFP expression was assayed over time. The histograms represent the % of GFP- and % of GFP+ cells. See FIG. 15.
• GCV was applied, as above, to kill off cells that retained the pENTR_FRT excision construct. See FIG. 16.
• the pENTR_B3RT_FRT recombinase-based excision construct encodes the construct B 3 RT_FRT_iC asp9_S V40p A_FRT_B 3 RT_EGFP_B GHp A, in which B3RT and FRT are recombination sequences for B3 and Flp, respectively; and iCasp9 is a counter selection marker (CSM). See FIG. 19
• FIG. 17 shows an example of a system in which guide RNAs (gRNAs) cleave and remove a genomically-integrated circuit.
• gRNAs guide RNAs
• the gRNAs target the 5'-UTR and 3'- UTR if a YFP reporter that has been stably integrated into cells.
• a transient transfection assay was performed to test the removal of a genomically- integrated circuit using CRISPR/Cas9.
• Vectors encoding a single gRNA and Cas9 were co- transfected along with a reporter plasmid (e.g., expressing BFP) into a cell line that expresses YFP.
• a reporter plasmid e.g., expressing BFP
• two vectors encoding different gRNAs were transfected along with a reporter plasmid.
• the cell populations were gated for BFP expression, and the % of YFP+ cells were plotted over time. Different combinations of gRNAs may be used to remove YFP. See FIG. 18.
• MethHC a database of DNA methylation and gene expression in human cancer. Nucleic Acids Res. 2015 ;43 (Database issue):D856-61. doi: 10.1093/nar/gkul l51. PubMed PMID: 25398901; PMCID: PMC4383953.
• Landgraf P Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V, Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B, Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G, Frezzetti D, Trompeter HI, Hornung V, Teng G,

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