Patent Application
20220307056
The application refers to sequences disclosed in a txt file named 574547SEQTXT.TXT, of 395,981 bytes, created Mar. 21, 2022, incorporated by reference.
The tet operon confers tetracycline resistance in bacteria. The operon includes tet-operator sites, a promoter, and a bicistronic transcriptional unit encoding a tet-repressor and a tetracycline-resistance protein. In the absence of tetracycline, the tet-repressor binds to the tet-operator sites inhibiting expression from the promoter of both the tet-repressor and tetracycline-resistance protein. When tetracycline is present it binds to the tet-repressor inhibiting its own binding to the tet-operators. Tetracycline-resistance protein is then expressed as is more tet-repressor, which again shuts downs expression of the tet operon when the tetracycline has been exhausted.
The components of the tet operon have been incorporated into various inducible expression systems for regulating expression of a coding segment of interest (see, e.g., U.S. Pat. Nos. 5,814,618, 5,654,168, 5,650,298 and 5,464,758 and 9,181,556). Generally, such systems have two components. A first construct includes one or more tet-operators, a promoter and a coding segment of interest. A second construct includes a promoter and a tet-repressor (or modified form thereof), sometimes fused to a transcriptional activation domain. The presence of tetracycline controls binding of the tet-repressor to the tet-operators, and consequently expression of the coding segment.
A hybrid mouse-human CMV promoter effective for transcriptional initiation comprising a segment of a mouse CMV promoter of SEQ ID NO:16 upstream from a segment of a human CMV promoter of SEQ ID NO:13 or 14, wherein the hybrid promoter lacks a CG motif at positions corresponding to positions 42 and 43 of SEQ ID NO:13 (human CMV). Optionally, the hybrid promoter comprises a contiguous segment of the mouse CMV promoter of SEQ ID NO:16 and a contiguous segment of the human CMV promoter of SEQ ID NO:13, wherein the junction between contiguous segments is within the sequence ACGTCAATGGGA, which is common to the mouse and human CMV promoter sequences. Optionally, the hybrid promoter of claim 2 having a sequence comprising SEQ ID NO:10. Optionally, the hybrid mouse-human-CMV promoter of claim 3 in operable linkage with first and second tet-operators. Optionally the hybrid mouse-human CMV promoter in in operable linkage with at least one cumate operator. Optionally, each cumate operator has a sequence selected independently from any of SEQ ID NOS: 156-158. Optionally, the hybrid mouse-human CMV promoter is in operable linkage with a coding segment to be expressed, optionally wherein the coding segment comprises an open reading frame encoding a polypeptide. Optionally, at least first and second tet-operators are situated between the promoter and coding segment. Optionally, the coding segment encodes a protein. Optionally, the protein is a membrane protein. Optionally, the protein is a therapeutic protein.
The invention further provides a nucleic acid comprising (a) the hybrid mouse-human CMV promoter as described above and (b) a promoter operably linked to a segment encoding a tet-repressor or cumate repressor. Optionally, the promoter of the second transcriptional unit is a weaker promoter than a human CMV promoter, for example, the promoter of the second construct is selected from SEQ ID NOS: 17-21, 33 or 34.
The invention further provides a transposon comprising a nucleic acid as described above flanked by inverted repeats of the transposon. Optionally, the transposon further comprises target sites flanking the inverted repeats. Optionally, the transposon is a piggyBac or piggyBac-like transposon.
The invention further provides a mouse-human-CMV promoter having a sequence comprising SEQ ID NO:12. Optionally, the hybrid mouse-human CMV promoter is in operable linkage with a coding segment to be expressed, optionally wherein the coding segment comprises an open reading frame encoding a polypeptide. Optionally, the coding segment encodes a protein, for example, a therapeutic protein.
The invention further provides a cell transformed with any of the nucleic acids or transposons described above. Optionally, the cell is mammalian.
The invention further provides a non-human animal transformed with any of the nucleic acids or transposons described above. Optionally, the non-human animal is transgenic.
The invention further provides a cell or nonhuman transgenic animal having a genome comprising (a) a hybrid mouse-human CMV promoter operably linked to at least two tet-operators and a coding segment, and (b) a promoter operably linked to a tet-repressor, wherein expression of the coding segment can be regulated by supplying tetracycline or doxycycline to the cell or nonhuman transgenic animal.
The invention further provides a cell or nonhuman transgenic animal having a genome comprising (a) a hybrid mouse-human CMV promoter operably linked to at least one cumate operators and a coding segment, and (b) a promoter operably linked to a cumate repressor, wherein expression of the coding segment can be regulated by supplying cumate or an analog to the cell or nonhuman transgenic animal.
The invention further provides a method for inducible expression of a coding segment comprising, providing a first transcriptional unit comprising in operable linkage a hybrid mouse-human CMV promoter comprising a segment of a mouse CMV promoter of SEQ ID NO: 16 upstream from a segment of a human CMV promoter of SEQ ID NO: 13, wherein the hybrid promoter lacks a CG motif at positions corresponding to positions 42 and 43 of SEQ ID NO:13 (human CMV), at least two tet-operators and a coding segment to be expressed, and a second transcriptional unit comprising in operable linkage a promoter and a segment encoding a tet-repressor, wherein the tet-repressor is expressed and in the absence of tetracycline or doxycycline, the tet-repressor binds to the tet-operators inhibiting expression of the coding segment, and in the presence of tetracycline or doxycycline, the tet-repressor binds to the tetracycline or doxycycline, which inhibits its binding to the tet-operators and thereby increasing expression of the open-reading frame.
The invention further provides a method for inducible expression of a coding segment comprising, providing a first transcriptional unit comprising in operable linkage a hybrid mouse-human CMV promoter comprising a segment of a mouse CMV promoter of SEQ ID NO: 16 upstream from a segment of a human CMV promoter of SEQ ID NO: 13, wherein the hybrid promoter lacks a CG motif at positions corresponding to positions 42 and 43 of SEQ ID NO:13 (human CMV), at least one cumate-operator(s) and a coding segment to be expressed, and a second transcriptional unit comprising in operable linkage a promoter and a segment encoding a cumate-repressor, wherein the cumate-repressor is expressed and in the absence of cumate, the cumate-repressor binds to the cumate-operator(s) inhibiting expression of the coding segment, and in the presence of cumate, the cumate-repressor binds to the cumate, which inhibits its binding to the cumate-operator(s) and thereby increasing expression of the open-reading frame.
Optionally, the first and second transcriptional units are components of the same contiguous DNA molecule. Optionally, the first and second transcriptional units are components of a transposon. Optionally, the transposon is a piggyBac or piggyBac-like transposon. Optionally, the method further comprises introducing the contiguous DNA molecule into a cell.
Optionally, the cell is mammalian. Optionally, the first and second transcriptional units integrate into the genome of the cell. Optionally, the method further comprises culturing the cell. Optionally, the method further comprises supplying tetracycline or doxycycline, or analog thereof, or cumate or an analog thereof to culture media of the cell.
The invention further provides a nucleic acid comprising a transcriptional unit comprising a promoter having a sequence comprising SEQ ID NO:24 in operable linkage with a heterologous coding segment.
Optionally, the promoter lacks a 5′ flanking sequence from a natural chimpanzee CMV promoter with which it is naturally associated. Optionally, the nucleic acid further comprises at least first and second tet-operators in operable linkage with the promoter. Optionally, the first and second tet-operators are 5′ to the promoter. Optionally, the nucleic acid comprises three, six or eight tet-operators 5′ to the promoter. Optionally, the nucleic acid further comprises at least one cumate operator in operable linkage with the promoter. Optionally, the at least one cumate operators is 5′ to the promoter. Optionally, the nucleic acid comprises three, six or eight cumate-operator 5′ to the promoter.
Optionally, the nucleic acid comprises any of SEQ ID NOS: 164-166 providing the promoter and cumate operators. Optionally, the nucleic acid comprises any of SEQ ID NOS: 167-169 providing the promoter, the operators and a 5′ UTR. Optionally, the three, six or eight tet-operators are separated by spacers of 10-25 nucleotides. Optionally, at least some of the spacers differ from one another. Optionally, the nucleic acid further comprises a segment encoding a 5′ UTR, for example a 5′ UTR having a sequence comprising SEQ ID NO:29. Optionally, the nucleic acid further comprises a second transcriptional unit comprising a second promoter operably linked to a segment encoding a tet-repressor effective to bind a tet-operator in the absence of tetracycline or doxycycline or modified-tet-repressor effective to bind a tet-operator in the presence of tetracycline or doxycycline, wherein the tet-repressor or modified tet-repressor is fused to a transcriptional activator. Optionally, the nucleic acid further comprises a second transcriptional unit comprising a second promoter operably linked to a segment encoding a cumate-repressor effective to bind a cumate-operator in the absence of cumate or modified-cumate-repressor effective to bind a cumate-operator in the presence of cumate, wherein the cumate-repressor or modified cumate-repressor is fused to a transcriptional activator. Optionally, the second transcriptional unit further comprises a polyadenylation sequence. Optionally, the tet-repressor has an amino acid sequence comprising SEQ ID NO:5. Optionally, the modified tet-repressor has an amino acid sequence comprising SEQ ID NO: 6. Optionally, the cumate repressor has an amino acid sequence comprising SEQ ID NO:170. Optionally, the modified cumate-repressor linked to the transcriptional activator has an amino acid sequence comprising SEQ ID NO:172. Optionally, the coding segment encodes a protein, for example a membrane protein, or a therapeutic protein.
The invention further provides a transposon comprising a nucleic acid as described above flanked by inverted repeats of the transposon. Optionally, the transposon further comprises target sites flanking the inverted repeats. Optionally, the transposon is a piggyBac or piggyBac-like transposon.
The invention further provides a cell transformed with the nucleic acid or transposon as described above. Optionally, the cell is mammalian.
The invention further provides a non-human animal transformed with a nucleic acid or transposon as described above. Optionally, the non-human animal is transgenic.
The invention further provides a cell or nonhuman transgenic animal having a genome comprising (a) a promoter having a sequence comprising SEQ ID NO:24 operably linked to at least two tet operons and a coding segment, and (b) a promoter operably linked to a tet-repressor or modified tet-repressor fused to transcriptional activation domain, wherein expression of the coding segment can be regulated by supplying tetracycline or doxycycline to the cell or nonhuman transgenic animal. The invention further provides a cell or nonhuman transgenic animal having a genome comprising (a) a promoter having a sequence comprising SEQ ID NO:24 operably linked to at least two cumate operators and a coding segment, and (b) a promoter operably linked to a cumate-repressor or modified cumate-repressor fused to transcriptional activation domain, wherein expression of the coding segment can be regulated by supplying cumate to the cell or nonhuman transgenic animal.
The invention further provides a method for inducible expression of a coding segment comprising; providing a first transcriptional unit comprising in operable linkage with a least two tet-operators, a promoter having a nucleotide sequence comprising SEQ ID NO: 24 and a coding segment, and a second transcriptional unit comprising in operable linkage a promoter, and a segment encoding a tet-repressor or modified tet-repressor fused to a transcriptional activator, wherein the tet-repressor fused to the transcriptional activator is expressed and in the absence of tetracycline or doxycycline the tet-repressor binds to the at least two tet-operators and expression of the coding segment is increased, or the modified tet-repressor fused to the transcriptional activator is expressed and in the presence of tetracycline or doxycycline the modified tet-repressor binds to the at least two tet-operators and expression of the coding segment is increased. The invention further provides a method for inducible expression of a coding segment comprising; providing a first transcriptional unit comprising in operable linkage with a least two cumate-operators, a promoter having a nucleotide sequence comprising SEQ ID NO: 24 and a coding segment, and a second transcriptional unit comprising in operable linkage a promoter, and a segment encoding a cumate-repressor or modified cumate-repressor fused to a transcriptional activator, wherein the cumate-repressor fused to the transcriptional activator is expressed and in the absence of cumate the cumate-repressor binds to the at least two tet-operators and expression of the coding segment is increased, or the modified cumate-repressor fused to the transcriptional activator is expressed and in the presence of tetracycline or doxycycline the modified cumate-repressor binds to the at least two cumate-operators and expression of the coding segment is increased. Optionally, the first and second transcriptional units are components of the same contiguous DNA molecule. Optionally, the first and second transcriptional units are components of a transposon. Optionally, the transposon is a piggyBac or piggyBac-like transposon. Optionally, the method further comprises comprising introducing the contiguous DNA molecule into a cell. Optionally, the cell is a mammalian cell. Optionally, the first and second transcriptional units integrate into the genome of the cell. Optionally, the method further comprises culturing the cell.
Optionally, the method further comprises supplying tetracycline or doxycycline or analog thereof, or cumate or an analog thereof to culture media of the cell.
The singular forms “a,” “an,” and “the” include plural references unless the context clearly dictates otherwise. Thus, for example, reference to “a nucleic acid” includes a plurality of nucleic acids, reference to “a substrate” includes a plurality of such substrates, reference to “a variant” includes a plurality of variants, and the like.
Terms such as “connected,” “attached,” “linked,” and “conjugated” are used interchangeably to encompass direct as well as indirect connection, attachment, linkage or conjugation unless the context indicates otherwise.
When a range of values is recited, it is to be understood that each intervening integer value, and each fraction thereof, between the recited upper and lower limits of that range is also specifically disclosed, along with each subrange between such values. The upper and lower limits of any range can independently be included in or excluded from the range, and each range where either, neither or both limits are included is also encompassed within the invention. When a value being discussed has inherent limits, for example where a component can be present at a concentration of from 0 to 100%, or where the pH of an aqueous solution can range from 1 to 14, those inherent limits are specifically disclosed. When a value is explicitly recited, it is to be understood that values which are about the same quantity or amount as the recited value are also within the scope of the invention. When a combination is disclosed, each sub combination of the elements of that combination is also specifically disclosed and is within the scope of the invention. Conversely, when different elements or groups of elements are individually disclosed, combinations thereof are also disclosed. When any element of an invention is disclosed as having a plurality of alternatives, examples of that invention in which each alternative is excluded singly or in any combination with the other alternatives are also hereby disclosed; more than one element of an invention can have such exclusions, and all combinations of elements having such exclusions are hereby disclosed.
Unless defined otherwise, all technical and scientific terms used have their ordinary meaning. Singleton, et. al., Dictionary of Microbiology and Molecular Biology, 2nd Ed., John Wiley and Sons, New York (1994), and Hale & Marham, The Harper Collins Dictionary of Biology, Harper Perennial, NY, 1991 provide guidance as to ordinary meaning.
Unless otherwise indicated, nucleic acids are written left to right in 5′ to 3′ orientation; amino acid sequences are written left to right in amino to carboxy orientation, respectively.
If a DNA sequence is provided, the specification should be understood as additional disclosing the sequence of the RNA, which will be the same with the exception that thymine (T) is replaced with uracil (U), and vice versa.
Nucleic acids are preferably provided with codon preferences for a cell in which expression is intended. The term “codon usage” or “codon bias” refers to the relative frequencies with which different synonymous codons are used to encode an amino acid within an open reading frame. A nucleic acid sequence having codon preferences for a particular target cell has a balance of synonymous codon choices that result in efficient translation in that cell type. This balance is often not calculable from observed genomic codon frequencies, but must be empirically determined, for example as described in U.S. Pat. Nos. 7,561,972 and 7,561,973 and 8,401,798 and in Welch et. al. (2009) “Design Parameters to Control Synthetic Gene Expression in Escherichia coli”. PLoS ONE 4(9): e7002. https://doi.org/10.1371/journal.pone.0007002. A nucleic acid originally isolated from one cell type to be introduced into a target cell of another type can undergo selection of codon preferences for the target site cell such that at least 1 and sometimes, 5, 20, 15, 20, 50, 100 or more choices among synonymous codons differ between the nucleic acid introduced into the target cell from the original nucleic acid.
Two nucleic acids are “complementary” if the bases of one hydrogen bond to the bases of the other. For perfect complementarity, adenine (A) in the first nucleic acid must correspond with thymine (T) (or uracil for RNA) in the second (and vice versa), and cytosine (C) in the first nucleic acid must correspond with guanine (G) in the second (and vice versa). The two nucleic acid s must also be antiparallel. If two nucleic acid are complementary, one may be described as the “reverse complement” of the other to indicate that their bases are complementary when one is in the 5′ to 3′ direction and the other is in the 3′ to 5′ direction. When one nucleic acid sequence is described as complementary to another, it is intended to indicate that the sequences are antiparallel and able to base-pair with one another.
The “configuration” of a nucleic acid refers to the presence, order and direction of functional segments with the nucleic acid.
A ‘transposase’ is a polypeptide that catalyzes the excision of a corresponding transposon from a donor nucleic acid, for example a vector, and (providing the transposase is not integration-deficient) the subsequent integration of the transposon into a target nucleic acid.
“Transposition” refers to action of a transposase in excising a transposon from one nucleic acid and then integrating it, either into a different site in the same nucleic acid, or into a second nucleic acid.
A “transposon” means a nucleic acid that can be excised from a first nucleic acid, for instance, a vector, and be integrated into a second position in the same nucleic acid, or into a second nucleic acid, for instance, the genomic or extrachromosomal DNA of a cell, by the action of a corresponding trans-acting transposase. A transposon comprises a first transposon end and a second transposon end, which are nucleic acid sequences recognized by and transposed by a transposase. The first and second transposon ends include inverted terminal repeats. Two copies of a transposon target site are usually present on the outside of the transposon ends (one on each side). A transposon usually further comprises a nucleic acid between the two transposon ends, which along with the two transposon ends is transposed by the action of the transposase. In natural transposons, the nucleic acid between the transposon ends is typically a corresponding transposase. Transposons of the present invention are “synthetic transposons” comprising a heterologous nucleic acid, which is transposable by virtue of its juxtaposition between two transposon ends. Synthetic transposons may or may not further comprise flanking nucleic acid sequence(s) outside the transposon ends, such as a sequence encoding a transposase, a vector sequence or sequence encoding a selectable marker.
A “transposon end” means the cis-acting nucleotide sequences that are sufficient for recognition by and transposition by a corresponding transposase. Transposon ends of piggyBac-like transposons comprise perfect or imperfect repeats such that the respective repeats in the two transposon ends are reverse complements of each other. These are referred to as inverted terminal repeats (ITR) or terminal inverted repeats (TIR). A transposon end may or may not include additional sequence proximal to the ITR that promotes or augments transposition.
The terms “corresponding transposon” and “corresponding transposase” are used to indicate an activity relationship between a transposase and a transposon. A transposase transposes its corresponding transposon. Many transposases correspond with a single transposon, and many transposons correspond with a single transposase. The term “orthogonal” refers to a lack of interaction between two systems. A first transposon and its corresponding first transposase and a second transposon and its corresponding second transposase are orthogonal if the first transposase does not excise or transpose the second transposon and the second transposase does not excise or transpose the first transposon.
A “target site” for a transposase is a site or sequence in a molecule into which a transposon can be inserted by a transposase. The piggyBac transposase from Trichoplusia ni inserts its transposon predominantly into the target sequence 5′-TTAA-3′. Other useable target sequences for piggyBac transposons are 5′-CTAA-3′, 5′-TTAG-3′, 5′-ATAA-3′, 5′-TCAA-3′, 5′-AGTT-3′, 5′-ATTA-3′, 5′-GTTA-3′, 5′-TTGA-3′, 5′-TTTA-3′, 5′-TTAC-3′, 5′-ACTA-3′, 5′-AGGG-3′, 5′-CTAG-3′, 5′-GTAA-3′, 5′-AGGT-3′, 5′-ATCA-3′, 5′-CTCC-3′, 5′-TAAA-3′, 5′-TCTC-3′, 5′-TGAA-3′, 5′-AAAT-3′, 5′-AATC-3′, 5′-ACAA-3′, 5′-ACAT-3′, 5′-ACTC-3′, 5′-AGTG-3′, 5′-ATAG-3′, 5′-CAAA-3′, 5′-CACA-3′, 5′-CATA-3′, 5′-CCAG-3′, 5′-CCCA-3′, 5′-CGTA-3′, 5′-CTGA-3′, 5′-GTCC-3′, 5′-TAAG-3′, 5′-TCTA-3′, 5′-TGAG-3′, 5′-TGTT-3′, 5′-TTCA-3′, 5′-TTCT-3′ and 5′-TTTT-3′ (Li et al., 2013. Proc. Natl. Acad. Sci vol. 110, no. 6, E478-487) and 5′-TTAT. PiggyBac-like transposases transpose their transposons using a cut-and-paste mechanism, which results in duplication of their 4 base pair target sequence on insertion into a DNA molecule. The target sequence is thus found on each side of an integrated piggyBac-like transposon.
A “coupling element” or “translational coupling element” means a DNA sequence that allows the expression of a first polypeptide to be linked to the expression of a second polypeptide. Internal ribosome entry site elements (IRES elements) and cis-acting hydrolase elements (CHYSEL elements) are examples of coupling elements.
A DNA sequence, segment of DNA, RNA sequence or RNA sequence means a contiguous nucleic acid sequence, which can be an oligonucleotide of 2 to 20 nucleotides in length to a full-length genomic sequence of thousands or hundreds of thousands of base pairs.
A vector is a nucleic acid that facilitates any of transfection, integration, replication or expression of a coding segment incorporated into the vector. An expression vector is a vector comprising a promoter which has been or can be operably linked to a coding segment to be expressed. Transfection of the expression vector into a cell allows the cell to express the coding segment. An expression vector can be a genetically engineered plasmid, virus, recombinant virus, or an artificial chromosome derived from, for example, a bacteriophage, adenovirus, adeno-associated virus, retrovirus, lentivirus, poxvirus, or herpesvirus. Such expression vectors can include sequences from bacteria, viruses or phages. Such vectors include chromosomal, episomal and virus-derived vectors, for example, vectors derived from bacterial plasmids, bacteriophages, yeast episomes, yeast chromosomal elements, and viruses, vectors derived from combinations thereof, such as those derived from plasmid and bacteriophage genetic elements, cosmids and phagemids.
A “gene” refers to a transcriptional unit including a promoter and sequence to be expressed from it as an RNA or polypeptide. The sequence to be expressed can be genomic or cDNA or one or more non-coding RNAs including siRNAs or microRNAs among other possibilities. Other elements, such as introns, and other regulatory sequences may or may not be present.
A gene transfer system refers to an expression vector and optionally one or more other features to facilitate gene transfer. For example, a gene transfer system may comprise an expression vector and a lipid or viral packaging mix for enabling a first nucleic acid to enter a cell, or it may comprise a nucleic acid that includes a transposon and a second nucleic acid encoding a corresponding transposase for genomic integration of the transposon. A transposase and transposon of a gene transfer system may be on the same nucleic acid molecule or on different nucleic acid molecules.
Two elements are “heterologous” to one another if not naturally associated. For example, a coding segment linked to a heterologous promoter means a promoter other than that which naturally drives expression of the coding segment. A heterologous nucleic acid flanked by transposon ends or ITRs means a heterologous nucleic acid not naturally flanked by those transposon ends or ITRs, such as a nucleic acid encoding a polypeptide other than a transposase, including an antibody heavy or light chain. A nucleic acid is heterologous to a cell if not naturally found in the cell or if naturally found in the cell but in a different location (e.g., episomal or different genomic location) than the location described.
A “hyperactive” transposase is a transposase that is more active than the naturally occurring transposase from which it is derived. “Hyperactive” transposases are thus not naturally occurring sequences.
An “IRES” or “internal ribosome entry site” means a specialized sequence that directly promotes ribosome binding, independent of a cap structure.
An ‘isolated’ object, such as a polypeptide or nucleic acid, means the object has been either removed from its natural environment, produced using recombinant techniques, or chemically or enzymatically synthesized. Objects can also be purified, that is, provided at least 90%, 95% or 99% free w/w of other materials with which they are naturally associated or are used in their production or purification. The terms isolated and purified do not exclude presence of other components not naturally associated with the object that facilitate its use, such as a heterologous promoter for a coding segment, or pharmaceutical excipient.
Unless otherwise apparent from the context, the terms “nucleoside” and “nucleotide” include those moieties which contain not only the standard purine and pyrimidine bases, but also other heterocyclic bases which have been modified. Such modifications include methylated purines or pyrimidines, acylated purines or pyrimidines, or other heterocycles. Modified nucleosides or nucleotides can also include modifications on the sugar moiety, for example, where one or more of the hydroxyl groups are replaced with halogen, aliphatic groups, or is functionalized as ethers, amines, or the like. The term “nucleotidic unit” encompasses nucleosides and nucleotides.
An “Open Reading Frame” or “ORF” means a portion of a nucleic acid that, when translated into amino acids, contains no stop codons. An open reading frame presumptively encodes a polypeptide. The genetic code reads DNA sequences in groups of three base pairs, which means that a double-stranded DNA molecule can read in any of six possible reading frames-three in the forward direction and three in the reverse. An ORF typically also includes an initiation codon at which translation may start.
The term “operably linked” refers to functional linkage between two sequences such that one sequence operationally modifies the behavior of the other. For example, a promoter is operably linked to a coding segment when the promoter can initiate transcription of the coding segment, optionally with subsequent translation of the transcript. A promoter is operably linked to one or more tet-operators, when initiation of transcription by the promoter can be regulated by binding of a tet-repressor or modified tet-repressor to the tet-operon. A mature polypeptide and signal peptide are operably linked when the signal peptide regulates secretion or subcellular location of the mature polypeptide.
The term “overhang” or “DNA overhang” means the single-stranded portion at the end of a double-stranded DNA molecule. Complementary overhangs are those which will base-pair with each other.
A “piggyBac-like transposase” means a transposase with at least 20% amino acid sequence identity as identified using the TBLASTP algorithm to the piggyBac transposase from Trichoplusia ni (SEQ ID NO:116), and as more fully described in Sakar, A. et. al., 2003. Mol. Gen. Genomics 270: 173-180. “Molecular evolutionary analysis of the widespread piggyBac transposon family and related ‘domesticated’ species”, and further characterized by a DDE-like DDD motif, with aspartate residues at positions corresponding to D268, D346, and D447 of Trichoplusia ni piggyBac transposase on maximal alignment. PiggyBac-like transposases are also characterized by their ability to excise their transposons precisely with a high frequency. A “piggyBac-like transposon” means a transposon having transposon ends which are the same or at least 80% and preferably at least 90, 95, 96, 97, 98, 99% or 100% identical to the nucleotide sequences of the transposon ends of a naturally occurring transposon that encodes a piggyBac-like transposase. A piggyBac-like transposon includes an inverted terminal repeat (ITR) sequence of approximately 12-16 bases at each end. These repeats may be identical at the two ends, or the repeats at the two ends may differ at 1 or 2 or 3 or 4 positions in the two ITRs. The transposon is flanked on each side by a 4 base sequence corresponding to the integration target sequence which is duplicated on transposon integration (the Target Site Duplication or Target Sequence Duplication or TSD). PiggyBac-like transposons and transposases occur naturally in a wide range of organisms including Argyrogramma agnate (GU477713), Anopheles gambiae (XP_312615; XP_320414; XP_310729), Aphis gossypii (GU329918), Acyrthosiphon pisum (XP_001948139), Agrotis ypsilon (GU477714), Bombyx mori (BAD11135), Ciona intestinalis (XP_002123602), Chilo suppressalis (JX294476), Drosophila melanogaster (AAL39784), Daphnia pulicaria (AAM76342), Helicoverpa armigera (ABS18391), Homo sapiens (NP_689808), Heliothis virescens (ABD76335), Macdunnoughia crassisigna (EU287451), Macaca fascicularis (AB179012), Mus musculus (NP_741958), Pectinophora gossypiella (GU270322), Rattus norvegicus (XP_220453), Tribolium castaneum (XP_001814566) and Trichoplusia ni (AAA87375) and Xenopus tropicalis (BAF82026), although transposition activity has been described for almost none of these.
A regulatory element such as promoter is active in a specified target cell, such as a mammalian cell, means a regulatory element configurable to result in a level of expression of at least 1 transcript and optionally at least ten, 100 or 1000 transcripts per cell in a mammalian cell into which the regulatory element has been introduced.
Sequence identity can be determined by aligning sequences using algorithms, such as BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package Release 7.0, Genetics Computer Group, 575 Science Dr., Madison, Wis.), using default gap parameters, or by inspection, and the best alignment (i.e., resulting in the highest percentage of sequence similarity over a comparison window). Percentage of sequence identity is calculated by comparing two optimally aligned sequences over a window of comparison, determining the number of positions at which the identical residues occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of matched and mismatched positions not counting gaps in the window of comparison (i.e., the window size), and multiplying the result by 100 to yield the percentage of sequence identity. Unless otherwise indicated the window of comparison between two sequences is defined by the longer of (a) entire length of the shorter of the two sequences being compared, or (b) at least 25 contiguous nucleotides. Matched positions in maximally aligned sequences can be referred to as corresponding to one another.
Specific binding between two entities refers to binding detectably higher in magnitude and distinguishable from non-specific binding of each of the entities to at least one unrelated target. Specific binding can be the result of formation of bonds between particular functional groups or particular spatial fit (e.g., lock and key type) whereas nonspecific binding is usually the result of van der Waals forces. Exemplary specific binding affinity can be at least 107, 108, 109, or 1010 M−1.
Preferential binding between two entities refers to a substantial difference in binding affinity between two different conditions, such as presence or absence of tetracycline. For example, the affinities can differ by a factor of a least 5, 10, 25, 50 or 100. Preferential expression in one condition compared with another likewise refers to variation in expression by a factor of at least 5, 10, 25, 50 or 100 between the conditions.
A polypeptide refers to any polymer of amino acids natural or synthetic regardless of length and thus includes full length proteins, fragments thereof, and peptides.
A promoter can be represented by a single-stranded sequence of nucleotides present on a transcribed strand or a double-stranded sequence of nucleotide formed of the single-stranded sequence of nucleotides just described duplexed with its complement. Depending on the context, reference to a promoter may refer to either single- or double-stranded forms or both.
Transfection is used generically for any process for introducing a nucleic into cells.
The term “comprising” indicates that other features besides those recited may or may not be present. Thus, for example, reference to a nucleic acid comprising a tet-operator comprising SEQ ID NO:5 means that additional flanking residues can be present on either or both sides of SEQ ID NO:5. The term “consisting essentially of” is used in accordance with convention to refer to the basic and novel features of an invention.
The invention provides inducible promoter systems and their components incorporating components of a tetracycline operon. By coordinating expression of different transcriptional units in these systems as a result of selection of promoters and/or linking the units into the same DNA molecule, these systems can achieve higher levels of expression of coding segments of interest, increased differential levels of expression between on- and off-states, and/or greater responsiveness to inducing agents than conventional systems.
The invention provides a hybrid mouse-human CMV promoter. The sequences of mouse and human CMV promoters are set out aligned in
The invention also provides a minimal chimpanzee CMV promoter. A minimal promoter is a promoter that by itself shows no or minimal transcription (e.g., a mean of <1, 5 or 10 transcripts per cell), but which can show substantially enhanced transcription (e.g., at least 10-fold, 50-fold or 100-fold), when combined with an upstream regulatory sequence, which serves to recruit a polymerase and transcriptional factors. A minimal promoter sequence is typically a contiguous sequence of nucleotides starting at or near the first nucleotide upstream of the transcriptional initiation site and including a TATA box. An exemplary minimal chimpanzee CMV promoter has a sequence comprising, consisting of or consisting essentially of SEQ ID NO:24. Optionally, up to 1, 2, 3, 4 or 5 nucleotides can be deleted from either end. Optionally, a few, e.g., up to 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides from the chimpanzee CMV promoter can be included upstream from the minimal promoter sequence, but inclusion of additional nucleotides is not preferred because this may reduce the differential levels of expression in the presence and absence of upstream activation.
The invention also uses intermediate strength promoters. Such promoters have reduced transcriptional activity relative to the hybrid promoters described above or their component promoters but greater activity than a minimal promoter. For example, the transcriptional activity can be reduced by 2-20 fold relative to the hybrid promoters described above or their components. Examples of such promoters have sequences comprising, consisting of or consisting essentially of any of SEQ ID NOS:17-21.
The invention can also make use of other strong promoters besides the hybrid promoters and their components described above. Such promoters are preferably active in eukaryotic cells, more preferably in mammalian cells. Examples of such strong promoters are CMV, EF1a (human elongation factor 1-alpha), SV40, PGK1 (phosphoglycerate kinase), human ubiquitin C, and human beta actin.
The promoters described above can be incorporated into transcriptional units, which in addition to the promoter include a coding segment, and sometimes other regulatory sequences, such as tet-operators as described further below or an enhancer, among other components. The heterologous coding segment can encode a polypeptide or RNA and can include a 5′UTR and/or a 3′ UTR and a polyadenylation sequence among other components. Such transcriptional units can be transformed into cells for expression.
Promoters can be compared by forming otherwise identical transcriptional units between promoters to be compared, transforming into the same cell type, e.g., CHO, HeLa, 293, COS, U20S, 3T3, or other mammalian cell and comparing transcription levels.
Some of the components of the present systems can be the same as those of conventional tet-dependent regulatory systems. Such components include tet-operators, tet-repressors, which bind tet-operators in the absence of tetracycline or other analogs thereof, modified tet-repressors, which bind tet-operators in the presence of tetracycline or other analogs thereof, and inducers, such as tetracycline and analogs thereof.
An exemplary tet-operator comprises, consists of, or consists essentially of the sequence of SEQ ID NO:1 Other tet-operators can have up to 1, 2, 3 or 4 substitutions, deletions or additions and/or have at least 90, 95, 97, 98 or 99% identity relative to the exemplified sequence and retain the ability of the exemplified sequence for preferential binding of a tet-repressor in the absence of tetracycline and preferential binding of a modified tet-repressor in the presence of tetracycline. Examples of other tet-operator sequences include 5′-TCGCTATCAGTGATAGAGA-3′ and 5′-ACTCTATCATTGATAGAGT-3′ (Wissmann et al, 1986, Nucl. Acids Res. 14: 4253-4266). Tet-operators are typically used in tandem arrays (i.e, including at least two tet operator sequences). Some arrays include 2 to 10 tet-operator sequences. Some such arrays include 2, 3, 4, 5, 6, 7, 8, 9 or 10 operator sequences. Some arrays have at least 2, 3, 4, 5, 6, 7, 8, 9 or 10 operator sequences. Some arrays have more than 10 operator sequences. The multiple operator sequences in such a tandem array are typically the same sequence. The operators are typically separated by spacers of e.g., 1-25 nucleotides. The identity and length of spacers can vary between different operators in an array. The number of operators and length of spacer can vary depending on the location of the operators relative to other components of a transcriptional unit as further described below.
An exemplary tet-repressor polypeptide comprises or consists of the amino acid sequence SEQ ID NO:5. Other tet-repressor polypeptides can have up to 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 substitutions, deletions or additions and/or have at least 90, 95, 97, 98 or 99% identity relative to this sequence. Examples of variants include those described in Gossen and Bujard, Proc. Natl. Acad. Sci. USA Vol. 89, pp. 5547-5551, 1992 and a T40A substitution described by Altschmied et al., EMBO J. 7:4011-4017, (1988). Substitutions are numbered according to position in SEQ ID NO:5 or if present in a sequence with a different number of residues than SEQ ID NO:5, the position of SEQ ID NO:5 corresponding to the substitution when the sequences are maximally aligned. A tet-repressor polypeptide has the property of specifically binding to a tet-operator or an array thereof in the absence of tetracycline. A tet-repressor shows at least preferential binding to a tet-operator or array thereof in the absence of tetracycline compared with the presence of tetracycline.
An exemplary modified tet-repressor polypeptide comprises or consists of the amino acid sequence SEQ ID NO:6. Other modified tet-repressor polypeptides can have up to 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 substitutions, deletions or additions and/or have at least 90, 95, 97, 98 or 99% identity relative to this sequence. Examples of variants include those described in Das et al. Current Gene Therapy, 2016, 16, 156-167, including tTA (E71K D95N L101S G102D), S2 (E19G A56P D148E H179R), M2 (S12G E19G A56P D148E H179R), 2s-S2 (E19G A56P D148E H179R), 2s-M2 (S12G E19G A56P D148E H179R), V1 (E19G A56P F86Y D148E H179R), rtTA3 (S12G E19G A56P F86Y D148E H179R), V10 (E19G A56P F67S F86Y D148E R171K H179R), V16 (V9I E19G A56P F67S F86Y D148E R171K H179R). Substitutions are numbered according to position in SEQ ID NO:6 or if present in a sequence with a different number of residues than SEQ ID NO:6, the position of SEQ ID NO:6 corresponding to the substitution when the sequences are maximally aligned. In contrast to a tet-repressor polypeptide, a modified tet-repressor polypeptide has the property of specifically binding to a tet-operator or an array thereof in the presence of tetracycline. A modified tet-repressor shows at least preferential binding to a tet-operator or array thereof in the presence of tetracycline compared with the absence of tetracycline.
Inducers of expression used in the present system include tetracycline itself, doxycycline and other tetracycline analogs. Unless otherwise apparent from the context, reference to tetracycline should be understood as alternatively disclosing that tetracycline analogs can be used. A tetracycline analog is a compound structurally related to tetracycline and which specifically binds to a tet-repressor or modified tet-repressor as described herein. Examples of tetracycline analogs are anhydrotetracycline (atc), chlorotetracycline, oxytetracycline, or deoxytetracycline and minocycline. Further analogs are disclosed by Hlavka and Boothe, “The Tetracyclines,” in Handbook of Experimental Pharmacology 78, R. K. Blackwood et al. (eds.), Springer-Verlag, Berlin, N.Y., 1985; Mitscher, “The Chemistry of the Tetracycline Antibiotics”, Medicinal Research 9, Dekker, N.Y., 1978; Noyee Development Corporation, “Tetracycline Manufacturing Processes” Chemical Process Reviews, Park Ridge, N.J., 2 volumes, 1969; Evans, “The Technology of the Tetracyclines,” Biochemical Reference Series 1, Quadrangle Press, New York, 1968; and Dowling, “Tetracycline,” Antibiotic Monographs, no. 3, Medical Encyclopedia, New York, 1955 and WO2007/133797 and WO2007/133798.
A cumulate regulatory system has analogous compounds and mode of operation to a tetracycline regulatory system. These include cumate operators, cumate repressors, which bind a cumate operator in the absence of cumate and modified cumate repressors, which bind cumate operators in the presence of cumate. The description in relation to tetracycline regulatory sequences applies mutatis mutandis to cumate operator systems.
An exemplary cumate operator comprises, consists of, or consists essentially of the sequence of any of SEQ ID NOS:156-158. Other cumate operators can have up to 1, 2, 3 or 4 substitutions, deletions or additions and/or have at least 90, 95, 97, 98 or 99% identity relative to the exemplified sequence and retain the ability of the exemplified sequence for preferential binding of a cumate repressor in the absence of cumate and preferential binding of a modified cumate repressor in the presence of cumate. Cumate operators can be used individually or in tandem arrays (i.e., including at least two cumate operators). Some arrays include 2 to 10 cumate operators. Some such arrays include 2, 3, 4, 5, 6, 7, 8, 9 or 10 operator sequences. Some arrays have at least 2, 3, 4, 5, 6, 7, 8, 9 or 10 operator sequences. Some arrays have more than 10 operator sequences. The multiple operators in such a tandem array can have the same or different sequences. The operators may be separated by spacers of e.g., 1-25 nucleotides. The identity and length of spacers can vary between different operators in an array. The number of operators and length of spacer can vary depending on the location of the operators relative to other components of a transcriptional unit as further described below.
An exemplary cumate repressor polypeptide comprises or consists of the amino acid sequence SEQ ID NO:170. Other cumate-repressor polypeptides can have up to 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 substitutions, deletions or additions and/or have at least 90, 95, 97, 98 or 99% identity relative to this sequence. A cumate repressor polypeptide has the property of specifically binding to a cumate operator or an array thereof in the absence of cumate. A cumate-repressor shows at least preferential binding to a cumate operator or array thereof in the absence of cumate compared with the presence of tetracycline.
An exemplary modified cumate repressor polypeptide comprises or consists of the amino acid sequence SEQ ID NO:171. Other modified cumate repressor polypeptides can have up to 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 substitutions, deletions or additions and/or have at least 90, 95, 97, 98 or 99% identity relative to this sequence. SEQ ID NO:171 includes three mutations relative to SEQ ID NO:170: E142G, I144M and V125A In contrast to a cumate repressor polypeptide, a modified cumate repressor polypeptide has the property of specifically binding to a cumate-operator or an array thereof in the presence of cumate. A modified cumate repressor shows at least preferential binding to a tet-operator or array thereof in the presence of tetracycline compared with the absence of tetracycline.
Inducers of expression used in the present system include cumate itself and analogs. An analog is a compound structurally related to cumate and which specifically binds to a cumate-repressor or modified cumate-repressor as described herein. Examples of cumate analogs include di-methyl p-aminobenzoic acid (DM PABA), trimethyl cumate, and ethylbenzoate, or a salt thereof, mainly para- or 4-substituted benzoate consisting of a bulky group of heteroatom, such as those selected from the group consisting of 3,4-dimethylbenzoate, 4-ethylbenzoate, 4-t-butylbenzoate, 4-phenylbenzoate, 4-benzylbenzoate, 4-ethoxybenzoate, 4-propyloxybenzoate, 4-n-butyloxybenzoate, 4-chlorobenzoate, 4-bromobenzoate, 4-iodobenzoate, 4-bromomethylbenzoate, 3,4-dichlorobenzoate, 4-trifluoromethylbenzoate, 4-ethyl-m-xylene, 4-vinyltoluene, 4-n-propyltoluene, 4-allytoluene, 4-fluoro-p-toluate, 3-chloro-p-toluate, and 4-bromo-m-toluate, an analogue of cumate such as Benzoic acid, p-methylbenzoic acid, p-ethylbenzoic acid, p-Propylbenzoic acid, cumic acid, p-isobutylbenzoic acid, p-tert-butylbenzoic acid, ibuprofen, p-aminobenzoic acid, p-N-methylaminobenzoic acid, p-N-dimethylaminobenzoic acid, p-N-methyl-N-ethylaminobenzoic acid and p-N-ethylaminobenzoic acid.
Some of the present systems include a transcriptional activation domain. Such a domain is expression as a fusion protein with a tet-repressor polypeptide or modified tet-repressor polypeptide. Fusion is preferably between the C-terminus of the tet-repressor or modified-tet-repressor and the N-terminus of the transcriptional activation domain. More than one transcriptional domain can be included as a tandem array of such domains in a fusion protein. Examples of transcriptional activations domains include the HSV VP16 activation domain (see, e.g., Hagmann et al., J. Virol. 71, 5952-5962 (1997)) nuclear hormone receptors (see, e.g., Torchia et al., Curr. Opin. Cell. Biol. 10:373-383 (1998)); the p65 subunit of nuclear factor kappa B (Bitko & Barik, J. Virol. 72:5610-5618 (1998) and Doyle & Hunt, Neuroreport 8:2937-2942 (1997)); Liu et al., Cancer Gene Ther. 5:3-28 (1998)), or artificial chimeric functional domains such as VP64 (Seifpal et al., EMBO J. 11, 4961-4968 (1992)). Other transcriptional activation domains include VP64, p300, CBP, PCAF, SRC1 PvALF, AtHD2A and ERF-2. See, for example, Robyr et al. (2000) Mol. Endocrinol. 14:329-347; Collingwood et al. (1999) J. Mol. Endocrinol. 23:255-275; Leo et al. (2000) Gene 245:1-11; Manteuffel-Cymborowska (1999) Acta Biochim. Pol. 46:77-89; McKenna et al. (1999) J. Steroid Biochem. Mol. Biol. 69:3-12; Malik et al. (2000) Trends Biochem. Sci. 25:277-283; and Lemon et al. (1999) Curr. Opin. Genet. Dev. 9:499-504. Additional exemplary activation domains include, but are not limited to, OsGAI, HALF-1, C1, AP1, ARF-5, -6, -7, and -8, CPRF1, CPRF4, MYC-RP/GP, and TRAB1. See, for example, Ogawa et al. (2000) Gene 245:21-29; Okanami et al. (1996) Genes Cells 1:87-99; Goff et al. (1991) Genes Dev. 5:298-309; Cho et al. (1999) Plant Mol. Biol. 40:419-429; Ulmason et al. (1999) Proc. Natl. Acad. Sci. USA 96:5844-5849; Sprenger-Haussels et al. (2000) Plant J. 22:1-8; Gong et al. (1999) Plant Mol. Biol. 41:33-44; and Hobo et al. (1999) Proc. Natl. Acad. Sci. USA 96:15, 348-15, 353. Exemplary VP16 activation domains comprises or consists of a sequence selected from SEQ ID NOS:7 or 40. Exemplary fusions of a modified tet-repressor to a VP16 activation domain comprises or consists of a sequence selected from SEQ ID NOS:8 or 9.
Coding segments can encode any polypeptide or RNA of interest. Coding segments can include an open reading frame encoding a polypeptide. Coding segments can also include a segment encoding a 5′ UTR, 3′ UTR or polyadenylation region. Examples of polypeptides includes therapeutic proteins, proteins associated with a disease phenotype, enzymes, proteins used as selection markers or counter-selection markers, or suicide proteins. Examples of RNA include mRNA, tRNA, rRNA as well as various RNA molecules used for interference of expression, such as anti-sense, siRNA, shRNA or micro-RNA including artificial micro-RNA. Some examples of therapeutic proteins include antibodies or their component heavy and light chains, or heavy and light chain fused to one another as a single-chain antibody, antibodies engineered to produce heteromeric multi-chain molecules capable of binding more than one target protein (e.g. bispecific or multi-specific antibodies), T cell engagers, chimeric antigen receptors combining an antigen binding region with transmembrane and T cell signalling domains, Fc fusion proteins, antigens from pathogens (e.g. for use in vaccines), anticoagulants, blood factors, bone morphogenetic proteins, enzymes, growth factor hormones, interferons, interleukins and thrombolytics. Proteins associated with disease are often mutated forms of human proteins. Some examples of such proteins are huntingtin, cystic fibrosis trans-membrane regulator, hemoglobin, alpha-1 antitrypsin, phenylalanine hydroxylase, beta-hexosaminidase, amyloid precursor protein, alpha-synuclein prion protein, transthyretin, crystallin and p53. It is particularly useful to be able to control the timing of expression of coding segments whose expression can be toxic for the cell that expresses them, for example so that the growth phase of an expression host can be decoupled from the expression phase. Examples of potentially toxic coding segments include open reading frames encoding membrane proteins such as ion channels, G-protein coupled receptors (GPCRs) and viral membrane proteins (such as the coronavirus spike proteins). Other examples of potentially toxic coding segments include open reading frames encoding proteins normally targeted to the lysozome, kinases and cytokines.
A selection marker is a nucleic acid or expression product that allows for selection of a molecule or cell containing the marker often under particular conditions. These markers can encode an activity, such as, production of RNA, peptide, or protein, or can provide a binding site for RNA, peptides, proteins, inorganic and organic compounds or compositions. Examples of selectable markers include: (1) DNA segments that encode products which provide resistance against otherwise toxic compounds (e.g., antibiotics); (2) DNA segments that encode products which are otherwise lacking in the recipient cell (e.g., tRNA genes, auxotrophic markers); (3) DNA segments that encode products which suppress the activity of a gene product; (4) DNA segments that encode products which can be readily identified (e.g., phenotypic markers such as beta-galactosidase, green fluorescent protein (GFP), and cell surface proteins); (5) DNA segments that bind products which are otherwise detrimental to cell survival and/or function; (6) DNA segments that otherwise inhibit the activity of any of the DNA segments described in Nos. 1-5 above (e.g., antisense oligonucleotides); (7) DNA segments that bind products that modify a substrate (e.g. restriction endonucleases); (8) DNA segments that can be used to isolate a desired molecule (e.g. specific protein binding sites); (9) DNA segments that encode a specific nucleotide sequence which can be otherwise non-functional (e.g., for PCR amplification of subpopulations of molecules); and/or (10) DNA segments, which when absent, directly or indirectly confer sensitivity to particular compounds. Some examples of selection markers include glutamine synthetase, dihydrofolate reductase, blasticidin-resistance, neo-resistance, hygromycin-resistance, puromycin-resistance and zeocin-resistance.
The term “counter-selectable marker” means a polynucleotide sequence that confers a selective disadvantage on a host cell. Examples of counter-selectable markers include sacB, rpsL, tetAR, pheS, thyA, gata-1, ccdB, kid and barnase (Bernard, 1995, Journal/Gene, 162: 159-160; Bernard et. al., 1994. Journal/Gene, 148: 71-74; Gabant et. al., 1997, Journal/Biotechniques, 23: 938-941; Gababt et. al., 1998, Journal/Gene, 207: 87-92; Gababt et. al., 2000, Journal/Biotechniques, 28: 784-788; Galvao and de Lorenzo, 2005, Journal/Appl Environ Microbiol, 71: 883-892; Hartzog et. al., 2005, Journal/Yeat, 22:789-798; Knipfer et. al., 1997, Journal/Plasmid, 37: 129-140; Reyrat et. al., 1998, Journal/Infect Immun, 66: 4011-4017; Soderholm et. al., 2001, Journal/Biotechniques, 31: 306-310, 312; Tamura et. al., 2005, Journal/Appl Environ Microbiol, 71: 587-590; Yazynin et. al., 1999, Journal/FEBS Lett, 452: 351-354).
A suicide gene is a gene that causes a cell to kill itself e.g., by inducing apoptosis or by metabolizing a pro-drug into a drug that is toxic to a cell, e.g., caspase-9 (see Yagyu et al., Mol. Ther. 23: 1475-85 (2015)). The present systems are particularly useful for regulated expression of coding segments whose expression is detrimental or lethal to a cell.
The present transcription units can be incorporated into one or more gene transfer systems. For inducible control systems including two transcriptional units, both are preferably included in the same gene transfer system as part of the same contiguous nucleic acid.
A gene transfer systems comprises a nucleic acid to be transferred into a host cell and one or more other elements to facilitate uptake, integration, expression or election of the nucleic acid. A gene transfer system can include a transposon and corresponding transposase. Although transposons are preferred gene transfer systems because of their large cargo sizes and because multiple different coding segments with all of their associated regulatory elements can be incorporated without compromising packaging and delivery of the gene transfer system, other genes transfer systems including a lentiviral system, an adenoviral system or an adeno-associated viral system, or other expression vector can be used.
A gene transfer system or one or more if its components can be transfected into one or more cells by techniques such as particle bombardment, electroporation, microinjection, combining the components with lipid-containing vesicles, such as cationic lipid vesicles, DNA condensing reagents (example, calcium phosphate, polyline or polyethyleneimine)
After transfection, introduced nucleic acids can remain the cytoplasm (e.g., as an episome) or can be integrated into the genome. Integration of a nucleic acid into the genome of a host cell generally makes it stably heritable, by subjecting it to the same mechanisms that ensure the replication and division of genomic DNA. Such stable heritability is desirable for achieving good and consistent expression over long growth periods.
Nucleic acid can be efficiently integrated into nucleic acids, such as a genome, by a transposase system. The nucleic acid into which a transposed nucleic acid is integrated is sometimes referred to as a target nucleic acid. A transposase system includes a transposon and a corresponding transposase. The transposon includes a heterologous nucleic acid to be transposed flanked by inverted transposon repeats (ITRs). The ITR on one side of the heterologous nucleic acid is a perfect or substantial (e.g., one or two mismatched nucleotides) reverse complement of the ITR on the other side. Between the ITRs and heterologous nucleic acids, additional transposon sequences may be present. Outside the ITRs (distal to the heterologous nucleic acid) are two copies, one for each side, of a target site, typically of four nucleotides. A benefit of a transposon is that the entire nucleic acid between transposon inverted terminal repeats (ITRs) can be integrated. There are several different classes of transposon. piggyBac and piggyBac-like transposons include the piggyBac transposon from the looper moth Trichoplusia ni, Xenopus piggyBac-like transposons, Bombyx piggyBac-like transposons, Heliothis piggyBac-like transposons, Helicoverpa piggyBac-like transposons, Agrotis piggyBac-like transposons, Amyelois piggyBac-like transposons, piggyBat piggyBac-like transposons and Oryzias piggyBac-like transposons. hAT transposons include TcBuster. Mariner transposons include Sleeping Beauty. Each of these transposons can be integrated into the genome of a mammalian cell by a corresponding transposase. A transposase can be provided as a protein or encoded by a nucleic acid. A transposon comprising a heterologous nucleic acid and its corresponding transposase can be transfected into a cell at the same time, or sequentially. For example, a transposase protein or its encoding nucleic acid may be transfected into a cell prior to, simultaneously with or subsequently to transfection of a corresponding transposon. Additionally, administration of either component of the gene transfer system may occur repeatedly, for example, by administering at least two doses of this component.
A nucleic acid encoding a transposase protein can be transfected into a cell as a nucleic acid vector such as a plasmid, a viral vector or as an mRNA molecule. The nucleic acid can be circular or linear. The nucleic acid encoding the transposase protein can be stably inserted into the genome of the cell or can remain in the cytoplasm. The transposase can be expressed constitutively or from an inducible system. DNA encoding a transposase is preferably linked to a promoter. A variety of promoters can be used including constitutive promoters, tissue-specific promoters, inducible promoters, species-specific promoters, cell-type specific promoters and the like. Alternatively, a transposase can be introduced into a cell directly as protein, for example using cell-penetrating peptides (e.g. as described in Ramsey and Flynn, 2015. Pharmacol. Ther. 154: 78-86 “Cell-penetrating peptides transport therapeutics into cells”); using small molecules including salt plus propane betaine (e.g. as described in Astolfo et. al., 2015. Cell 161: 674-690); or electroporation (e.g. as described in Morgan and Day, 1995. Methods in Molecular Biology 48: 63-71 “The introduction of proteins into mammalian cells by electroporation”).
Transposase proteins can be introduced into cells encoded as an mRNA molecule. RNA molecules can include substitutions to reduce toxicity effects on the cell, for example substitution of uridine with pseudouridine, and substitution of cytosine with 5-methyl cytosine. mRNA encoding the transposase can be prepared with a 5′-cap structure to improve expression in a target cell. Exemplary cap structures are a cap analog (G(5′)ppp(5′)G), an anti-reverse cap analog (3′-O-Me-m.sup.7G(5′)ppp(5′)G, a clean cap(m7G(5′)ppp(5′)(2′OMeA)pG), an mCap (m7G(5′)ppp(5)G). mRNA encoding the transposase may be prepared such that some bases are partially or fully substituted, for example uridine may be substituted with pseudo-uridine, cytosine may be substituted with 5-methyl-cytosine. Any combinations of these caps and substitutions may be made. Similarly, a nucleic acid encoding a transposase protein or the transposon of this invention can be transfected into the cell as a linear fragment or as a circularized fragment, either as a plasmid or as recombinant viral DNA. If the transposase is introduced as a DNA sequence encoding the transposase, then the coding segment encoding the transposase is preferably operably linked to a promoter suitable for use in the intended target cell.
An exemplary piggyBac-like transposon for modifying the genome of a mammalian cell is a Xenopus transposon which comprises an ITR with the with sequence given by SEQ ID NO:41, a heterologous nucleic acid to be transposed and a second ITR with sequence given by SEQ ID NO:42. The transposon may further be flanked by a copy of the tetranucleotide5′-TTAA-3′ on each side, immediately adjacent to the ITRs and distal to the heterologous nucleic acid. The transposon may further comprise a sequence immediately adjacent to the ITR and proximal to the heterologous nucleic acid that is at least 95% or 100% identical to SEQ ID NO:43 or 44 on one side of the heterologous nucleic acid, preferably the left side, and a sequence immediately adjacent to the ITR and proximal to the heterologous nucleic acid that is at least 95% or 100% identical to SEQ ID NO:45 or 46 on the other side of the heterologous nucleic acid, preferably the right side. This transposon may be transposed by a corresponding Xenopus transposase comprising a sequence at least 90% or 100% identical to the sequence given by SEQ ID NO:47 or 48, for example, any of SEQ ID NOS:47-79. Preferably the transposase is a hyperactive variant of a naturally occurring transposase. Preferably the hyperactive variant transposase comprises one or more of the following amino acid changes, relative to the sequence of SEQ ID NO:47: Y6L, Y6H, Y6V, Y6I, Y6C, Y6G, Y6A, Y6S, Y6F, Y6R, Y6P, Y6D, Y6N, S7G, S7V, S7D, E9W, E9D, E9E, M16E, M16N, M16D, M16S, M16Q, M16T, M16A, M16L, M16H, M16F, M16I, S18C, 518Y, S18M, S18L, S18Q, S18G, S18P, S18A, S18W, S18H, S18K, S18I, S18V, S19C, S19V, S19L, S19F, S19K, S19E, S19D, S19G, S19N, S19A, S19M, S19P, 519Y, S19R, S19T, S19Q, S20G, 520M, S20L, S20V, S20H, S20W, S20A, S20C, S20Q, S20D, S20F, S20N, S20R, E21N, E21W, E21G, E21Q, E21L, E21D, E21A, E21P, E21T, E21S, E21Y, E21V, E21F, E21M, E22C, E22H, E22R, E22L, E22K, E22S, E22G, E22M, E22V, E22Q, E22A, E22Y, E22W, E22D, E22T, F23Q, F23A, F23D, F23W, F23K, F23T, F23V, F23M, F23N, F23P, F23H, F23E, F23C, F23R, F23Y, S24L, S24W, 524H, S24V, S24P, S24I, S24F, S24K, 524Y, S24D, S24C, 524N, 524G, S24A, S26F, S26H, S26V, S26Q, S26Y, S26W, S28K, S28Y, S28C, S28M, S28L, S28H, S28T, S28Q, V31L, V31T, V31I, V31Q, V31K, A34L, A34E, L67A, L67T, L67M, L67V, L67C, L67H, L67E, L67Y, G73H, G73N, G73K, G73F, G73V, G73D, G735, G73W, G73L, A76L, A76R, A76E, A76I, A76V, D77N, D77Q, D77Y, D77L, D77T, P88A, P88E, P88N, P88H, P88D, P88L, N91D, N91R, N91A, N91L, N91H, N91V, Y141I, Y141M, Y141Q, Y141S, Y141E, Y141W, Y141V, Y141F, Y141A, Y141C, Y141K, Y141L, Y141H, Y141R, N145C, N145M, N145A, N145Q, N145I, N145F, N145G, N145D, N145E, N145V, N145H, N145W, N145Y, N145L, N145R, N145S, P146V, P146T, P146W, P146C, P146Q, P146L, P146Y, P146K, P146N, P146F, P146E, P148M, P148R, P148V, P148F, P148T, P148C, P148Q, P148H, Y150W, Y150A, Y150F, Y150H, Y150S, Y150V, Y150C, Y150M, Y150N, Y150D, Y150E, Y150Q, Y150K, H157Y, H157F, H157T, H157S, H157W, A162L, A162V, A162C, A162K, A162T, A162G, A162M, A162S, A162I, A162Y, A162Q, A179T, A179K, A179S, A179V, A179R, L182V, L182I, L182Q, L182T, L182W, L182R, L182S, T189C, T189N, T189L, T189K, T189Q, T189V, T189A, T189W, T189Y, T189G, T189F, T189S, T189H, L192V, L192C, L192H, L192M, L192I, S193P, S193T, S193R, S193K, S193G, S193D, S193N, S193F, S193H, S193Q, S193Y, V196L, V196S, V196W, V196A, V196F, V196M, V196I, S198G, S198R, S198A, S198K, T200C, T200I, T200M, T200L, T200N, T200W, T200V, T200Q, T200Y, T200H, T200R, S202A, S202P, L210H, L210A, F212Y, F212N, F212M, F212C, F212A, N218V, N218R, N218T, N218C, N218G, N218I, N218P, N218D, N218E, A248S, A248L, A248H, A248C, A248N, A248I, A248Q, A248Y, A248M, A248D, L263V, L263A, L263M, L263R, L263D, Q270V, Q270K, Q270A, Q270C, Q270P, Q270L, Q270I, Q270E, Q270G, Q270Y, Q270N, Q270T, Q270W, Q270H, S294R, S294N, S294G, 5294T, S294C, T297C, T297P, T297V, T297M, T297L, T297D, E304D, E304H, E304S, E304Q, E304C, S308R, S308G, L310R, L310I, L310V, L333M, L333W, L333F, Q336Y, Q336N, Q336M, Q336A, Q336T, Q336L, Q336I, Q336G, Q336F, Q336E, Q336V, Q336C, Q336H, A354V, A354W, A354D, A354C, A354R, A354E, A354K, A354H, A354G, C357Q, C357H, C357W, C357N, C357I, C357V, C357M, C357R, C357F, C357D, L358A, L358F, L358E, L358R, L358Q, L358V, L358H, L358C, L358M, L358Y, L358K, L358N, L358I, D359N, D359A, D359L, D359H, D359R, D359S, D359Q, D359E, D359M, L377V, L377I, V423N, V423P, V423T, V423F, V423H, V423C, V423S, V423G, V423A, V423R, V423L, P426L, P426K, P426Y, P426F, P426T, P426W, P426V, P426C, P426S, P426Q, P426H, P426N, K428R, K428Q, K428N, K428T, K428F, S434A, S434T, S438Q, S438A, S438M, T447S, T447A, T447C, T447Q, T447N, T447G, L450M, L450V, L450A, L450I, L450E, A462M, A462T, A462Y, A462F, A462K, A462R, A462Q, A462H, A462E, A462N, A462C, V467T, V467C, V467A, V467K, I469V, I469N, I472V, I472L, 1472W, I472M, I472F, L476I, L476V, L476N, L476F, L476M, L476C, L476Q, P488E, P488H, P488K, P488Q, P488F, P488M, P488L, P488N, P488D, Q498V, Q498L, Q498G, Q498H, Q498T, Q498C, Q498E, Q498M, L502I, L502M, L502V, L502G, L502F, E517M, E517V, E517A, E517K, E517L, E517G, E517S, E517I, P520W, P520R, P520M, P520F, P520Q, P520V, P520G, P520D, P520K, P520Y, P520E, P520L, P520T, S521A, S521H, S521C, S521V, S521W, S521T, S521K, S521F, S521G, N523W, N523A, N523G, N523S, N523P, N523M, N523Q, N523L, N523K, N523D, N523H, N523F, N523C, I533M, I533V, I533T, I533S, I533F, I533G, I533E, D534E, D534Q, D534L, D534R, D534V, D534C, D534M, D534N, D534A, D534G, D534F, D534T, D534H, D534K, D534S, F576L, F576K, F576V, F576D, F576W, F576M, F576C, F576R, F576Q, F576A, F576Y, F576N, F576G, F576I, F576E, K577L, K577G, K577D, K577R, K577H, K577Y, K577I, K577E, K577V, K577N, I582V, 1582K, I582R, I582M, I582G, I582N, 1582E, I582A, I582Q, Y583L, Y583C, Y583F, Y583D, Y583Q, L587F, L587D, L587R, L587I, L587P, L587N, L587E, L587S, L587Y, L587M, L587Q, L587G, L587W, L587K or L587T.
Another exemplary piggyBac-like transposon for modifying the genome of a cell is a Bombyx transposon which comprises an ITR with the sequence of SEQ ID NO:80, a heterologous nucleic acid to be transposed and a second ITR with the sequence of SEQ ID NO:81. The transposon may further be flanked by a copy of the tetranucleotide5′-TTAA-3′ on each side, immediately adjacent to the ITRs and distal to the heterologous nucleic acid. The transposon may further comprise a sequence immediately adjacent to the ITR and proximal to the heterologous nucleic acid that is at least 95% or 100% identical to SEQ ID NO:82 on one side of the heterologous nucleic acid, preferably the left side, and a sequence immediately adjacent to the ITR and proximal to the heterologous nucleic acid that is at least 95% or 100% identical to SEQ ID NO:83 on the other side of the heterologous nucleic acid, preferably the right side. This transposon may be transposed by a corresponding Bombyx transposase comprising a sequence at least 90% or 100% identical to SEQ ID NO:84, for example. any of SEQ ID NOS:84-106. Preferably the transposase is a hyperactive variant of a naturally occurring transposase of SEQ ID NO:84 including one or more of the following mutations: Q92A, Q92P, Q92N, Q92I, Q92Y, Q92H, Q92F, Q92R, Q92D, Q92M, Q92W, Q92C, Q92G, Q92L, Q92V, Q92T, V93P, V93K, V93M, V93F, V93W, V93L, V93A, V93I, V93Q, P96A, P96T, P96M, P96R, P96G, P96V, P96E, P96Q, P96C, F97Q, F97K, F97H, F97T, F97C, F97W, F97V, F97E, F97P, F97D, F97A, F97R, F97G, F97N, F97Y, H165E, H165G, H165Q, H165T, H165M, H165V, H165L, H165C, H165N, H165D, H165K, H165W, H165A, E178S, E178H, E178Y, E178F, E178C, E178A, E178Q, E178G, E178V, E178D, E178L, E178P, E178W, C189D, C189Y, C189I, C189W, C189T, C189K, C189M, C189F, C189P, C189Q, C189V, A196G, L200I, L200F, L200C, L200M, L200Y, A201Q, A201L, A201M, L203V, L203D, L203G, L203E, L203C, L203T, L203M, L203A, L203Y, N207G, N207A, L211G, L211M, L211C, L211T, L211V, L211A, W215Y, T217V, T217A, T217I, T217P, T217C, T217Q, T217M, T217F, T217D, T217K, G2195, G219A, G219C, G219H, G219Q, Q235C, Q235N, Q235H, Q235G, Q235W, Q235Y, Q235A, Q235T, Q235E, Q235M, Q235F, Q238C, Q238M, Q238H, Q238V, Q238L, Q238T, Q238I, R242Q, K246I, K253V, M258V, F261L, S263K, C271S, N303C, N303R, N303G, N303A, N303D, N303S, N303H, N303E, N303R, N303K, N303L, N303Q, I312F, I312C, I312A, I312L, I312T, I312V, I312G, I312M, F321H, F321R, F321N, F321Y, F321W, F321D, F321G, F321E, F321M, F321K, F321A, F321Q, V323I, V323L, V323T, V323M, V323A, V324N, V324A, V324C, V324I, V324L, V324T, V324K, V324Y, V324H, V324F, V324S, V324Q, V324M, V324G, A330K, A330V, A330P, A330S, A330C, A330T, A330L, Q333P, Q333T, Q333M, Q333H, Q333S, P337W, P337E, P337H, P337I, P337A, P337M, P337N, P337D, P337K, P337Q, P337G, P337S, P337C, P337L, P337V, F368Y, L373C, L373V, L373I, L373S, L373T, V389I, V389M, V389T, V389L, V389A, R394H, R394K, R394T, R394P, R394M, R394A, Q395P, Q395F, Q395E, Q395C, Q395V, Q395A, Q395H, Q395S, Q395Y, S399N, S399E, S399K, S399H, S399D, S399Y, S399G, S399Q, S399R, S399T, S399A, S399V, S399M, R402Y, R402K, R402D, R402F, R402G, R402N, R402E, R402M, R402S, R402Q, R402T, R402C, R402L, R402V, T403W, T403A, T403V, T403F, T403L, T403Y, T403N, T403G, T403C, T403I, T403S, T403M, T403Q, T403K, T403E, D404I, D404S, D404E, D404N, D404H, D404C, D404M, D404G, D404A, D404Q, D404L, D404P, D404V, D404W, D404F, N408F, N408I, N408A, N408E, N408M, N408S, N408D, N408Y, N408H, N408C, N408Q, N408V, N408W, N408L, N408P, N408K, S409H, S409Y, S409N, S409I, S409D, S409F, S409T, S409C, S409Q, N441F, N441R, N441M, N441G, N441C, N441D, N441L, N441A, N441V, N441W, G448W, G448Y, G448H, G448C, G448T, G448V, G448N, G448Q, E449A, E449P, E449T, E449L, E449H, E449G, E449C, E449I, V469T, V469A, V469H, V469C, V469L, L472K, L472Q, L472M, C473G, C473Q, C473T, C473I, C473M, R484H, R484K, T507R, T507D, T507S, T507G, T507K, T507I, T507M, T507E, T507C, T507L, T507V, G523Q, G523T, G523A, G523M, G523S, G523C, G523I, G523L, I527M, I527V, Y528N, Y528W, Y528M, Y528Q, Y528K, Y528V, Y528I, Y528G, Y528D, Y528A, Y528E, Y528R, Y543C, Y543W, Y543I, Y543M, Y543Q, Y543A, Y543R, Y543H, E549K, E549C, E549I, E549Q, E549A, E549H, E549C, E549M, E549S, E549F, E549L, K550R, K550M, K550Q, S556G, S556V, S556I, P557W, P557T, P557S, P557A, P557Q, P557K, P557D, P557G, P557N, P557L, P557V, H559K, H559S, H559C, H559I, H559W, V560F, V560P, V560I, V560H, V560Y, V560K, N561P, N561Q, N561G, N561A, V562Y, V562I, V562S, V562M, V567I, V567H, V567N, S583M, E601V, E601F, E601Q, E601W, E605R, E605W, E605K, E605M, E605P, E605Y, E605C, E605H, E605A, E605Q, E605S, E605V, E605I, E605G, D607V, D607Y, D607C, D607N, D607W, D607T, D607A, D607H, D607Q, D607E, D607L, D607K, D607G, S609R, S609W, S609H, S609V, S609Q, S609G, S609T, S609K, S609N, S609Y, L610T, L610I, L610K, L610G, L610A, L610W, L610D, L610Q, L610S, L610F or L610N.
Another exemplary piggyBac-like transposon for modifying the genome of a cell is a piggyBat transposon which comprises an ITR with the sequence of SEQ ID NO:107, a heterologous nucleic acid to be transposed and a second ITR with the sequence of SEQ ID NO:108. The transposon may further be flanked by a copy of the tetranucleotide5′-TTAA-3′ on each side, immediately adjacent to the ITRs and distal to the heterologous nucleic acid. The transposon may further comprise a sequence immediately adjacent to the ITR and proximal to the heterologous nucleic acid that is at least 95% or 100% identical to SEQ ID NO:109 on one side of the heterologous nucleic acid, preferably the left side, and a sequence immediately adjacent to the ITR and proximal to the heterologous nucleic acid that is at least 95% or 100% identical to SEQ ID NO:110 on the other side of the heterologous nucleic acid, preferably the right side. This transposon may be transposed by a corresponding piggyBat transposase comprising a sequence at least 90% or 100% identical to SEQ ID NO:111. Preferably the transposase is a hyperactive variant of a naturally occurring transposase. Preferably the hyperactive variant transposase comprises one or more of the following amino acid changes, relative to the sequence of SEQ ID NO:111: A14V, D475G, P491Q, A561T, T546T, T300A, T294A, A520T, G239S, S5P, S8F, S54N, D9N, D9G, I345V. M481V, EI1G, K130T, G9G, R427H, S8P, S36G, D1OG, S36G.
Another exemplary piggyBac-like transposon for modifying the genome of a cell comprises an ITR with the sequence of SEQ ID NO:112, a heterologous nucleic acid to be transposed and a second ITR with the sequence of SEQ ID NO:113. The transposon may further be flanked by a copy of the tetranucleotide5′-TTAA-3′ on each side, immediately adjacent to the ITRs and distal to the heterologous nucleic acid. The transposon may further comprise a sequence immediately adjacent to the ITR and proximal to the heterologous nucleic acid that is at least 95% or 100% identical to SEQ ID NO:114 on one side of the heterologous nucleic acid, preferably the left side, and a sequence immediately adjacent to the ITR and proximal to the heterologous nucleic acid that is at least 95% or 100% identical to SEQ ID NO:115 on the other side of the heterologous nucleic acid preferably the right side. This transposon may be transposed by a corresponding piggyBac transposase comprising a sequence at least 90% or 100% identical to SEQ ID NO:116. Preferably the transposase is a hyperactive variant of a naturally occurring transposase. Preferably the hyperactive variant transposase comprises one or more of the following amino acid changes, relative to the sequence of SEQ ID NO:116: G2C, Q40R, I30V, G1655, T43A, S61R, S103P, S103T, M194V, R281G, M282V, G316E, I426V, Q497L, N505D, Q573L, S509G, N570S, N538K, Q591P, Q591R, F594L, M194V, I30V, S103P, G165S, M282V, S509G, N538K, N571S, C41T, A1424G, C1472A, G1681A, T150C, A351G, A279G, T1638C, A898G, A880G, G1558A, A687G, G715A, T13C, C23T, G161A, G25A, T1050C, A1356G, A26G, A1033G, A1441G, A32G, A389C, A32G, A389C, A32G, T1572A, G456A, T1641C, TI 155C, G1280A, T22C, A106G, A29G, C137T, A14V, D475G, P491Q, A561T, T546T, T300A, T294A, A520T, G239S, SSP, SBF, S54N, D9N, D9G, 1345V, M481V, E11G, K130T, G9G, R427H, S8P, S36G, DI0G, S36G, A51T, C153A, C277T, G201A, G202A, T236A, A103T, A104C, T140C, G138T, T118A, C74T, A179C, S3N, I30V, A46S, A46T, I82W, S103P, R119P, C125A, C125L, G165S, Y177K, Y177H, F180L, F180I, F180V, M185L, A187G, F200W, V207P, V209F, M226F, L235R, V240K, F241L, P243K, N258S, M282Q, L296W, L296Y, L296F, M298V, M298A, M298L, P311V, P311I, R315K, T319G, Y327R, Y328V, C340G, C340L, D421H, V436I, M456Y, L470F, S486K, M503I, M503L, V552K, A570T, Q591P, Q591R, R65A, R65E, R95A, R95E, R97A, R97E, R135A, R135E, R161A, R161E, R192A, R192E, R208A, R208E, K176A, K176E, K195A, K195E, S171E, M14V, D270N, 130V, G165S, M282L, M282I, M282V or M282A.
Another example of a piggyBac-like transposon for modifying the genome of a cell is an Amyelois transposon comprising an ITR with the sequence of SEQ ID NO:117, a heterologous nucleic acid, and a second ITR with the sequence of SEQ ID NO:118. The transposon may further be flanked by a copy of the tetranucleotide 5′-TTAA-3′ on each side, immediately adjacent to the ITRs and distal to the heterologous nucleic acid. The transposon may further comprise a sequence that is at least 95% or 100% identical to SEQ ID NO:119 on one side of the heterologous nucleic acid, and a sequence that is at least 95% or 100%identical to SEQ ID NO:120 on the other side of the heterologous nucleic acid. This transposon may be transposed by a corresponding Amyelois transposase comprising a sequence at least 90% identical to SEQ ID NO:121. Preferably the transposase is a hyperactive variant of a naturally occurring transposase. Preferably the hyperactive variant transposase comprises one or more of the following amino acid changes, relative to the sequence of SEQ ID NO:121: P65E, P65D, R95S, R95T, V100I, V100L, V100M, L115D, L115E, E116P, H121Q, H121N, K139E, K139D, T159N, T159Q, V166F, V166Y, V166W, G179N, G179Q, W187F, W187Y, P198R, P198K, L203R, L203K, I209L, 1209V, 1209M, N211R, N211K, E238D, L273I, L273V, L273M, D304K, D304R, I323L, I323M, I323V, Q329G, Q329R, Q329K, T345L, T345I, T345V, T345M, K362R, T366R, T366K, T380S, L408M, L408I, L408V, E413S, E413T, S416E, S416D, I426M, I426L, I426V, S435G, L458M, L458I, L458V, A472S, A472T, V475I, V475L, V475M, N483K, N483R, I491M, I491V, I491L, A529P, K540R, S560K, S560R, T562K, T562R, S563K, S563R.
Another exemplary piggyBac-like transposon for modifying the genome of a cell is a Heliothis transposon comprising an ITR with the sequence of SEQ ID NO:122, a heterologous nucleic acid and a second ITR with the sequence of SEQ ID NO:123. The transposon may further be flanked by a copy of the tetranucleotide 5′-TTAA-3′ on each side, immediately adjacent to the ITRs and distal to the heterologous nucleic acid. The transposon may further comprise a sequence that is at least 95% or 100% identical to SEQ ID NO:124 on one side of the heterologous nucleic acid, and a sequence that is at least 95% or 100% identical to SEQ ID NO: 125 on the other side of the heterologous nucleic acid. This transposon may be transposed by a corresponding Heliothis transposase comprising a sequence at least 90% or 100% identical to SEQ ID NO:126. Preferably the transposase is a hyperactive variant of a naturally occurring transposase. Preferably the hyperactive variant transposase comprises one or more of the following amino acid changes, relative to the sequence of SEQ ID NO:126: S41V, 541I, S41L, L43S, L43T, V81E, V81D, D83S, D83T, V85L, V85I, V85M, P125S, P125T, Q126S, Q126T, Q131R, Q131K, Q131T, Q131S, S136V, S136I, S136L, S136M, E140C, E140A, N151Q, K169E, K169D, N212S, I239L, I239V, I239M, H241N, H241Q, T268D, T268E, T297C, M300R, M300K, M305N, M305Q, L312I, C316A, C316M, L321V, L321M, N322T, N322S, P351G, H357R, H357K, H357D, H357E, K360Q, K360N, E379P, K397S, K397T, Y421F, Y421W, V450I, V450L, V450M, Y495F, Y495W, A447N, A447D, A449S, A449V, K476L, V492A, 1500M, L585K and T595K.
An advantageous piggyBac-like transposon for modifying the genome of a cultured mammalian cell is an Oryzias transposon comprising an ITR with the sequence of SEQ ID NO:127, a heterologous nucleic acid and a second ITR with the sequence of SEQ ID NO:128. The transposon may further be flanked by a copy of the tetranucleotide 5′-TTAA-3′ on each side, immediately adjacent to the ITRs and distal to the heterologous nucleic acid. The transposon may further comprise a sequence that is at least 95% or 100% identical to SEQ ID NO:129 on one side of the heterologous nucleic acid, and a sequence that is at least 95% or 100% identical to SEQ ID NO:130 on the other side of the heterologous nucleic acid. This transposon may be transposed by a corresponding Oryzias transposase comprising a sequence at least 90% or 100% identical to SEQ ID NO:131. Preferably the transposase is a hyperactive variant of a naturally occurring transposase. Preferably the hyperactive variant transposase comprises one or more of the following amino acid changes, relative to the sequence of SEQ ID NO:131: E22D, A124C, Q131D, Q131E, L138V, L138I, L138M, D160E, Y164F, Y164W, I167L, I167V, I167M, T202R, T202K, I206L, I206V, I206M, I210L, I210V, I210M, N214D, N214E, V253I, V253L, V253M, V258L, V258I, V258M, A284L, A284I, A284M, A284V, V386I, V386M, V386L, M400L, M400I, M400V, S408E, S408D, L409I, L409V, L409M, V458L, V458M, V458I, V467I, V467M, V467L, L468I, L468V, L468M, A514R, A514K, V515I, V515M, V515L, R548K, D549K, D549R, D550R, D550K, S551K and S551R
Another exemplary piggyBac-like transposon for modifying the genome of a cell is an Agrotis transposon comprising an ITR with the sequence of SEQ ID NO:132, a heterologous nucleic acid, and a second ITR with the sequence of SEQ ID NO:133. The transposon may further be flanked by a copy of the tetranucleotide 5′-TTAA-3′ on each side, immediately adjacent to the ITRs and distal to the heterologous nucleic acid. The transposon may further comprise a sequence that is at least 95% or 100% identical to SEQ ID NO:134 on one side of the heterologous nucleic acid, and a sequence that is at least 95% or 100% identical to SEQ ID NO:135 on the other side of the heterologous nucleic acid. This transposon may be transposed by a corresponding Agrotis transposase comprising a sequence at least 90% or 100% identical to SEQ ID NO:136. Preferably the transposase is a hyperactive variant of a naturally occurring transposase.
Another piggyBac-like transposon for modifying the genome of a cell is a Helicoverpa transposon comprising an ITR with the sequence of SEQ ID NO:137, a heterologous nucleic acid and a second ITR with the sequence of SEQ ID NO:138. The transposon may further be flanked by a copy of the tetranucleotide 5′-TTAA-3′ on each side, immediately adjacent to the ITRs and distal to the heterologous nucleic acid. The transposon may further comprise a sequence that is at least 95% or 100% identical to SEQ ID NO:139 on one side of the heterologous nucleic acid, and a sequence that is at least 95% or 100% identical to SEQ ID NO:140 on the other side of the heterologous nucleic acid. This transposon may be transposed by a corresponding Helicoverpa transposase comprising a sequence at least 90% or 100% identical to SEQ ID NO:141. Preferably the transposase is a hyperactive variant of a naturally occurring transposase.
Another exemplary transposon for modifying the genome of cell is a Sleeping Beauty transposon from the Mariner family of transposons, for example one that comprises an ITR with the sequence of SEQ ID NO:142, a heterologous nucleic acid and a second ITR with the sequence of SEQ ID NO:143. Such a transposon can comprise a first transposon end with at least 90% or 100% sequence identity to SEQ ID NO:144, and a second transposon end with at least 90% or 100% sequence identity to SEQ ID NO:145. This transposon may be transposed by a corresponding Sleeping Beauty transposase comprising a sequence at least 90% or 100% identical to SEQ ID NO:146, including hyperactive variants thereof.
Another example transposon for modifying the genome of a mammalian cell is a TcBuster transposon, from the hAT family of transposons, for example one that comprises an ITR with the sequence of SEQ ID NO:147, a heterologous nucleic acid and a second ITR with the sequence of SEQ ID NO:148. Such a transposon can comprise a first transposon end with at least 90% or 100% sequence identity to SEQ ID NO:149, and a second transposon end with at least 90% or 100% sequence identity to SEQ ID NO:150. This transposon may be transposed by a corresponding TcBuster transposase comprising a sequence at least 90% or 100% identical to SEQ ID NO:151, including hyperactive variants thereof.
Nucleic acids comprising one or more transcriptional units as further described herein and gene transfer systems including the nucleic acids can be introduced into various cells and transgenic non-human animals. Cells into which nucleic acids are introduced are sometimes referred to as host cells or target cells or target host cells. Cells can be prokaryotic or eukaryotic. Mammalian cells, such as human, primate, or rodent are preferred. Insect cells can also be used. Cells can be a cell line of substantially identical cells obtained by expansion of a single cell or a mixed population of cells. Cells can be an immortal cell line or cells of finite life span. Some exemplary cell lines include CHO cell lines, various COS cell lines, HeLa cells, COS cells, 293 cells, U20S, HEK293 cells, L cells, and non-antibody-producing myelomas including Sp2/0 and NS0. Examples of cell types include hepatocytes, neural cells, muscle cells, blood cells, lymphocytes (B cells, natural killer cells and T cells), embryonic stem cells, somatic stem cells, hematopoietic cells, embryos, zygotes and sperm cells (some of which are open to be manipulated in an in vitro setting). Cells can be totipotent (i.e., a cell whose descendants can become any cell type in an organism, e.g., embryonic stem cells), pluripotent (cells whose descendants can differentiate into several restricted cell types, such as hematopoietic stem cells or other stem cells). Nucleic acid introduced into cells can also be used to generate transgenic nonhuman animals, e.g., rodents, such as mice, rats and rabbits, insects, fish, farm animals, such as goats, sheep, pigs, and cattle and non-human primates. Such transgenic animals typically incorporate an introduced heterologous nucleic acid into the genome of their germline and other cells. Such cells and transgenic animals can be used for production of proteins, e.g., therapeutic proteins or enzymes. Cells and transgenic animals can also be used for analyzing phenotypes conferred by expressed proteins, e.g., disease-associated phenotypes, and screening compounds for activity against such disease. Introduced nucleic acids can also be used to modify expression of genes of cells and transgenic animals, as for example, when the introduced nucleic acid encodes an inhibitor RNA to suppress expression of an endogenous gene. Suitable cells into which a nucleic acid has been introduced, particularly stem cells, can also be used for gene therapy. In some such application, the introduced nucleic acid includes a coding segment under inducible control, such that the coding segment encodes a polypeptide, which when expressed is lethal to the cell. Such a system allows an introduced cell to be eliminated by supplying an inducer of expression should the cell start undergoing inappropriate growth (e.g., becoming cancerous). After introduction of transcriptional units into cells, cells can be cultured and tetracycline or an analog be introduced into the culture medium to turn on or off expression of a coding segment. Likewise animals into which transcriptional units have been introduced can be contacted with tetracycline or an analog when a developmental stage is reached at which induction or suppression of expression of the coding segment on the first transcriptional unit is desired. Contacting can be by any conventional route including intravenous, intraperitoneal, subcutaneous, oral, transdermal, and intramuscular. Nucleic acid encoding one or more transcriptional units as described below can also be used in a coupled in vitro transcription and translation systems kits for which are commercially available from e.g., Thermo Fisher Scientific or New England Biolabs.
The invention provides several systems for placing a coding segment of interest under inducible control depending on the presence or absence of tetracycline, doxycycline or other analog. Such systems typically include two transcriptional units, one for expressing a coding segment of interest, the other for expressing a tet-repressor or modified tet-repressor to make expression of the first transcriptional unit dependent on the presence or absence of tetracycline or an analog thereof.
One expression system has a first transcriptional unit including in operable linkage and in order from 5′ to 3′, a promoter, one or more tet-operator sites, and a coding segment to be expressed. An exemplary transcriptional unit is shown in
A second transcriptional unit includes a promoter operably linked to a segment encoding a tet-repressor. An exemplary transcriptional unit is shown in
The invention further provides several systems for placing a coding segment of interest under inducible control depending on the presence or absence of cumate or other analog. Such systems typically include two transcriptional units, one for expressing a coding segment of interest, the other for expressing a cumate repressor or modified cumate repressor to make expression of the first transcriptional unit dependent on the presence or absence of cumate or an analog thereof.
One expression system has a first transcriptional unit including in operable linkage and in order from 5′ to 3′, a promoter, one or more cumate operators, and a coding segment to be expressed. An exemplary transcriptional unit is shown in
A second transcriptional unit includes a promoter operably linked to a segment encoding a cumate repressor. An exemplary transcriptional unit is shown in
The promoter of the first transcriptional unit (tet and cumate systems) is preferably a strong promoter to increase expression of the coding sequence after induction. The promoter is preferably a chimeric mouse-human CMV promoter as described above. Such a promoter is a preferred promoter to a human CMV promoter, which has been used for tetracycline-inducible expression previously. This is because elimination of one or more CpG sites from the human CMV promoter reduces the silencing effects of CpG methylation.
The promoter for the second transcriptional unit (tet and cumate systems) is preferably a promoter of reduced strength compared with the chimeric mouse-human CMV promoter described above or even with the human CMV promoter used in some conventional systems. Use of a reduced strength promoter reduces the expression of the tet repressor and thus allows induction of expression from the first transcriptional unit at lower levels of tetracycline or analog than when the same or similar strength promoters are used for both transcriptional units.
The first and second transcriptional units of this system (tet and cumate systems) are preferably combined on the same contiguous nucleic acid for introduction into cells. The nucleic acid can then be part of a transposon or other vector or gene delivery system as described above. Incorporating both transcriptional units on the same nucleic acid facilitates introduction of both units into cells because only one transfection and identification of transformed cells is necessary, but also contributes to cells integrating the same number of copies of each of the transcriptional units. The presence of equal numbers of both transcriptional units allows reproducible control of the ratio of tet-repressor to the number of copies of the first transcriptional unit. This reproducible control, preferably in combination with appropriate promoter selection as described above, can result in any of high levels of inducible expression, greater differentiation between levels of expression in presence and absence of inducer and inducible expression using lower levels of inducer.
A second tet system for inducible expression has a first transcriptional unit comprising in operable linkage and in order from 5′ to 3′, one or more tet-operators, a minimal promoter and a coding segment to be expressed.
The reverse form of induction occurs when the tet-repressor is replaced with a modified form of tet-repressor, which binds to tet-operators in the presence of tetracycline or analog. Here, in the absence of tetracycline or analog, the modified tet-repressor linked to transcriptional activation domain is expressed but does not bind significantly if at all to the tet-operators resulting in little or no recruitment of polymerase and other transcription factors, and little if any expression from the minimal promoter. When tetracycline or analog is supplied, the tetracycline or analog binds to the modified tet-repressor, which in turn binds to the tet-operators. The linked transcriptional activation domain then recruits polymerase and other transcriptional factor resulting in transcription of the coding segment from the minimal promoter. The coding segment is thus placed under inducible control of tetracycline or analog, being expressed in the presence of tetracycline and not expressed or expressed at much lower levels in the absence of tetracycline (e.g., least 2-, 5-, 10-, 20-, 50- or 100-fold increased expression on inductions).
Exemplary tet operator arrays can have a nucleotide sequence selected from SEQ ID NOS:8 and 9. An exemplary minimal human CMV promoter has SEQ ID NO:22. Exemplary 5′ UTRs comprising the Xenopus globin 5′ UTR can have a nucleotide sequence selected from SEQ ID NOS:29, 30 and 31. The exemplary arrays are linked in the order from 5′ to 3′: tet operator array, minimal human CMV promoter, 5′ UTR. Any of the exemplified tet operator arrays, can be used with any exemplified minimal human CMV promoter, and any exemplified 5′ UTR in the order specified. An exemplary tet operator array fused to the 5′ end of a chimpanzee minimal CMV promoter has a nucleotide sequence SEQ ID NO:26. Preferably the 3′ end of the minimal chimpanzee CMV promoter is joined to a 5′ UTR comprising the Xenopus globin 5′ UTR with nucleotide sequence SEQ ID NO:29. An exemplary sequence comprising the minimal chimpanzee CMV promoter joined to a 5′ UTR comprising the Xenopus globin 5′ UTR has nucleotide sequence SEQ ID NO:25. An exemplary sequence comprising a tet operator array fused to the minimal chimpanzee CMV promoter joined to a 5′ UTR comprising the Xenopus globin 5′ UTR has nucleotide sequence SEQ ID NO:27.
A second cumate system for inducible expression has a first transcriptional unit comprising in operable linkage and in order from 5′ to 3′, one or more cumate-operators, a minimal promoter and a coding segment to be expressed. FIG. 7_shows an exemplary form of this transcriptional unit with an array of cumate operators separated by spacers upstream of a minimal promoter, operably linked to a coding segment encoding a 5′ UTR and open reading frame to be expressed. The 5′ UTR preferably comprises Xenopus globin UTR of SEQ ID NO:29. Preferably 2-10 or 3-8, e.g., 2, 3, 4, 5, 6, 7, 9, or 10 operators are present in the array, optionally separated by spacers of 1-25 bp. A second transcriptional unit includes in operable linkage a promoter and a segment encoding either a cumate repressor or a modified cumate repressor fused to a transcriptional activation domain, such as VP16. When the cumate repressor fused to the transcriptional activation domain is expressed from the second transcriptional unit, it binds to the array of cumate operators in the absence of cumate or analog. The transcriptional activation domain recruits polymerase and other transcription factors resulting in transcription from the minimal promoter and expression of the coding segment. In the presence of cumate or analog, the cumate repressor can no longer bind the cumate operator array or does so to a much-reduced extent, inhibiting or eliminating expression of the coding segment. Thus, the coding segment is placed under cumate or analog inducible control being expressed in the absence of cumate or analog.
The reverse form of induction occurs when the cumate repressor is replaced with a modified form of cumate repressor, which binds to cumate-operators in the presence of cumate or analog. Here, in the absence of cumate or analog, the modified cumate repressor linked to transcriptional activation domain is expressed but does not bind significantly if at all to the cumate operators resulting in little or no recruitment of polymerase and other transcription factors, and little if any expression from the minimal promoter. When cumate or analog is supplied, the cumate or analog binds to the modified cumate repressor, which in turn binds to the cumate operators. The linked transcriptional activation domain then recruits polymerase and other transcriptional factor resulting in transcription of the coding segment from the minimal promoter. The coding segment is thus placed under inducible control of cumate or analog, being expressed in the presence of cumate and not expressed or expressed at much lower levels in the absence of cumate (e.g., least 2-, 5-, 10-, 20-, 50- or 100-fold increased expression on inductions).
Exemplary cumate operator array-promoter fusions are SEQ ID NOS:164-166. Exemplary cumate operator promoter fusions including a 5′ UTR are SEQ ID NOS:167-169.
Again (tet and cumate systems), selection of promoters for the first and second transcriptional units and combination of the units into the same contiguous molecule can improve the efficiency and reproducibility of inducible control. As already mentioned, the promoter for the first transcriptional unit is a minimal promoter. A preferred promoter is the minimal chimp CMV promoter described above, which results in higher level expression of a coding segment in the present systems than a minimal human CMV promoter used in conventional systems. The minimal chimp promoter, when activated by binding of a transcriptional activation domain as described above, is more active than a minimal human CMV promoter used in conventional tetracycline-inducible vectors. Preferred promoters for the second transcriptional unit are the intermediate strength promoters described above, although other promoters can also be used. Again, incorporation of both transcriptional units on the same nucleic acid for introduction into cells is advantageous for obtaining a cell that has integrated both transcription units and coordinating expression of the second transcriptional unit with the number of copies of the first transcriptional unit to be regulated. This reproducible control preferably in combination with appropriate promoter selection as described above can result in any of high levels of inducible expression, greater differentiation between levels of expression in presence and absence of inducer and inducible expression using lower levels of inducer.
We tested several embodiments of tet-inducible promoters for their ability to respond to increasing concentrations of doxycycline after transient transfection into (human) HEK 293 cells. Two promoters were constructed in which the 12 bp to the 5′ of the transcriptional start site were removed and replaced by a pair of tet operators with nucleotide sequence SEQ ID NO:2. The first promoter was constructed by modification of the human CMV promoter with nucleotide sequence SEQ ID NO:14. Removal of the 12 bp to the 5′ of the transcriptional start site produced nucleotide sequence SEQ ID NO:36. Addition of 2x tet operators to this truncated promoter produced nucleotide sequence SEQ ID NO:15. The second promoter constructed by modification of a chimeric murine-human CMV promoter comprising the first 161 bp of the murine CMV promoter with nucleotide sequence SEQ ID NO:16 fused to the last 127 bp of the human CMV promoter with nucleotide sequence SEQ ID NO:13: the junction between the two promoters comprised a 12 bp sequence common to both: 5′-ACGTCAATGGGA-3′, and the sequence of the resulting chimeric promoter had nucleotide sequence SEQ ID NO:12. Removal of the 12 bp to the 5′ of the transcriptional start site produced nucleotide sequence SEQ ID NO:10. Addition of 2x tet operators to this truncated promoter produced nucleotide sequence SEQ ID NO:11.
The 3′ end of the second tet operator in each of the two promoters described above, was fused to a 5′ UTR with nucleotide sequence SEQ ID NO:31, which comprised a Xenopus globin 5′UTR modified to include a Kozak sequence (the modified Xenopus globin 5′UTR has nucleotide sequence SEQ ID NO:29). The UTR was fused to an open reading frame encoding Dasher GFP with amino acid sequence of SEQ ID NO:32, such that transcription from the promoter would result in expression of the GFP.
Each of the two different tet-inducible promoter-GFP transcriptional units was cloned onto a plasmid comprising a second transcriptional unit. The second transcriptional unit comprised an open reading frame encoding a tet repressor with amino acid sequence of SEQ ID NO:5. The open reading frame encoding the repressor was linked to a promoter operable in mammalian cells. Promoters selected were a PGK promoter with nucleotide sequence SEQ ID NO:18, an EEF2 promoter with nucleotide sequence SEQ ID NO:17, a murine CMV promoter with nucleotide sequence SEQ ID NO:16, and a human CMV promoter with nucleotide sequence SEQ ID NO:13.
HEK293 suspension cells were grown in flasks in Expi293 media at 37° C. with 8% CO2, in an incubator with 25 mm throw at 125 RPM. The cells were passaged at a density of 2.5×106 cells/ml 24 hours prior to transfection. Cells were diluted to 3×106 cells/ml, and 700 ul were aliquoted into 96 deep well plates. Each DNA construct was transfected three independent times using ExpiFectamine™ 293 Transfection Reagent at a 1:2.7 DNA:Transfection reagent ratio. After transfection, the cells were placed in an incubator at 3° C. with 8% CO2, with a 3 mm throw shaking at 1,000 RPM. 24 hours post-transfection, the cultures were fed with ExpiFectamine™ 293 Transfection Enhancer 1 and ExpiFectamine™ 293 Transfection Enhancer 2. After this feeding, the cultures were induced by the addition doxycycline at either 10, 30, or 100 ng/ml, with a control to which no doxycycline was added. After doxycycline addition, 100 ul of culture was taken and diluted with 100 ul of PBS. Expression was measured using a SpectroMax M2. OD600 was measured in a flat-bottom, clear-well plate. Green fluorescent protein expression was measured in a black-well plate, with excitation at 485 nm and emission at 525 nm. Sampling was repeated 24, 48, and 72 hours post-induction. The average fluorescence at 525 nm for each set of 3 replicates was divided by optical density at 600 nm for each set of 3 replicates to provide an average measure of fluorescence normalized by cell number. Results are shown in Table 1.
Row 6 of Table 1 shows the behavior of a construct in which the human CMV promoter was modified by addition of tet operators to serve as the inducible promoter, and where the human CMV promoter was also used as the promoter from which the tet repressor was transcribed. Expression from this construct was induced only at the highest concentration of doxycycline tested (100 ng/ml). Similar performance was observed when the human-murine chimeric CMV promoter was modified by addition of tet operators to serve as the inducible promoter, and where the murine CMV promoter was also used as the promoter from which the tet repressor was transcribed (Table 1 row 5), except that the maximum inducible expression was about twice as high as obtained using the human CMV promoter. When weaker promoters EEF2 or PGK were used to drive expression of the tet repressor, induction of expression was seen at lower levels of doxycycline (rows 4 and 3 respectively). This shows that the threshold for doxycycline induction of expression can be modulated by choice of promoter used to express the tet repressor: weaker promoters express lower levels of tet repressor, so less doxycycline is required to bind to the tet repressor to prevent repressor binding to the operators and remove the block to transcriptional initiation.
We tested several embodiments of tet-inducible promoters for their ability to respond to increasing concentrations of doxycycline after transient transfection into CHO cells. The same DNA constructs were used as described in Example 1.
CHO-s cells were grown in flasks in ExpiCHO media at 37° C. with 5% CO2, in an incubator with 25 mm throw at 125 RPM. The cells were passaged at a density of 4.5×106 cells/ml 24 hours prior to transfection. Cells were diluted to 6×106 cells/ml, and 800 ul were aliquoted into 96 deep well plates. Each DNA construct was transfected three independent times using ExpiFectamine™ CHO Transfection Reagent at a 1:4 DNA:Transfection reagent ratio. After transfection, the cells were placed in an incubator at 37° C. with 5% CO2, with a 3 mm throw shaking at 1,000 RPM. 24 hours post-transfection, the cultures were fed with ExpiFectamine™ CHO Enhancer and ExpiCHO Feed. After feeding the cells, the cultures were induced by the addition doxycycline at either 10, 30, or 100 ng/ml, with a control to which no doxycycline was added. After doxycycline addition, 100 ul of culture was taken and diluted with 100 ul of PBS. Expression was measured using a SpectroMax M2. OD600 was measured in a flat-bottom, clear-well plate. Green fluorescent protein expression was measured in a black-well plate, with excitation at 485 nm and emission at 525 nm. Sampling was repeated 24, 48, and 72 hours post-induction. The average fluorescence at 525 nm for each set of 3 replicates was divided by optical density at 600 nm for each set of 3 replicates to provide an average measure of fluorescence normalized by cell number. Results are shown in Table 2.
Table 2 shows a similar pattern to inducible expression in transient HEK cells, except that the human and murine CMV constructs shown in rows 5 and 6 have reversed places. Expression from the construct in which the murine CMV promoter was used as the promoter from which the tet repressor was transcribed (Table 2 row 5) was induced only at the higher concentrations of doxycycline tested (a little at 30 ng/ml, more at 100 ng/ml). In contrast, higher expression at lower doxycycline concentrations was observed when the human CMV promoter was used as the promoter from which the tet repressor was transcribed (Table 2 row 6). This is consistent with the murine CMV promoter being stronger than the human CMV promoter in rodent cells and the human CMV promoter being stronger than the murine CMV promoter human cells. Again, when weaker promoters EEF2 or PGK were used to drive expression of the tet repressor, induction of expression was seen at lower levels of doxycycline (rows 4 and 3 respectively). Inducible expression was higher from the chimeric human murine CMV promoter than from the human CMV promoter. Again the threshold for doxycycline induction of expression can be modulated by choice of promoter used to express the tet repressor: weaker promoters express lower levels of tet repressor, so less doxycycline is required to bind to the tet repressor to prevent repressor binding to the operators and remove the block to transcriptional initiation.
We tested several embodiments of tet-inducible promoters for their ability to respond to increasing concentrations of doxycycline when stably integrated into CHO-K1 cells. DNA constructs were used as described in Example 1. Each construct further comprised a third transcriptional unit expressing glutamine synthetase. The three transcriptional units were flanked by a pair of insulators: an HS4 insulator on one side and a D4Z4 core insulator on the other side. The three transcriptional units and the insulators were all placed into a Xenopus piggyBac-like transposon. On one side of the transposon was a 5′-TTAA′3′ target integration sequence, immediately followed by a first ITR with nucleotide sequence SEQ ID NO:41 immediately followed by a left transposon end with nucleotide sequence SEQ ID NO:44. On the other side of the transposon was a right transposon end with nucleotide sequence SEQ ID NO:45, immediately followed by a second ITR with nucleotide sequence SEQ ID NO:42, immediately followed by a 5′-TTAA′3′ target integration sequence.
Transposons were co-transfected with mRNA encoding transposase with amino acid sequence SEQ ID NO:54 into a CHO cell line with no functional glutamine synthetase gene. Cells were grown in the absence of glutamine added to the media until their viability reached 95%. Three cultures for each selected cell pool were then grown in EX-CELL® Advanced™ CHO Fed-batch Medium media at 37° C. with 5% CO2, in an incubator with 25 mm throw at 120 RPM. The cells were passaged at a density of 2×106 cells/ml 24 hours prior to induction. Cells were diluted to 6×106 cells/ml, and 800 ul were aliquoted into 96 deep well plates. Cultures were induced by the addition doxycycline at either 10, 30, 100, 300, 1000 or 3000 ng/ml, with a control to which no doxycycline was added. After doxycycline addition, 100 ul of culture was taken and diluted with 100 ul of PBS. Expression was measured using a SpectroMax M2. OD600 was measured in a flat-bottom, clear-well plate. Green fluorescent protein expression was measured in a black-well plate, with excitation at 485 nm and emission at 525 nm. Sampling was repeated 24 and 48 hours post-induction. The average fluorescence at 525 nm for each set of 3 replicates was divided by optical density at 600 nm for each set of 3 replicates to provide an average measure of fluorescence normalized by cell number. Results are shown in Table 3.
Table 3 shows a similar pattern to inducible expression in transiently transfected CHO cells, except that the overall induction levels were substantially lower. Lowest inducible expression was seen where the tet repressor was transcribed from the very active human or murine CMV promoters (Table 3 rows 5 and 6). The constructs in which tet repressor was transcribed from the more weakly active promoters showed expression that was induced at lower levels of doxycycline (expression started at 30 ng/ml when the tet repressor was transcribed from EEF2 or PGK promoters, while 300 ng/ml doxycycline) and reached 1.7-fold higher levels at high concentrations of doxycycline than constructs where the tet repressor was transcribed from a CMV promoter.
We tested several embodiments of tet-inducible promoters for their ability to respond to increasing concentrations of doxycycline when stably integrated into CHO-K1 cells. DNA transposon constructs were similar to those described in Example 3, except that additional versions were made with other promoters driving expression of the tet repressor. Transposon compositions are indicated in Table 4.
Transposons were co-transfected with mRNA encoding transposase with amino acid sequence SEQ ID NO:54 into a CHO cell line with no functional glutamine synthetase gene. Cells were grown in the absence of glutamine added to the media until their viability reached 95%. Three cultures of each stably selected cell pool were then grown in EX-CELL® Advanced™ CHO Fed-batch Medium media at 37° C. with 5% CO2, in an incubator with 25 mm throw at 120 RPM. The cells were passaged at a density of 2×106 cells/ml 24 hours prior to induction. Cells were diluted to 6×106 cells/ml, and 800 ul were aliquoted into 96 deep well plates. Cultures were induced by the addition doxycycline at either 10, 30, 100, 300 or 1000 ng/ml, with a control to which no doxycycline was added. After doxycycline addition, 100 ul of culture was taken and diluted with 100 ul of PBS. Expression was measured using a SpectroMax M2. OD600 was measured in a flat-bottom, clear-well plate. Green fluorescent protein expression was measured in a black-well plate, with excitation at 485 nm and emission at 525 nm. Sampling was repeated 24 and 48 hours post-induction. The average fluorescence at 525 nm for each set of 3 replicates was divided by optical density at 600 nm for each set of 3 replicates to provide an average measure of fluorescence normalized by cell number. Results are shown in Table 4.
Table 4 shows a similar pattern to the inducible expression in stably transfected CHO cells shown in Table 3. Most notably, two constructs whose inducible expression is shown in Table 4 differed only in the 6 nucleotides preceding the tet repressor open reading frame (Table 4 rows 6 and 7). The construct shown in row 6 had an optimal Kozak sequence (5′-GCCGCCACC-3′), while the construct shown in row 7 had a de-optimized Kozak (5′-GCCTTTTTT-3′). The de-optimized Kozak results in reduced translational initiation and thus in less tet repressor being present. The consequence of this was that this inducible promoter was induced at only 10 ng/ml doxycycline, and was fully induced at 30 ng/ml doxycycline, whereas the otherwise identical construct with the optimal Kozak initiating translation of the tet repressor did not begin induction until 100 ng/ml doxycycline, and only became fully induced by 1,000 ng/ml doxycycline.
Tables 1, 2, 3 and 4 show that expression levels obtained from tet-inducible promoters, and the amount of inducer required to induce expression, differ depending on the level of expression of the tet repressor. The benefit of combining the transcriptional unit expressing the tet repressor onto the same transposon as the inducible transcriptional unit, is that it minimizes the potential variation in relative expression of tet repressor compared with the number of copies of the inducible promoter in the cell. This improves the predictability of the performance of the system.
We tested several embodiments of tet-inducible promoters for their ability to respond to increasing concentrations of doxycycline after transient transfection into HEK 293 cells.
Three different minimal CMV promoters, from human, mouse and chimpanzee CMV (with nucleotide sequences SEQ ID NO:22, 23 and 24 respectively) were each fused, at their 5′ ends, to an array of 8 tet operators with nucleotide sequence SEQ ID NO:3, to create 3 tet-inducible promoters. The 3′ end of each minimal promoter was fused to a 5′UTR with nucleotide sequence SEQ ID NO:30. A control inducible promoter was also constructed by fusing a previously described array of 7 tet operators with nucleotide sequence SEQ ID NO:4 to the 5′ end of a previously described modified minimal human CMV promoter with nucleotide sequence SEQ ID NO:38. The 3′ end of this control minimal promoter was fused to a 5′UTR with nucleotide sequence SEQ ID NO:39. The 3′ end of each 5′UTR was fused to an open reading frame encoding Dasher GFP with amino acid sequence SEQ ID NO:32.
Each of the different tet-inducible promoter-GFP transcriptional units was cloned onto a plasmid comprising a second transcriptional unit. The second transcriptional unit comprised an open reading frame encoding a transcriptional activator comprising a modified tet repressor with amino acid sequence of SEQ ID NO:6, fused to a VP16 transcriptional activator with amino acid sequence SEQ ID NO:7. In addition the control tet-inducible promoter GFP transcriptional unit was cloned onto a plasmid comprising a second transcriptional unit comprising an open reading frame encoding a transcriptional activator comprising a modified tet repressor with amino acid sequence of SEQ ID NO:6, fused to an alternative VP16 transcriptional activator with amino acid sequence SEQ ID NO:40. In each case the open reading frame encoding the transcriptional activator was linked to an SV40 promoter with nucleotide sequence SEQ ID NO:28, which promoter is operable in mammalian cells.
HEK293 suspension cells were grown in flasks in Expi293 media at 37° C. with 8% CO2, in an incubator with 25 mm throw at 125 RPM. The cells were passaged at a density of 2.5×106 cells/ml 24 hours prior to transfection. Cells were diluted to 3×106 cells/ml, and 700 ul were aliquoted into 96 deep well plates. Each DNA construct was transfected three independent times using ExpiFectamine™ 293 Transfection Reagent at a 1:2.7 DNA:Transfection reagent ratio. After transfection, the cells were placed in an incubator at 37° C. with 8% CO2, with a 3 mm throw shaking at 1,000 RPM. 24 hours post-transfection, the cultures were fed with ExpiFectamine™ 293 Transfection Enhancer 1 and ExpiFectamine™ 293 Transfection Enhancer 2. After this feeding, the cultures were induced by the addition doxycycline at either 10, 30, or 100 ng/ml, with a control to which no doxycycline was added. After doxycycline addition, 100 ul of culture was taken and diluted with 100 ul of PBS. Expression was measured using a SpectroMax M2. OD600 was measured in a flat-bottom, clear-well plate. Green fluorescent protein expression was measured in a black-well plate, with excitation at 485 nm and emission at 525 nm. Sampling was repeated 24, 48, and 72 hours post-induction. The average fluorescence at 525 nm for each set of 3 replicates was divided by optical density at 600 nm for each set of 3 replicates to provide an average measure of fluorescence normalized by cell number. Results are shown in Table 5.
Table 5 (rows 4 and 5) shows that the control tet-inducible minimal human CMV promoter resulted in similar induction profiles using either of the different transcriptional activators (with amino acid sequences SEQ ID NOS:8 and 9, which comprise the VP16-derived activation domains with amino acid sequences SEQ ID NOS:7 and 40 respectively). Table 5 also shows that the array of 8 tet operators joined to minimal human CMV promoter with nucleotide sequence SEQ ID NO:22 performs very comparably to the control tet-inducible minimal human CMV promoter (compare Table 5 row 6 with row 5). The minimal murine CMV promoter showed substantially lower levels of induced gene expression than the human minimal CMV promoter sequences (Table 5 row 7). However the inducible promoter comprising the chimpanzee minimal CMV promoter resulted in consistently higher levels of expression than any of the other inducible promoters (Table 5 row 8).
Thus a tet operator array fused to the 5′ end of a chimpanzee minimal CMV promoter with nucleotide sequence SEQ ID NO:24 produces a highly effective tet-inducible promoter.
We tested several embodiments of tet-inducible promoters for their ability to respond to increasing concentrations of doxycycline after transient transfection into CHO-S cells.
Constructs were as described in Example 5. CHO-s cells were grown in flasks in ExpiCHO media at 37° C. with 5% CO2, in an incubator with 25 mm throw at 125 RPM. The cells were passaged at a density of 4.5×106 cells/ml 24 hours prior to transfection. Cells were diluted to 6×106 cells/ml, and 800 ul were aliquoted into 96 deep well plates. Each DNA construct was transfected three independent times using ExpiFectamine™ CHO Transfection Reagent at a 1:4 DNA:Transfection reagent ratio. After transfection, the cells were placed in an incubator at 37° C. with 5% CO2, with a 3 mm throw shaking at 1,000 RPM. 24 hours post-transfection, the cultures were fed with ExpiFectamine™ CHO Enhancer and ExpiCHO Feed. After feeding the cells, the cultures were induced by the addition doxycycline at either 10, 30, or 100 ng/ml, with a control to which no doxycycline was added. After doxycycline addition, 100 ul of culture was taken and diluted with 100 ul of PBS. Expression was measured using a SpectroMax M2. OD600 was measured in a flat-bottom, clear-well plate. Green fluorescent protein expression was measured in a black-well plate, with excitation at 485 nm and emission at 525 nm. Sampling was repeated 24, 48, and 72 hours post-induction. The average fluorescence at 525 nm for each set of 3 replicates was divided by optical density at 600 nm for each set of 3 replicates to provide an average measure of fluorescence normalized by cell number. Results are shown in Table 6.
Table 6 shows that the tet-inducible promoters performed similarly in transiently transfected CHO cells as they did in transiently transfected HEK 293 cells. The inducible promoter comprising the chimpanzee minimal CMV promoter resulted in consistently higher levels of expression than any of the other inducible promoters (Table 6 row 8).
We tested several embodiments of tet-inducible promoters for their ability to respond to increasing concentrations of doxycycline after stable integration into CHO-K1 cells.
DNA constructs were used as described in Example 5. Each construct further comprised a third transcriptional unit expressing glutamine synthetase. The three transcriptional units were flanked by a pair of insulators: an HS4 insulator on one side and a D4Z4 core insulator on the other side. The three transcriptional units and the insulators were all placed into a Xenopus piggyBac-like transposon. On one side of the transposon was a 5′-TTAA′3′ target integration sequence, immediately followed by a first ITR with nucleotide sequence SEQ ID NO:41, immediately followed by a left transposon end with nucleotide sequence SEQ ID NO:44. On the other side of the transposon was a right transposon end with nucleotide sequence SEQ ID NO:45, immediately followed by a second ITR with nucleotide sequence SEQ ID NO:42, immediately followed by a 5′-TTAA′3′ target integration sequence.
Transposons were co-transfected with mRNA encoding transposase with amino acid sequence SEQ ID NO:54 into a CHO cell line with no functional glutamine synthetase gene. Cells were grown in the absence of glutamine added to the media until their viability reached 95%. Three cultures for each selected cell pool were then grown in EX-CELL® Advanced™ CHO Fed-batch Medium media at 37° C. with 5% CO2, in an incubator with 25 mm throw at 120 RPM. The cells were passaged at a density of 2×106 cells/ml 24 hours prior to induction. Cells were diluted to 6×106 cells/ml, and 800 ul were aliquoted into 96 deep well plates. Cultures were induced by the addition doxycycline at either 10, 30 or 100 ng/ml, with a control to which no doxycycline was added. After doxycycline addition, 100 ul of culture was taken and diluted with 100 ul of PBS. Expression was measured using a SpectroMax M2. OD600 was measured in a flat-bottom, clear-well plate. Green fluorescent protein expression was measured in a black-well plate, with excitation at 485 nm and emission at 525 nm. Sampling was repeated 24 and 48 hours post-induction. The average fluorescence at 525 nm for each set of 3 replicates was divided by optical density at 600 nm for each set of 3 replicates to provide an average measure of fluorescence normalized by cell number. Results are shown in Table 7. Table 7 shows that the minimal chimpanzee CMV tet-inducible promoter shows very good inducible expression when stably integrated into the genome of a host cell.
We tested three embodiments of tet-inducible promoters with different numbers of tet operators for their ability to respond to increasing concentrations of doxycycline after stable integration into CHO-K1 cells.
A minimal CMV promoter from chimpanzee CMV (with nucleotide sequence SEQ ID NO:24) was fused at its 5′ end, to an array of 3, 6 or 8 tet operators (with nucleotide sequences SEQ ID NOs: 153, 152 and 3 respectively), to create 3 tet-inducible promoters. The 3′ end of each minimal promoter was fused to a 5′UTR with nucleotide sequence SEQ ID NO:30. The 3′ end of each 5′UTR was fused to an open reading frame encoding Dasher GFP with amino acid sequence SEQ ID NO:32.
Each of the different tet-inducible promoter-GFP transcriptional units was cloned onto a plasmid comprising a second transcriptional unit. The second transcriptional unit comprised an open reading frame encoding a transcriptional activator comprising a modified tet repressor with amino acid sequence of SEQ ID NO:6, fused to a VP16 transcriptional activator with amino acid sequence SEQ ID NO:7. In each case the open reading frame encoding the transcriptional activator was linked to an SV40 promoter with nucleotide sequence SEQ ID NO:28, which promoter is operable in mammalian cells. Each construct further comprised a third transcriptional unit expressing glutamine synthetase. The three transcriptional units were flanked by a pair of insulators: an HS4 insulator on one side and a D4Z4 core insulator on the other side. The three transcriptional units and the insulators were all placed into a Xenopus piggyBac-like transposon. On one side of the transposon was a 5′-TTAA′3′ target integration sequence, immediately followed by a first ITR with nucleotide sequence SEQ ID NO:41, immediately followed by a left transposon end with nucleotide sequence SEQ ID NO:44. On the other side of the transposon was a right transposon end with nucleotide sequence SEQ ID NO:45, immediately followed by a second ITR with nucleotide sequence SEQ ID NO:42, immediately followed by a 5′-TTAA′3′ target integration sequence.
Transposons were co-transfected with mRNA encoding transposase with amino acid sequence SEQ ID NO:54 into a CHO cell line with no functional glutamine synthetase gene. Cells were grown in the absence of glutamine added to the media until their viability reached 95%. Three cultures for each selected cell pool were then grown in EX-CELL® Advanced™ CHO Fed-batch Medium media at 37° C. with 5% CO2, in an incubator with 25 mm throw at 120 RPM. The cells were passaged at a density of 2×106 cells/ml 24 hours prior to induction. Cells were diluted to 6×106 cells/ml, and 800 ul were aliquoted into 96 deep well plates. Cultures were induced by the addition doxycycline at either 10, 30, 100 or 300 ng/ml, with a control to which no doxycycline was added. After doxycycline addition, 100 ul of culture was taken and diluted with 100 ul of PBS. Expression was measured using a SpectroMax M2. OD600 was measured in a flat-bottom, clear-well plate. Green fluorescent protein expression was measured in a black-well plate, with excitation at 485 nm and emission at 525 nm. Sampling was repeated 24, 48 and 72 hours post-induction. The average fluorescence at 525 nm for each set of 3 replicates was divided by optical density at 600 nm for each set of 3 replicates to provide an average measure of fluorescence normalized by cell number. Results are shown in Table 8. Table 8 shows that the minimal chimpanzee CMV tet-inducible promoter, operably linked to 3, 6 or 8 repeats of the tet operator, shows very good inducible expression when stably integrated into the genome of a host cell. It also shows that a smaller number of repeats resulted in a higher level of expression in the absence of doxycycline (compare Table 8 columns B, G, L and Q for row 3 with 8 tet operator repeats, row 4 with 6 tet operator repeats, and row 5 with 3 tet operator repeats. As a control, Table 8 row 6 shows the average fluorescence in cells with no integrated inducible transposon).
We tested a hybrid human-mouse promoter comprising a segment of a mouse CMV promoter of SEQ ID NO:16 upstream from a segment of a human CMV promoter of SEQ ID NO:13, wherein the hybrid promoter lacks a CG motif at positions corresponding to positions 42 and 43 of SEQ ID NO:13. The junction between contiguous segments is within the sequence ACGTCAATGGGA, which is common to the mouse and human CMV promoter sequences. The promoter has nucleotide sequence SEQ ID NO: 12, which comprises SEQ ID NO: 10 plus 13 bases (5′-GTTTAGTGAACCG-3′) immediately 5′ of the transcriptional start site.
The hybrid promoter was operably linked to an open reading frame encoding an antibody heavy chain with amino acid sequence SEQ ID NO: 154. The construct further comprised a mouse CMV promoter with nucleotide sequence SEQ ID NO: 16 operably linked to an open reading frame with amino acid sequence SEQ ID NO: 155. The construct further comprised a third transcriptional unit expressing glutamine synthetase. The three transcriptional units were flanked by a pair of insulators: an HS4 insulator on one side and a D4Z4 core insulator on the other side. The three transcriptional units and the insulators were all placed into a Xenopus piggyBac-like transposon. On one side of the transposon was a 5′-TTAA′3′ target integration sequence, immediately followed by a first ITR with nucleotide sequence SEQ ID NO:41, immediately followed by a left transposon end with nucleotide sequence SEQ ID NO:44. On the other side of the transposon was a right transposon end with nucleotide sequence SEQ ID NO:45, immediately followed by a second ITR with nucleotide sequence SEQ ID NO:42, immediately followed by a 5′-TTAA′3′ target integration sequence.
Two additional transposon constructs were prepared, in which the hybrid promoter operably linked to the antibody heavy chain was replaced by either a murine CMV promoter with nucleotide sequence SEQ ID NO: 16, or by a human CMV promoter with nucleotide sequence SEQ ID NO: 13.
Transposons were co-transfected with mRNA encoding transposase with amino acid sequence SEQ ID NO:54 into a CHO cell line with no functional glutamine synthetase gene. Cells were grown in the absence of glutamine added to the media until their viability reached 95%. Recovered pools were then grown in a 7-day fed-batch using Sigma Advanced Fed Batch media. Antibody titers were measured in culture supernatant using an Octet. Table 9 shows the titers measured at day 7, and the specific productivities (calculated as the amount of antibody produced per cell per day).
As shown in Table 9, the volumetric (Table 9 column D) and specific (Table 9 column C) productivities obtained using the hybrid promoter with nucleotide sequence comprising SEQ ID NO: 10 operably linked to the heavy chain open reading frame (Table 9 row 1) were higher than those obtained using either of the promoters from which the hybrid promoter was derived (Table 9 rows 2 and 3). We conclude that the hybrid human/murine CMV promoter comprising SEQ ID NO: 10 is advantageous for expression of heterologous proteins in CHO cells.
Table 1. DNA constructs comprising two transcriptional units were prepared as described in Example 3. Each construct comprised a first transcriptional unit comprising an inducible promoter whose name is given in column A, operably linked to an open reading frame encoding a green fluorescent protein. The SEQ ID NO giving the nucleotide sequence of the inducible promoter, lacking the 12 bp before the transcriptional start site is shown in column B, and the SEQ ID NO giving the nucleotide sequence of the inducible promoter including the pair of tet operators is shown in column C. Each construct further comprised a second transcriptional unit comprising a constitutive promoter operable in a mammalian cell, operably linked to an open reading frame encoding a tet repressor with amino acid sequence SEQ ID NO:5. This promoter name is shown in column D, and the SEQ ID NO giving the nucleotide sequence of the promoter linked to the tet repressor is shown in column E. Each construct was transfected into HEK 293 cells in 3 independent transfections, induced with doxycycline and cell numbers and fluorescence were measured as described in Example 1. Fluorescence was measured at 525 nm and cell density was measured as optical density at 600 nm, with each condition measured for 3 independent transfections. The average fluorescence at 525 nm for each set of 3 replicates was divided by optical density at 600 nm for each set of 3 replicates to provide an average measure of fluorescence normalized by cell number, shown in columns F to U. Days post-induction are shown in row 1, doxycycline concentrations are shown in row 2.
Table 2. DNA constructs comprising two transcriptional units were prepared as described in Example 1. Each construct comprised a first transcriptional unit comprising an inducible promoter whose name is given in column A, operably linked to an open reading frame encoding a green fluorescent protein. The SEQ ID NO giving the nucleotide sequence of the inducible promoter, lacking the 12 bp before the transcriptional start site is shown in column B, and the SEQ ID NO giving the nucleotide sequence of the inducible promoter including the pair of tet operators is shown in column C. Each construct further comprised a second transcriptional unit comprising a constitutive promoter operable in a mammalian cell, operably linked to an open reading frame encoding a tet repressor with amino acid sequence SEQ ID NO:5. This promoter name is shown in column D, and the SEQ ID NO giving the nucleotide sequence of the promoter linked to the tet repressor is shown in column E. Each construct was transfected into CHO-s cells in 3 independent transfections, induced with doxycycline and cell numbers and fluorescence were measured as described in Example 2. Fluorescence was measured at 525 nm and cell density was measured as optical density at 600 nm, with each condition measured for 3 independent transfections. The average fluorescence at 525 nm for each set of 3 replicates was divided by optical density at 600 nm for each set of 3 replicates to provide an average measure of fluorescence normalized by cell number, shown in columns F to U. Days post-induction are shown in row 1, doxycycline concentrations are shown in row 2.
Table 3. DNA transposons comprising two transcriptional units were prepared as described in Example 1. Each transposon comprised a first transcriptional unit comprising an inducible promoter whose name is given in column A, operably linked to an open reading frame encoding a green fluorescent protein. The SEQ ID NO giving the nucleotide sequence of the inducible promoter, lacking the 12 bp before the transcriptional start site is shown in column B, and the SEQ ID NO giving the nucleotide sequence of the inducible promoter including the pair of tet operators is shown in column C. Each transposon further comprised a second transcriptional unit comprising a constitutive promoter operable in a mammalian cell, operably linked to an open reading frame encoding a tet repressor with amino acid sequence SEQ ID NO:5. This promoter name is shown in column D, and the SEQ ID NO giving the nucleotide sequence of the promoter linked to the tet repressor is shown in column E. Transposons were stably transfected into CHO cells and selected, after recovery three separate cultures for each stable cell line were induced with doxycycline and cell numbers and fluorescence were measured as described in Example 3. Fluorescence was measured at 525 nm and cell density was measured as optical density at 600 nm. The average fluorescence at 525 nm for each set of 3 replicates was divided by optical density at 600 nm for each set of 3 replicates to provide an average measure of fluorescence normalized by cell number shown in columns F to Z. Days post-induction are shown in row 1, doxycycline concentrations are shown in row 2.
Table 4. DNA transposons comprising two transcriptional units were prepared as described in Example 4. Each transposon comprised a first transcriptional unit comprising an inducible promoter whose name is given in column A, operably linked to an open reading frame encoding a green fluorescent protein. The SEQ ID NO giving the nucleotide sequence of the inducible promoter, lacking the 12 bp before the transcriptional start site is shown in column B, and the SEQ ID NO giving the nucleotide sequence of the inducible promoter including the pair of tet operators is shown in column C. Each transposon further comprised a second transcriptional unit comprising a constitutive promoter operable in a mammalian cell, operably linked to an open reading frame encoding a tet repressor with amino acid sequence SEQ ID NO:5. This promoter name is shown in column D, and the SEQ ID NO giving the nucleotide sequence of the promoter linked to the tet repressor is shown in column E. The promoter sequences indicated in column E in rows 6 and 7 also include the 5′UTR including the Kozak sequence immediately before the translational initiation site for the tet repressor. Transposons were stably transfected into CHO cells and selected, after recovery three separate cultures for each stable cell line were induced with doxycycline and cell numbers and fluorescence were measured as described in Example 4. Fluorescence was measured at 525 nm and cell density was measured as optical density at 600 nm, with each condition measured for 3 independent transfections. The average fluorescence at 525 nm for each set of 3 replicates was divided by optical density at 600 nm for each set of 3 replicates to provide an average measure of fluorescence normalized by cell number and is shown in columns F to W. Days post-induction are shown in row 1, doxycycline concentrations are shown in row 2.
Table 5. DNA constructs comprising two transcriptional units were prepared as described in Example 5. Each construct comprised a first transcriptional unit comprising a minimal promoter whose name is given in column A, with nucleotide sequence given by the SEQ ID NO shown in column C. The 5′ of the minimal promoter was fused to an array of tet operators with nucleotide sequence given by the SEQ ID NO shown in column B. The 3′ of the minimal promoter was fused to a 5′ UTR with nucleotide sequence given by the SEQ ID NO shown in column D. The 5′UTR was joined to an open reading frame encoding Dasher GFP, with amino acid sequence SEQ ID NO:32. Each construct further comprised a second transcriptional unit comprising a constitutive SV40 promoter operable in a mammalian cell, operably linked to an open reading frame encoding a modified tet repressor fused to a VP16 transcriptional activation domain, the amino acid sequence of the open reading frame given by the SEQ ID NO in column E. Each construct was transfected into HEK 293 cells in 3 independent transfections, induced with doxycycline and cell numbers and fluorescence were measured as described in Example 5. Fluorescence was measured at 525 nm and cell density was measured as optical density at 600 nm, with each condition measured for 3 independent transfections. The average fluorescence at 525 nm for each set of 3 replicates was divided by optical density at 600 nm for each set of 3 replicates to provide an average measure of fluorescence normalized by cell number, shown in columns F to U. Days post-induction are shown in row 1, doxycycline concentrations are shown in row 2.
Table 6. DNA constructs comprising two transcriptional units were prepared as described in Example 5. Each construct comprised a first transcriptional unit comprising a minimal promoter whose name is given in column A, with nucleotide sequence given by the SEQ ID NO shown in column C. The 5′ of the minimal promoter was fused to an array of tet operators with nucleotide sequence given by the SEQ ID NO shown in column B. The 3′ of the minimal promoter was fused to a 5′ UTR with nucleotide sequence given by the SEQ ID NO shown in column D. The 5′UTR was joined to an open reading frame encoding Dasher GFP, with amino acid sequence SEQ ID NO:32. Each construct further comprised a second transcriptional unit comprising a constitutive SV40 promoter operable in a mammalian cell, operably linked to an open reading frame encoding a modified tet repressor fused to a VP16 transcriptional activation domain, the amino acid sequence of the open reading frame given by the SEQ ID NO in column E. Each construct was transfected into CHO-S cells in 3 independent transfections, induced with doxycycline and cell numbers and fluorescence were measured as described in Example 6. Fluorescence was measured at 525 nm and cell density was measured as optical density at 600 nm, with each condition measured for 3 independent transfections. The average fluorescence at 525 nm for each set of 3 replicates was divided by optical density at 600 nm for each set of 3 replicates to provide an average measure of fluorescence normalized by cell number, shown in columns F to Q. Days post-induction are shown in row 1, doxycycline concentrations are shown in row 2.
Table 7. DNA transposons comprising two transcriptional units were prepared as described in Example 7. Each transposon comprised a first transcriptional unit comprising a minimal promoter whose name is given in column A, with nucleotide sequence given by the SEQ ID NO shown in column C. The 5′ of the minimal promoter was fused to an array of tet operators with nucleotide sequence given by the SEQ ID NO shown in column B. The 3′ of the minimal promoter was fused to a 5′ UTR with nucleotide sequence given by the SEQ ID NO shown in column D. The 5′UTR was joined to an open reading frame encoding Dasher GFP, with amino acid sequence SEQ ID NO:32. Each construct further comprised a second transcriptional unit comprising a constitutive SV40 promoter operable in a mammalian cell, operably linked to an open reading frame encoding a modified tet repressor fused to a VP16 transcriptional activation domain, the amino acid sequence of the open reading frame given by the SEQ ID NO in column E. Transposons were stably transfected into CHO cells and selected, after recovery three separate cultures for each stable cell line were induced with doxycycline and cell numbers and fluorescence were measured as described in Example 7. Fluorescence was measured at 525 nm and cell density was measured as optical density at 600 nm, with each condition measured for 3 independent transfections. The average fluorescence at 525 nm for each set of 3 replicates was divided by optical density at 600 nm for each set of 3 replicates to provide an average measure of fluorescence normalized by cell number, shown in columns F to Q. Days post-induction are shown in row 1, doxycycline concentrations are shown in row 2.
Table 8. DNA transposons comprising two transcriptional units were prepared as described in Example 8. Each transposon comprised a first transcriptional unit comprising a minimal chimpanzee promoter whose 5′ end was fused to an array of tet operators with nucleotide sequence given by the SEQ ID NO shown in column A. The promoter was operably linked to an open reading frame encoding Dasher GFP, with amino acid sequence SEQ ID NO:32. Each construct further comprised a second transcriptional unit comprising a constitutive SV40 promoter operable in a mammalian cell, operably linked to an open reading frame encoding a modified tet repressor fused to a VP16 transcriptional activation domain, the amino acid sequence of the open reading frame given by the SEQ ID NO in column E. Transposons were stably transfected into CHO cells and selected, after recovery three separate cultures for each stable cell line were induced with doxycycline and cell numbers and fluorescence were measured as described in Example 8. Fluorescence was measured at 525 nm and cell density was measured as optical density at 600 nm, with each condition measured for 3 independent transfections. The average fluorescence at 525 nm for each set of 3 replicates was divided by optical density at 600 nm for each set of 3 replicates to provide an average measure of fluorescence normalized by cell number, shown in columns B to U. Days post-induction are shown in row 1, doxycycline concentrations are shown in row 2. Control cells with no integrated transposon are shown in row 6.
Table 9. DNA transposons comprising two transcriptional units were prepared as described in Example 9. Each transposon comprised a first transcriptional unit comprising a mouse CMV promoter operably linked to an open reading frame encoding an antibody light chain. Each transposon further comprised a second transcriptional unit comprising a promoter named in column A and with nucleotide given by the SEQ ID NO in column B, operably linked to an open reading frame encoding an antibody heavy chain. Transposons were stably transfected into CHO cells and selected as described in Example 9. The specific productivity of each CHO cell pool is shown in column C, the volumetric productivity is shown in column D.
All publications, patents and patent applications, accession numbers, websites and the like mentioned in this specification are incorporated by reference to the same extent as if each individual publication, patent or patent application was so individually denoted. To the extent different content is associated with an accession number or other reference at different times, the content in effect as of the effective filing date of this application is meant. The effective filing date is the date of the earliest priority application disclosing the accession number in question. Unless otherwise apparent from the context any element, embodiment, step, feature or aspect of the invention can be performed in combination with any other.
The present application claims the benefit of 63/165,484 filed Mar. 24, 2021 incorporated by reference in its entirety for all purposes.
| Number | Date | Country | |
|---|---|---|---|
| 63165484 | Mar 2021 | US |
