WO2015157386A1 - Production of engineered t-cells by sleeping beauty transposon coupled with methotrexate selection - Google Patents

Production of engineered t-cells by sleeping beauty transposon coupled with methotrexate selection Download PDF

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Publication number
WO2015157386A1
WO2015157386A1 PCT/US2015/024868 US2015024868W WO2015157386A1 WO 2015157386 A1 WO2015157386 A1 WO 2015157386A1 US 2015024868 W US2015024868 W US 2015024868W WO 2015157386 A1 WO2015157386 A1 WO 2015157386A1
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WO
WIPO (PCT)
Prior art keywords
sequence
alternatives
selection
cells
concentration range
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Ceased
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PCT/US2015/024868
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English (en)
French (fr)
Inventor
Michael C. Jensen
Suzie Pun
Nataly KACHEROVSKY
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
University of Washington
Seattle Childrens Hospital
Original Assignee
University of Washington
Seattle Childrens Hospital
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
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Family has litigation
First worldwide family litigation filed litigation Critical https://patents.darts-ip.com/?family=54288361&utm_source=google_patent&utm_medium=platform_link&utm_campaign=public_patent_search&patent=WO2015157386(A1) "Global patent litigation dataset” by Darts-ip is licensed under a Creative Commons Attribution 4.0 International License.
Priority to KR1020167031069A priority Critical patent/KR20160144431A/ko
Priority to BR112016023517A priority patent/BR112016023517A2/pt
Priority to RU2016143389A priority patent/RU2016143389A/ru
Priority to EP15776501.7A priority patent/EP3129480A4/en
Priority to CN201580030815.7A priority patent/CN106661570B/zh
Priority to CA2945303A priority patent/CA2945303C/en
Priority to JP2017504604A priority patent/JP6788573B6/ja
Priority to US15/302,449 priority patent/US20170029774A1/en
Priority to AU2015243922A priority patent/AU2015243922B2/en
Application filed by University of Washington, Seattle Childrens Hospital filed Critical University of Washington
Priority to NZ725081A priority patent/NZ725081A/en
Priority to MX2016013149A priority patent/MX2016013149A/es
Publication of WO2015157386A1 publication Critical patent/WO2015157386A1/en
Anticipated expiration legal-status Critical
Priority to US17/096,138 priority patent/US12258397B2/en
Ceased legal-status Critical Current

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    • A—HUMAN NECESSITIES
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    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
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    • C07K2317/622—Single chain antibody (scFv)
    • C—CHEMISTRY; METALLURGY
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    • C07K2317/73—Inducing cell death, e.g. apoptosis, necrosis or inhibition of cell proliferation
    • C—CHEMISTRY; METALLURGY
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    • C07K2319/00—Fusion polypeptide
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    • C—CHEMISTRY; METALLURGY
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    • C12N2740/00011—Details
    • C12N2740/10011—Retroviridae
    • C12N2740/15011—Lentivirus, not HIV, e.g. FIV, SIV
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    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
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    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids

Definitions

  • aspects of the invention described herein include methods of treating, inhibiting, ameliorating and/or eliminating a virus or cancer cells in a subject utilizing genetically engineered human T-cells having receptors for a molecule presented by the virus or the cancer cells.
  • Engineered human T-cells are a promising therapeutic route for cancer immunotherapy and viral therapy.
  • T-cells expressing chimeric antigen receptors combined with additional genes to enhance T-cell proliferation, survival, or tumor homing can further improve efficacy but require multiple stable gene transfer events. Accordingly, methods are needed to increase production efficiency for multiplexed engineered cells.
  • Efficient, stable transduction of T-cells can be achieved using a Sleeping Beauty transposon system in minicircles that are introduced by nucleofection. Rapid selection of transduced cells with methotrexate (MTX) for cells expressing a mutant dihydrofolate reductase (DHFRdm) resistant to metabolic inhibition can also be achieved.
  • MTX methotrexate
  • DHFRdm mutant dihydrofolate reductase
  • Described herein are approaches for the preferential amplification of T cells expressing multiple transgenes, preferably encoding receptors or chimeric receptors specific for a molecule presented by a virus or a cancer cell.
  • selection pressure on transformed T cells is applied in a two-stage MTX selection utilizing increasing concentrations of MTX.
  • a gene delivery polynucleotide for stable insertion of a nucleic acid into an oligonucleotide wherein the nucleic acid for insertion is flanked by inverted terminal repeat gene sequences in the gene delivery polynucleotide and wherein the gene delivery polynucleotide is selectable
  • the gene delivery polynucleotide comprises a first sequence, wherein the first sequence comprises a first inverted terminal repeat gene sequence, a second sequence, wherein the second sequence comprises a second inverted terminal repeat gene sequence, a third sequence, wherein the third sequence comprises a promoter region sequence, a fourth sequence, wherein the fourth sequence comprises at least one gene encodes a protein or encodes a sequence for mRNA transcription, and wherein the fourth sequence is optimized, a fifth sequence, wherein the fifth sequence comprises at least one selectable marker cassette encoding a double mutant of dihydrofolate reductase, wherein the double mutant of dihydrof
  • the double mutant of human dihydrofolate reductase comprises the protein sequence: MVGSLNCIVA VSQNMGIGKN GDFPWPPLRN ESRYFQRMTT TSSVEGKQNL VIMGK TWFS IPEKNRPLKG RINLVLSREL KEPPQGAHFL SRSLDDALKL TEQPELANKV DMVWIVGGSS VYKEAMNHPG HLKLFVTRIM QDFESDTFFP EIDLEKYKLL PEYPGVLSDV QEEKGIKYKF EVYEKND (SEQ ID NO: 3).
  • the gene delivery polynucleotide is circular.
  • the gene delivery polynucleotide is at least lkB to 5kB. In some alternatives, the gene delivery polynucleotide is a minicircle. In some alternatives, the promoter region comprises an EF1 promoter sequence. In some alternatives, the fourth sequence comprises one, two, three, four, or five genes that encode proteins. In some alternatives, the fourth sequence is codon optimized to reduce the total GC/AT ratio of the fourth sequence. In some alternatives, the fourth sequence is optimized by codon optimization for expression in humans. In some alternatives, the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins.
  • the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins, such as a plurality of antibody binding domains, which are specific for the same epitope.
  • the plurality of related proteins comprise a plurality of antibody binding domains, wherein the plurality of antibody binding domains are specific for the same epitope.
  • the fifth sequence is codon optimized for expression in humans and/or to reduce the total GC/AT ratio of the fifth sequence. In preferred alternatives, the fifth sequence is optimized by codon optimization for expression in humans.
  • the protein is a protein for therapy.
  • the codon optimization and/or a consensus sequence is generated by comparing the variability of sequence and/or nucleobases utilized in a plurality of related sequences.
  • the protein comprises an antibody or a portion thereof, which may be humanized.
  • the double mutant of dihydro folate reductase comprises amino acid mutations of L22F and F31S.
  • the T cells are precursor T cells. In some alternatives, the precursor T cells are hematopoietic stem cells.
  • a method of generating engineered multiplexed T- cells for adoptive T-cell immunotherapy comprises providing a gene delivery polynucleotide, introducing the gene delivery polynucleotide into a T-cell, providing a vector encoding a Sleeping Beauty transposase, introducing the vector encoding the Sleeping Beauty transposase into the T-cell, selecting the cells comprising the gene delivery polynucleotide wherein selecting comprises a first round of selection and a second round of selection, wherein the first round of selection comprises adding a selection reagent at a first concentration range and the second round of selection comprises adding the selection reagent at a second concentration range, wherein the second concentration range is higher than the first concentration range and, wherein the second concentration range is at least 1.5 fold higher than that of the first concentration range and isolating the T-cells expressing a phenotype under selective pressure.
  • the gene delivery polynucleotide comprises a first sequence, wherein the first sequence comprises a first inverted terminal repeat gene sequence, a second sequence, wherein the second sequence comprises a second inverted terminal repeat gene sequence, a third sequence, wherein the third sequence comprises a promoter region sequence, a fourth sequence, wherein the fourth sequence comprises at least one gene encoding a protein, and wherein the fourth sequence is optimized, a fifth sequence, wherein the fifth sequence comprises at least one selectable marker cassette encoding a double mutant of dihydrofolate reductase, wherein the double mutant of dihydrofolate reductase has a 15,000 fold or about 15,000 fold reduced affinity for methotrexate, wherein the methotrexate can be used as a selection mechanism to selectively amplify cells transduced with the gene delivery polynucleotide and wherein the fifth sequence is optimized, a sixth sequence, wherein the sixth sequence comprises a first attachment site (attP) and a seventh sequence, wherein
  • the gene encoding the double mutant of human dihydrofolate reductase comprises the DNA sequence: ATGGTTGGTTCGCTAAACTGCATCGTCGCTGTGTCCCAGAACATGGGCATCGGCA AGAACGGGGACTTCCCCTGGCCACCGCTCAGGAATGAATCCAGATATTTCCAGA GAATGACCACAACCTCTTCAGTAGAAGGTAAACAGAATCTGGTGATTATGGGTA AGAAGACCTGGTTCTCCATTCCTGAGAAGAATCGACCTTTAAAGGGTAGAATTA ATTTAGTTCTCAGCAGAGAACTCAAGGAACCTCCACAAGGAGCTCATTTTCTTTC CAGAAGTCTAGATGATGCCTTAAAACTTACTGAACAACCAGAATTAGCAAATAA AGTAGACATGGTCTGGATAGTTGGTGGCAGTTCTGTTTATAAGGAAGCCATGAAT CACCCAGGCCATCTTAAACTATTTGTGACAAGGATCATGCAAGACTTTGAAAGTG ACACGTTTTCCAGAAATTGATTTG
  • the double mutant of human dihydro folate reductase comprises the protein sequence: MVGSLNCIVA VSQNMGIGKN GDFPWPPLRN ESRYFQRMTT TSSVEGKQNL VIMGK TWFS IPEKNRPLKG RINLVLSREL KEPPQGAHFL SRSLDDALKL TEQPELANKV DMVWIVGGSS VYKEAMNHPG HLKLFVTRIM QDFESDTFFP EIDLEKYKLL PEYPGVLSDV QEEKGIKYKF EVYEKND (SEQ ID NO: 3).
  • the gene delivery polynucleotide is circular.
  • the gene delivery polynucleotide is at least lkB to 5kB. In some alternatives, the gene delivery polynucleotide is a minicircle. In some alternatives, the promoter region comprises an EF1 promoter sequence. In some alternatives, the fourth sequence comprises one, two, three, four, or five genes that encode proteins. In some alternatives, the fourth sequence is codon optimized to reduce the total GC/AT ratio of the fourth sequence. In some alternatives, the fourth sequence is optimized by codon optimization for expression in humans. In some alternatives, the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins.
  • the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins, such as a plurality of antibody binding domains, which are specific for the same epitope.
  • the plurality of related proteins comprise a plurality of antibody binding domains, wherein the plurality of antibody binding domains are specific for the same epitope.
  • the fifth sequence is codon optimized to reduce the total GC/AT ratio of the fifth sequence.
  • the fifth sequence is optimized by codon optimization for expression in humans.
  • the protein is a protein for therapy.
  • the codon optimization and/or consensus sequence is generated by comparing the variability of sequence and/or nucleobases utilized in a plurality of related sequences.
  • the protein comprises an antibody or a portion thereof, which may be humanized.
  • the double mutant of dihydrofolate reductase comprises amino acid mutations of L22F and F31S.
  • the double mutant of dihydrofolate reductase comprises amino acid mutations of L22F and F31S.
  • the introducing is performed by electroporation.
  • the selecting is performed by increasing selective pressure through the selective marker cassette.
  • the selection reagent comprises an agent for selection.
  • the agent for selection is methotrexate.
  • the first concentration range is at least 50nM - lOOnM and the second concentration range is at least 75 to 150nM.
  • the first concentration is 50 nM, 60 nM, 70 nM, 80 nM, 90 nM, or lOOnM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 75 nM, 80 nM, 90 nM, 100 nM, 110 nM, 120 nM, 130 nM, 140 nM, or 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 75 nM - 150 nM and the second concentration range is at least 112.5 nM to 225 nM.
  • the first concentration is 75 nM, 85 nM, 95 nM, 105 nM, 115 nM, 125 nM, 135 nM, 145 nM, or 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 112 nM, 122 nM, 132 nM, 142 nM, 152 nM, 162 nM, 172 nM, 182 nM, 192 nM, 202 nM, 212 nM, or 225 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 300 nM - 675 nM and the first concentration range is at least 450 nM to 1012 nM.
  • the first concentration is 300 nM, 350 nM, 400 nM, 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, or 675 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, 700 nM, 750 nM, 800 nM, 850 nM, 900 nM, 1000 nM, or 1012 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first round of selection comprises exposing the T-cells to the selection agent for 2, 3, 4, 5, 6 or 7 days before the second round of selection.
  • the second round of selection comprises exposing the T-cells to the selection agent for at least 2, 3, 4, 5, 6,7, 8, 9, 10, 11, 12, 13, or 14 days or any time that is between a range of times defined by any two of the aforementioned time points before isolation.
  • the T cells are precursor T cells.
  • the precursor T cells are hematopoietic stem cells.
  • a method of increasing protein production in a T-cell comprises providing a polynucleotide of, introducing the polynucleotide into a cell, providing a vector encoding a Sleeping Beauty transposase, introducing the vector encoding the Sleeping Beauty transposase into the T-cell, selecting the cells comprising the gene delivery polynucleotide wherein selecting comprises a first round of selection and a second round of selection, wherein the first round of selection comprises adding a selection reagent at a first concentration range and the second round of selection comprises adding the selection reagent at a second concentration range, wherein the second concentration range is higher than the first concentration range and, wherein the second concentration range is at least 1.5 fold higher than that of the first concentration range and isolating the cells expressing a phenotype under selective pressure.
  • the gene delivery polynucleotide comprises a first sequence, wherein the first sequence comprises a first inverted terminal repeat gene sequence, a second sequence, wherein the second sequence comprises a second inverted terminal repeat gene sequence, a third sequence, wherein the third sequence comprises a promoter region sequence, a fourth sequence, wherein the fourth sequence comprises at least one gene encoding a protein, and wherein the fourth sequence is optimized, a fifth sequence, wherein the fifth sequence comprises at least one selectable marker cassette encoding a double mutant of dihydrofolate reductase, wherein the double mutant of dihydrofolate reductase has a 15,000 fold or about 15,000 fold reduced affinity for methotrexate, wherein the methotrexate can be used as a selection mechanism to selectively amplify cells transduced with the gene delivery polynucleotide and wherein the fifth sequence is optimized, a sixth sequence, wherein the sixth sequence comprises a first attachment site (attP) and a seventh sequence, wherein
  • the gene encoding the double mutant of human dihydrofolate reductase comprises the DNA sequence: ATGGTTGGTTCGCTAAACTGCATCGTCGCTGTGTCCCAGAACATGGGCATCGGCA AGAACGGGGACTTCCCCTGGCCACCGCTCAGGAATGAATCCAGATATTTCCAGA GAATGACCACAACCTCTTCAGTAGAAGGTAAACAGAATCTGGTGATTATGGGTA AGAAGACCTGGTTCTCCATTCCTGAGAAGAATCGACCTTTAAAGGGTAGAATTA ATTTAGTTCTCAGCAGAGAACTCAAGGAACCTCCACAAGGAGCTCATTTTCTTTC CAGAAGTCTAGATGATGCCTTAAAACTTACTGAACAACCAGAATTAGCAAATAA AGTAGACATGGTCTGGATAGTTGGTGGCAGTTCTGTTTATAAGGAAGCCATGAAT CACCCAGGCCATCTTAAACTATTTGTGACAAGGATCATGCAAGACTTTGAAAGTG ACACGTTTTCCAGAAATTGATTTG
  • the double mutant of human dihydro folate reductase comprises the protein sequence: MVGSLNCIVA VSQNMGIGKN GDFPWPPLRN ESRYFQRMTT TSSVEGKQNL VIMGK TWFS IPEKNRPLKG RINLVLSREL KEPPQGAHFL SRSLDDALKL TEQPELANKV DMVWIVGGSS VYKEAMNHPG HLKLFVTRIM QDFESDTFFP EIDLEKYKLL PEYPGVLSDV QEEKGIKYKF EVYEKND (SEQ ID NO: 3).
  • the gene delivery polynucleotide is circular.
  • the gene delivery polynucleotide is at least lkB to 5kB. In some alternatives, the gene delivery polynucleotide is a minicircle. In some alternatives, the promoter region comprises an EF1 promoter sequence. In some alternatives, the fourth sequence comprises one, two, three, four, or five genes that encode proteins. In some alternatives, the fourth sequence is codon optimized to reduce the total GC/AT ratio of the fourth sequence. In some alternatives, the fourth sequence is optimized by codon optimization for expression in humans. In some alternatives, the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins.
  • the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins, such as a plurality of antibody binding domains, which are specific for the same epitope.
  • the plurality of related proteins comprise a plurality of antibody binding domains, wherein the plurality of antibody binding domains are specific for the same epitope.
  • the fifth sequence is codon optimized to reduce the total GC/AT ratio of the fifth sequence.
  • the fifth sequence is optimized by codon optimization for expression in humans.
  • the protein is a protein for therapy.
  • the codon optimization and/or consensus sequence is generated by comparing the variability of sequence and/or nucleobases utilized in a plurality of related sequences.
  • the protein comprises an antibody or a portion thereof, which may be humanized.
  • the double mutant of dihydrofolate reductase comprises amino acid mutations of L22F and F31S.
  • the double mutant of dihydrofolate reductase comprises amino acid mutations of L22F and F31S.
  • the introducing is performed by electroporation.
  • the selecting is performed by increasing selective pressure through the selective marker cassette.
  • the selection reagent comprises an agent for selection.
  • the agent for selection is methotrexate.
  • the first concentration range is at least 50nM - lOOnM and the second concentration range is at least 75 to 150nM.
  • the first concentration is 50 nM, 60 nM, 70 nM, 80 nM, 90 nM, or lOOnM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 75 nM, 80 nM, 90 nM, 100 nM, 110 nM, 120 nM, 130 nM, 140 nM, or 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 75 nM - 150 nM and the second concentration range is at least 112.5 nM to 225 nM.
  • the first concentration is 75 nM, 85 nM, 95 nM, 105 nM, 115 nM, 125 nM, 135 nM, 145 nM, 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 112 nM, 122 nM, 132 nM, 142 nM, 152 nM, 162 nM, 172 nM, 182 nM, 192 nM, 202 nM, 212 nM, or 225 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 300 nM - 675 nM and the first concentration range is at least 450 nM to 1012 nM.
  • the first concentration is 300 nM, 350 nM, 400 nM, 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, or 675 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, 700 nM, 750 nM, 800 nM, 850 nM, 900 nM, 1000 nM, or 1012 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first round of selection comprises exposing the T-cells to the selection agent for 2, 3, 4, 5, 6 or 7 days before the second round of selection.
  • the second round of selection comprises exposing the T-cells to the selection agent for at least 2, 3, 4, 5, 6,7, 8, 9, 10, 11, 12, 13, or 14 days or any time that is between a range of times defined by any two of the aforementioned time points before isolation.
  • the T cells are precursor T cells.
  • the precursor T cells are hematopoietic stem cells.
  • an engineered multiplexed T-cell for adoptive T-cell immunotherapy generated by any one of the methods of is provided.
  • the engineered multiplexed T-cells for adoptive T-cell immunotherapy is generated by a method, wherein the method comprises providing a gene delivery polynucleotide, introducing the gene delivery polynucleotide into a T-cell, providing a vector encoding a Sleeping Beauty transposase, introducing the vector encoding the Sleeping Beauty transposase into the T-cell, selecting the cells comprising the gene delivery polynucleotide wherein selecting comprises a first round of selection and a second round of selection, wherein the first round of selection comprises adding a selection reagent at a first concentration range and the second round of selection comprises adding the selection reagent at a second concentration range, wherein the second concentration range is higher than the first concentration range and, wherein the second concentration range is at least 1.5 fold higher than that of the first concentration range and iso
  • the gene delivery polynucleotide comprises a first sequence, wherein the first sequence comprises a first inverted terminal repeat gene sequence, a second sequence, wherein the second sequence comprises a second inverted terminal repeat gene sequence, a third sequence, wherein the third sequence comprises a promoter region sequence, a fourth sequence, wherein the fourth sequence comprises at least one gene encoding a protein, and wherein the fourth sequence is optimized, a fifth sequence, wherein the fifth sequence comprises at least one selectable marker cassette encoding a double mutant of dihydrofolate reductase, wherein the double mutant of dihydrofolate reductase has a 15,000 fold or about 15,000 fold reduced affinity for methotrexate, wherein the methotrexate can be used as a selection mechanism to selectively amplify cells transduced with the gene delivery polynucleotide and wherein the fifth sequence is optimized, a sixth sequence, wherein the sixth sequence comprises a first attachment site (attP) and a seventh sequence, wherein
  • the double mutant of human dihydrofolate reductase comprises the protein sequence: MVGSLNCIVA VSQNMGIGKN GDFPWPPLRN ESRYFQRMTT TSSVEGKQNL VIMGK TWFS IPEKNRPLKG RINLVLSREL KEPPQGAHFL SRSLDDALKL TEQPELANKV DMVWIVGGSS VYKEAMNHPG HLKLFVTRIM QDFESDTFFP EIDLEKYKLL PEYPGVLSDV QEEKGIKYKF EVYEKND (SEQ ID NO: 3).
  • the gene delivery polynucleotide is circular.
  • the gene delivery polynucleotide is at least lkB to 5kB. In some alternatives, the gene delivery polynucleotide is a minicircle. In some alternatives, the promoter region comprises an EF1 promoter sequence. In some alternatives, the fourth sequence comprises one, two, three, four, or five genes that encode proteins. In some alternatives, the fourth sequence is codon optimized to reduce the total GC/AT ratio of the fourth sequence. In some alternatives, the fourth sequence is optimized by codon optimization for expression in humans. In some alternatives, the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins.
  • the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins, such as a plurality of antibody binding domains, which are specific for the same epitope.
  • the plurality of related proteins comprise a plurality of antibody binding domains, wherein the plurality of antibody binding domains are specific for the same epitope.
  • the fifth sequence is codon optimized to reduce the total GC/AT ratio of the fifth sequence.
  • the fifth sequence is optimized by codon optimization for expression in humans.
  • the protein is a protein for therapy.
  • the codon optimization and/or consensus sequence is generated by comparing the variability of sequence and/or nucleobases utilized in a plurality of related sequences.
  • the protein comprises an antibody or a portion thereof, which may be humanized.
  • the double mutant of dihydrofolate reductase comprises amino acid mutations of L22F and F31S.
  • the double mutant of dihydrofolate reductase comprises amino acid mutations of L22F and F31S.
  • the introducing is performed by electroporation.
  • the selecting is performed by increasing selective pressure through the selective marker cassette.
  • the selection reagent comprises an agent for selection.
  • the agent for selection is methotrexate.
  • the first concentration range is at least 50nM - lOOnM and the second concentration range is at least 75 to 150nM.
  • the first concentration is 50 nM, 60 nM, 70 nM, 80 nM, 90 nM, or lOOnM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 75 nM, 80 nM, 90 nM, 100 nM, 110 nM, 120 nM, 130 nM, 140 nM, or 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 75 nM - 150 nM and the second concentration range is at least 112.5 nM to 225 nM.
  • the first concentration is 75 nM, 85 nM, 95 nM, 105 nM, 115 nM, 125 nM, 135 nM, 145 nM, or 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 112 nM, 122 nM, 132 nM, 142 nM, 152 nM, 162 nM, 172 nM, 182 nM, 192 nM, 202 nM, 212 nM, or 225 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 300 nM - 675 nM and the first concentration range is at least 450 nM to 1012 nM.
  • the first concentration is 300 nM, 350 nM, 400 nM, 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, or 675 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, 700 nM, 750 nM, 800 nM, 850 nM, 900 nM, 1000 nM, or 1012 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first round of selection comprises exposing the T-cells to the selection agent for 2, 3, 4, 5, 6 or 7 days before the second round of selection.
  • the second round of selection comprises exposing the T-cells to the selection agent for at least 2, 3, 4, 5, 6,7, 8, 9, 10, 11, 12, 13, or 14 days or any time that is between a range of times defined by any two of the aforementioned time points before isolation.
  • the gene delivery polynucleotide comprises a first sequence, wherein the first sequence comprises a first inverted terminal repeat gene sequence, a second sequence, wherein the second sequence comprises a second inverted terminal repeat gene sequence, a third sequence, wherein the third sequence comprises a promoter region sequence, a fourth sequence, wherein the fourth sequence comprises at least one gene encoding a protein, and wherein the fourth sequence is optimized, a fifth sequence, wherein the fifth sequence comprises at least one selectable marker cassette encoding a double mutant of dihydrofolate reductase, wherein the double mutant of dihydrofolate reductase has a 15,000 fold or about 15,000 fold reduced affinity for methotrexate, wherein the methotrexate can be used as a selection mechanism to selectively amplify cells transduced with the gene delivery polynucleotide and wherein the fifth sequence is optimized, a sixth sequence, wherein the sixth sequence comprises a first attachment site (attP) and a seventh sequence, wherein
  • the gene encoding the double mutant of human dihydro folate reductase comprises the DNA sequence: ATGGTTGGTTCGCTAAACTGCATCGTCGCTGTGTCCCAGAACATGGGCATCGGCA AGAACGGGGACTTCCCCTGGCCACCGCTCAGGAATGAATCCAGATATTTCCAGA GAATGACCACAACCTCTTCAGTAGAAGGTAAACAGAATCTGGTGATTATGGGTA AGAAGACCTGGTTCTCCATTCCTGAGAAGAATCGACCTTTAAAGGGTAGAATTA ATTTAGTTCTCAGCAGAGAACTCAAGGAACCTCCACAAGGAGCTCATTTTCTTTC CAGAAGTCTAGATGATGCCTTAAAACTTACTGAACAACCAGAATTAGCAAATAA AGTAGACATGGTCTGGATAGTTGGTGGCAGTTCTGTTTATAAGGAAGCCATGAAT CACCCAGGCCATCTTAAACTATTTGTGACAAGGATCATGCAAGACTTTGAAAGTG ACACGTTTTCCAGAAATTGATTTG
  • the double mutant of human dihydro folate reductase comprises the protein sequence: MVGSLNCIVA VSQNMGIGKN GDFPWPPLRN ESRYFQRMTT TSSVEGKQNL VIMGK TWFS IPEKNRPLKG RINLVLSREL KEPPQGAHFL SRSLDDALKL TEQPELANKV DMVWIVGGSS VYKEAMNHPG HLKLFVTRIM QDFESDTFFP EIDLEKYKLL PEYPGVLSDV QEEKGIKYKF EVYEKND (SEQ ID NO: 3).
  • the gene delivery polynucleotide is circular.
  • the gene delivery polynucleotide is at least lkB to 5kB. In some alternatives, the gene delivery polynucleotide is a minicircle. In some alternatives, the promoter region comprises an EF1 promoter sequence. In some alternatives, the fourth sequence comprises one, two, three, four, or five genes that encode proteins. In some alternatives, the fourth sequence is codon optimized to reduce the total GC/AT ratio of the fourth sequence. In some alternatives, the fourth sequence is optimized by codon optimization for expression in humans. In some alternatives, the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins.
  • the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins, such as a plurality of antibody binding domains, which are specific for the same epitope.
  • the plurality of related proteins comprise a plurality of antibody binding domains, wherein the plurality of antibody binding domains are specific for the same epitope.
  • the fifth sequence is codon optimized to reduce the total GC/AT ratio of the fifth sequence.
  • the fifth sequence is optimized by codon optimization for expression in humans.
  • the protein is a protein for therapy.
  • the codon optimization and/or consensus sequence is generated by comparing the variability of sequence and/or nucleobases utilized in a plurality of related sequences.
  • the protein comprises an antibody or a portion thereof, which may be humanized.
  • the double mutant of dihydrofolate reductase comprises amino acid mutations of L22F and F31S.
  • the introducing is performed by electroporation.
  • the selecting is performed by increasing selective pressure through the selective marker cassette.
  • the selection reagent comprises an agent for selection.
  • the agent for selection is methotrexate.
  • the first concentration range is at least 50nM - lOOnM and the second concentration range is at least 75 to 150nM.
  • the first concentration is 50 nM, 60 nM, 70 nM, 80 nM, 90 nM, or lOOnM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 75 nM, 80 nM, 90 nM, 100 nM, 110 nM, 120 nM, 130 nM, 140 nM, or 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 75 nM - 150 nM and the second concentration range is at least 112.5 nM to 225 nM.
  • the first concentration is 75 nM, 85 nM, 95 nM, 105 nM, 115 nM, 125 nM, 135 nM, 145 nM, or 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 112 nM, 122 nM, 132 nM, 142 nM, 152 nM, 162 nM, 172 nM, 182 nM, 192 nM, 202 nM, 212 nM, or 225 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 300 nM - 675 nM and the first concentration range is at least 450 nM to 1012 nM.
  • the first concentration is 300 nM, 350 nM, 400 nM, 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, or 675 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, 700 nM, 750 nM, 800 nM, 850 nM, 900 nM, 1000 nM, or 1012 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first round of selection comprises exposing the T-cells to the selection agent for 2, 3, 4, 5, 6 or 7 days before the second round of selection.
  • the second round of selection comprises exposing the T- cells to the selection agent for at least 2, 3, 4, 5, 6,7, 8, 9, 10, 11, 12, 13, or 14 days or any time that is between a range of times defined by any two of the aforementioned time points before isolation.
  • the T cells are precursor T cells.
  • the precursor T cells are hematopoietic stem cells.
  • a method of treating, inhibiting, or ameliorating cancer or a disease in a subject comprises administering to the subject the modified or engineered multiplexed T-cell generated as described below.
  • the engineered multiplexed T-cells for adoptive T-cell immunotherapy is generated by a method, wherein the method comprises providing a gene delivery polynucleotide, introducing the gene delivery polynucleotide into a T-cell, providing a vector encoding a Sleeping Beauty transposase, introducing the vector encoding the Sleeping Beauty transposase into the T-cell, selecting the cells comprising the gene delivery polynucleotide wherein selecting comprises a first round of selection and a second round of selection, wherein the first round of selection comprises adding a selection reagent at a first concentration range and the second round of selection comprises adding the selection reagent at a second concentration range, wherein the second concentration range is higher than the first concentration range and,
  • the gene delivery polynucleotide comprises a first sequence, wherein the first sequence comprises a first inverted terminal repeat gene sequence, a second sequence, wherein the second sequence comprises a second inverted terminal repeat gene sequence, a third sequence, wherein the third sequence comprises a promoter region sequence, a fourth sequence, wherein the fourth sequence comprises at least one gene encoding a protein, and wherein the fourth sequence is optimized, a fifth sequence, wherein the fifth sequence comprises at least one selectable marker cassette encoding a double mutant of dihydrofolate reductase, wherein the double mutant of dihydrofolate reductase has a 15,000 fold or about 15,000 fold reduced affinity for methotrexate, wherein the methotrexate can be used as a selection mechanism to selectively amplify cells transduced with the gene delivery polynucleotide and wherein the fifth sequence is optimized, a sixth sequence, wherein the sixth sequence comprises a first attachment site (attP) and a seventh sequence, wherein
  • the gene encoding the double mutant of human dihydrofolate reductase comprises the DNA sequence: ATGGTTGGTTCGCTAAACTGCATCGTCGCTGTGTCCCAGAACATGGGCATCGGCA AGAACGGGGACTTCCCCTGGCCACCGCTCAGGAATGAATCCAGATATTTCCAGA GAATGACCACAACCTCTTCAGTAGAAGGTAAACAGAATCTGGTGATTATGGGTA AGAAGACCTGGTTCTCCATTCCTGAGAAGAATCGACCTTTAAAGGGTAGAATTA ATTTAGTTCTCAGCAGAGAACTCAAGGAACCTCCACAAGGAGCTCATTTTCTTTC CAGAAGTCTAGATGATGCCTTAAAACTTACTGAACAACCAGAATTAGCAAATAA AGTAGACATGGTCTGGATAGTTGGTGGCAGTTCTGTTTATAAGGAAGCCATGAAT CACCCAGGCCATCTTAAACTATTTGTGACAAGGATCATGCAAGACTTTGAAAGTG ACACGTTTTCCAGAAATTGATTTG
  • the double mutant of human dihydrofolate reductase comprises the protein sequence: MVGSLNCIVA VSQNMGIGKN GDFPWPPLRN ESRYFQRMTT TSSVEGKQNL VIMGK TWFS IPEK RPLKG RINLVLSREL KEPPQGAHFL SRSLDDALKL TEQPELANKV DMVWIVGGSS VYKEAMNHPG HLKLFVTRIM QDFESDTFFP EIDLEKYKLL PEYPGVLSDV QEEKGIKYKF EVYEK D (SEQ ID NO: 3).
  • the gene delivery polynucleotide is circular.
  • the gene delivery polynucleotide is a minicircle. In some alternatives, the gene delivery polynucleotide is at least lkB to 5kB. In some alternatives, the promoter region comprises an EF1 promoter sequence. In some alternatives, the fourth sequence comprises one, two, three, four, or five genes that encode proteins. In some alternatives, the fourth sequence is codon optimized to reduce the total GC/AT ratio of the fourth sequence. In some alternatives, the fourth sequence is optimized by codon optimization for expression in humans. In some alternatives, the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins.
  • the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins, such as a plurality of antibody binding domains, which are specific for the same epitope.
  • the plurality of related proteins comprise a plurality of antibody binding domains, wherein the plurality of antibody binding domains are specific for the same epitope.
  • the fifth sequence is codon optimized to reduce the total GC/AT ratio of the fifth sequence.
  • the fifth sequence is optimized by codon optimization for expression in humans.
  • the protein is a protein for therapy.
  • the codon optimization and/or consensus sequence is generated by comparing the variability of sequence and/or nucleobases utilized in a plurality of related sequences.
  • the protein comprises an antibody or a portion thereof, which may be humanized.
  • the double mutant of dihydrofolate reductase comprises amino acid mutations of L22F and F31S.
  • the double mutant of dihydrofolate reductase comprises amino acid mutations of L22F and F31S.
  • the T cells are precursor T cells.
  • the precursor T cells are hematopoietic stem cells.
  • the introducing is performed by electroporation.
  • the selecting is performed by increasing selective pressure through the selective marker cassette.
  • the selection reagent comprises an agent for selection.
  • the agent for selection is methotrexate.
  • the first concentration range is at least 50nM - lOOnM and the second concentration range is at least 75 to 150nM.
  • the first concentration is 50 nM, 60 nM, 70 nM, 80 nM, 90 nM, or ⁇ or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 75 nM, 80 nM, 90 nM, 100 nM, 110 nM, 120 nM, 130 nM, 140 nM, or 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 75 nM - 150 nM and the second concentration range is at least 112.5 nM to 225 nM.
  • the first concentration is 75 nM, 85 nM, 95 nM, 105 nM, 115 nM, 125 nM, 135 nM, 145 nM, or 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 112 nM, 122 nM, 132 nM, 142 nM, 152 nM, 162 nM, 172 nM, 182 nM, 192 nM, 202 nM, 212 nM, or 225 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 300 nM - 675 nM and the first concentration range is at least 450 nM to 1012 nM.
  • the first concentration is 300 nM, 350 nM, 400 nM, 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, or 675 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, 700 nM, 750 nM, 800 nM, 850 nM, 900 nM, 1000 nM, or 1012 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first round of selection comprises exposing the T-cells to the selection agent for 2, 3, 4, 5, 6 or 7 days before the second round of selection.
  • the second round of selection comprises exposing the T- cells to the selection agent for at least 2, 3, 4, 5, 6,7, 8, 9, 10, 11, 12, 13, or 14 days or any time that is between a range of times defined by any two of the aforementioned time points before isolation.
  • the subject is human.
  • a method of generating engineered multiplexed T- cells for adoptive T-cell immunotherapy comprises providing a gene delivery polynucleotide, introducing the gene delivery polynucleotide into a T-cell, providing a vector encoding a Sleeping Beauty transposase, introducing the vector encoding the Sleeping Beauty transposase into the T-cell, selecting the cells comprising the gene delivery polynucleotide wherein selecting comprises a first round of selection and a second round of selection, wherein the first round of selection comprises adding a selection reagent at a first concentration range and the second round of selection comprises adding the selection reagent at a second concentration range, wherein the second concentration range is higher than the first concentration range and, wherein the second concentration range is at least 1.5 fold higher than that of the first concentration range and isolating the T-cells expressing a phenotype under selective pressure.
  • the gene delivery polynucleotide comprises a first sequence, wherein the first sequence comprises a first inverted terminal repeat gene sequence, a second sequence, wherein the second sequence comprises a second inverted terminal repeat gene sequence, a third sequence, wherein the third sequence comprises a promoter region sequence, a fourth sequence, wherein the fourth sequence comprises at least one gene encoding a protein, and wherein the fourth sequence is optimized, a fifth sequence, wherein the fifth sequence comprises at least one selectable marker cassette encoding a double mutant of dihydrofolate reductase, wherein the double mutant of dihydrofolate reductase has a 15,000 fold or about 15,000 fold reduced affinity for methotrexate, wherein the methotrexate can be used as a selection mechanism to selectively amplify cells transduced with the gene delivery polynucleotide and wherein the fifth sequence is optimized, a sixth sequence, wherein the sixth sequence comprises a first attachment site (attP) and a seventh sequence, wherein
  • the gene encoding the double mutant of human dihydrofolate reductase comprises the DNA sequence: ATGGTTGGTTCGCTAAACTGCATCGTCGCTGTGTCCCAGAACATGGGCATCGGCA AGAACGGGGACTTCCCCTGGCCACCGCTCAGGAATGAATCCAGATATTTCCAGA GAATGACCACAACCTCTTCAGTAGAAGGTAAACAGAATCTGGTGATTATGGGTA AGAAGACCTGGTTCTCCATTCCTGAGAAGAATCGACCTTTAAAGGGTAGAATTA ATTTAGTTCTCAGCAGAGAACTCAAGGAACCTCCACAAGGAGCTCATTTTCTTTC CAGAAGTCTAGATGATGCCTTAAAACTTACTGAACAACCAGAATTAGCAAATAA AGTAGACATGGTCTGGATAGTTGGTGGCAGTTCTGTTTATAAGGAAGCCATGAAT CACCCAGGCCATCTTAAACTATTTGTGACAAGGATCATGCAAGACTTTGAAAGTG ACACGTTTTCCAGAAATTGATTTG
  • the double mutant of human dihydro folate reductase comprises the protein sequence: MVGSLNCIVA VSQNMGIGKN GDFPWPPLRN ESRYFQRMTT TSSVEGKQNL VIMGK TWFS IPEKNRPLKG RINLVLSREL KEPPQGAHFL SRSLDDALKL TEQPELANKV DMVWIVGGSS VYKEAMNHPG HLKLFVTRIM QDFESDTFFP EIDLEKYKLL PEYPGVLSDV QEEKGIKYKF EVYEKND (SEQ ID NO: 3).
  • the gene delivery polynucleotide is circular.
  • the gene delivery polynucleotide is at least lkB to 5kB. In some alternatives, the gene delivery polynucleotide is a minicircle. In some alternatives, the promoter region comprises an EF1 promoter sequence. In some alternatives, the fourth sequence comprises one, two, three, four, or five genes that encode proteins. In some alternatives, the fourth sequence is codon optimized to reduce the total GC/AT ratio of the fourth sequence. In some alternatives, the fourth sequence is optimized by codon optimization for expression in humans. In some alternatives, the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins.
  • the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins, such as a plurality of antibody binding domains, which are specific for the same epitope.
  • the plurality of related proteins comprise a plurality of antibody binding domains, wherein the plurality of antibody binding domains are specific for the same epitope.
  • the fifth sequence is codon optimized to reduce the total GC/AT ratio of the fifth sequence.
  • the fifth sequence is optimized by codon optimization for expression in humans.
  • the protein is a protein for therapy.
  • the codon optimization and/or consensus sequence is generated by comparing the variability of sequence and/or nucleobases utilized in a plurality of related sequences.
  • the protein comprises an antibody or a portion thereof, which may be humanized.
  • the double mutant of dihydrofolate reductase comprises amino acid mutations of L22F and F31S.
  • the double mutant of dihydrofolate reductase comprises amino acid mutations of L22F and F31S.
  • the introducing is performed by electroporation.
  • the selecting is performed by increasing selective pressure through the selective marker cassette.
  • the selection reagent comprises an agent for selection.
  • the agent for selection is methotrexate.
  • the first concentration range is at least 50nM - lOOnM and the second concentration range is at least 75 to 150nM.
  • the first concentration is 50 nM, 60 nM, 70 nM, 80 nM, 90 nM, or lOOnM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 75 nM, 80 nM, 90 nM, 100 nM, 110 nM, 120 nM, 130 nM, 140 nM, or 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 75 nM - 150 nM and the second concentration range is at least 112.5 nM to 225 nM.
  • the first concentration is 75 nM, 85 nM, 95 nM, 105 nM, 115 nM, 125 nM, 135 nM, 145 nM, or 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 112 nM, 122 nM, 132 nM, 142 nM, 152 nM, 162 nM, 172 nM, 182 nM, 192 nM, 202 nM, 212 nM, or 225 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 300 nM - 675 nM and the first concentration range is at least 450 nM to 1012 nM.
  • the first concentration is 300 nM, 350 nM, 400 nM, 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, or 675 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, 700 nM, 750 nM, 800 nM, 850 nM, 900 nM, 1000 nM, or 1012 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first round of selection comprises exposing the T-cells to the selection agent for 2, 3, 4, 5, 6 or 7 days before the second round of selection.
  • the second round of selection comprises exposing the T-cells to the selection agent for at least 2, 3, 4, 5, 6,7, 8, 9, 10, 11, 12, 13, or 14 days or any time that is between a range of times defined by any two of the aforementioned time points before isolation.
  • the T cells comprise precursor T cells.
  • the precursor T cells are hematopoietic stem cells.
  • a method of generating engineered cells for adoptive T-cell immunotherapy comprising, providing a gene delivery polynucleotide, introducing the gene delivery polynucleotide into a precursor T cell, providing a vector encoding a Sleeping Beauty transposase, introducing the vector encoding the Sleeping Beauty transposase into the precursor T cell, selecting the precursor T cells comprising the gene delivery polynucleotide; wherein selecting comprises a first round of selection and a second round of selection, wherein the first round of selection comprises adding a selection reagent at a first concentration range and the second round of selection comprises adding the selection reagent at a second concentration range, wherein the second concentration range is higher than the first concentration range and, wherein the second concentration range is at least 1.5 fold higher than that of the first concentration range and isolating the precursor T-cells expressing a phenotype under selective pressure.
  • the gene delivery polynucleotide is for stable insertion of a nucleic acid into an oligonucleotide wherein the nucleic acid for insertion is flanked by inverted terminal repeat gene sequences in the gene delivery polynucleotide and wherein the gene delivery polynucleotide is selectable, wherein the gene delivery polynucleotide comprises a first sequence, wherein the first sequence comprises a first inverted terminal repeat gene sequence, a second sequence, wherein the second sequence comprises a second inverted terminal repeat gene sequence, a third sequence, wherein the third sequence comprises a promoter region sequence, a fourth sequence, wherein the fourth sequence comprises at least one gene, wherein the at least one gene encodes a protein or encodes a sequence for mR A transcription, and wherein the fourth sequence is optimized, a fifth sequence, wherein the fifth sequence comprises at least one selectable marker cassette encoding a double mutant of dihydrofolate reductase, wherein the double mutant of dihydrof
  • the gene delivery polynucleotide is circular. In some alternatives, the gene delivery polynucleotide is at least lkB to 5kB. In some alternatives, the promoter region comprises an EF1 promoter sequence. In some alternatives, the fourth sequence comprises one, two, three, four, or five genes that encode proteins. In some alternatives, the fourth sequence is codon optimized to reduce the total GC/AT ratio of the fourth sequence. In some alternatives, the fourth sequence is optimized by codon optimization for expression in humans. In some alternatives, the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins.
  • the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins, such as a plurality of antibody binding domains, which are specific for the same epitope.
  • the plurality of related proteins comprise a plurality of antibody binding domains, wherein the plurality of antibody binding domains are specific for the same epitope.
  • the fifth sequence is codon optimized to reduce the total GC/AT ratio of the fifth sequence.
  • the fifth sequence is optimized by codon optimization for expression in humans.
  • the codon optimization and/or consensus sequence is generated by comparing the variability of sequence and/or nucleobases utilized in a plurality of related sequences.
  • the protein is a protein for therapy.
  • the protein comprises an antibody or a portion thereof, which may be humanized.
  • the double mutant of dihydro folate reductase comprises amino acid mutations of L22F and F31 S.
  • the gene delivery polynucleotide is a minicircle.
  • the introducing is performed by electroporation.
  • the selecting is performed by increasing selective pressure through the selective marker cassette.
  • the selection reagent comprises an agent for selection.
  • the agent for selection is methotrexate.
  • the first concentration range is at least 50nM - lOOnM and the second concentration range is at least 75 to 150nM.
  • the first concentration range is at least 75 nM - 150 nM and the second concentration range is at least 112.5 nM to 225 nM. In some alternatives, the first concentration range is at least 300 nM - 675 nM and the first concentration range is at least 450 nM to 1012 nM. In some alternatives, the first round of selection comprises exposing the T-cells to the selection agent for 2, 3, 4, 5, 6 or 7 days before the second round of selection. In some alternatives, the second round of selection comprises exposing the T-cells to the selection agent for at least 2, 3, 4, 5, 6,7, 8, 9, 10, 11, 12, 13, or 14 days or any time that is between a range of times defined by any two of the aforementioned time points before isolation. In some alternatives, the T cell precursor is a hematopoietic stem cell.
  • a method of increasing protein production in a precursor T-cell comprising providing a polynucleotide, introducing the polynucleotide into a cell, providing a vector encoding a Sleeping Beauty transposase; introducing the vector encoding the Sleeping Beauty transposase into the precursor T-cell, selecting the precursor T cells comprising the gene delivery polynucleotide, wherein selecting comprises a first round of selection and a second round of selection, wherein the first round of selection comprises adding a selection reagent at a first concentration range and the second round of selection comprises adding the selection reagent at a second concentration range, wherein the second concentration range is higher than the first concentration range and, wherein the second concentration range is at least 1.5 fold higher than that of the first concentration range and isolating the precursor T cells expressing a phenotype under selective pressure.
  • the gene delivery polynucleotide is for stable insertion of a nucleic acid into an oligonucleotide wherein the nucleic acid for insertion is flanked by inverted terminal repeat gene sequences in the gene delivery polynucleotide and wherein the gene delivery polynucleotide is selectable, wherein the gene delivery polynucleotide comprises a first sequence, wherein the first sequence comprises a first inverted terminal repeat gene sequence, a second sequence, wherein the second sequence comprises a second inverted terminal repeat gene sequence, a third sequence, wherein the third sequence comprises a promoter region sequence, a fourth sequence, wherein the fourth sequence comprises at least one gene, wherein the at least one gene encodes a protein or encodes a sequence for mR A transcription, and wherein the fourth sequence is optimized, a fifth sequence, wherein the fifth sequence comprises at least one selectable marker cassette encoding a double mutant of dihydrofolate reductase, wherein the double mutant of dihydrof
  • the gene delivery polynucleotide is circular. In some alternatives, the gene delivery polynucleotide is at least lkB to 5kB. In some alternatives, the promoter region comprises an EF1 promoter sequence. In some alternatives, the fourth sequence comprises one, two, three, four, or five genes that encode proteins. In some alternatives, the fourth sequence is codon optimized to reduce the total GC/AT ratio of the fourth sequence. In some alternatives, the fourth sequence is optimized by codon optimization for expression in humans. In some alternatives, the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins.
  • the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins, such as a plurality of antibody binding domains, which are specific for the same epitope.
  • the plurality of related proteins comprise a plurality of antibody binding domains, wherein the plurality of antibody binding domains are specific for the same epitope.
  • the fifth sequence is codon optimized to reduce the total GC/AT ratio of the fifth sequence.
  • the fifth sequence is optimized by codon optimization for expression in humans.
  • the codon optimization and/or consensus sequence is generated by comparing the variability of sequence and/or nucleobases utilized in a plurality of related sequences.
  • the protein is a protein for therapy.
  • the protein comprises an antibody or a portion thereof, which may be humanized.
  • the double mutant of dihydro folate reductase comprises amino acid mutations of L22F and F31S.
  • the gene delivery polynucleotide is a minicircle.
  • the introducing is performed by electroporation.
  • the selecting is performed by increasing selective pressure through the selective marker cassette.
  • the selection reagent comprises an agent for selection.
  • the agent for selection is methotrexate.
  • the first concentration range is at least 50nM - 100 nM and the second concentration range is at least 75 to 150 nM. In some alternatives, the first concentration range is at least 75nM - 150nM and the second concentration range is at least 112.5 nM to 225 nM. In some alternatives, the first concentration range is at least 300 nM - 675 nM and the second concentration range is at least 450 nM to 1012 nM. In some alternatives, the first round of selection comprises exposing the cells to the selection agent for 2, 3, 4, 5, 6 or 7 days before the second round of selection. In some alternatives, the second round of selection comprises exposing the cells to the selection agent for at least 2, 3, 4, 5, 6, or 7 days before isolation. In some alternatives, the precursor T cells are hematopoietic stem cells.
  • FIG. 1 shows an overall schematic of the gene delivery minicircle producer plasmid, MC_T3/FP-DHFRdm.
  • the minicircle with T3 generation of Sleeping Beauty transposon comprises an EFla promoter, a fusion of fluorescent protein (FP; maxGFP, mCherry, or Blue Fluorescent protein (BFP)), Thosea asigna virus 2A peptide (T2A), and double mutant of dihydrofolate reductase (DHFRdm) insensitive to methotrexate (MTX), positioned between inverted terminal repeats (ITRs, arrows). Recombination at attB/attP sites generates a minicircle while the remaining bacterial backbone is enzymatically degraded.
  • FP fluorescent protein
  • maxGFP maxGFP
  • mCherry mCherry
  • BFP Blue Fluorescent protein
  • DHFRdm double mutant of dihydrofolate reductase
  • FIG. 2 shows a series of bar graphs that demonstrate the optimization of the transposon:transposase DNA ratio.
  • H9 cells were nucleofected with 2 ⁇ g of MC_T3/eGFP-T2 A-DHFRdm DNA (transposon) and increasing amounts of MC SB100X (transposase) DNA (0.5, 1, 2, 4, 8 ug).
  • Flow cytometry was performed at 24 hours (striped bars) and at 7 days (black bars) after nucleofection to assess transient and stable transfection efficiency. Numbers above the bars indicate integration efficiency, which is calculated as percent of stable over transient GFP expression.
  • Figure 3 shows a series of bar graphs, which demonstrate the effect of MTX concentration during the selection process.
  • Flow cytometric analysis of H9 cell populations stably transfected with T3/GFP-T2 A-DHFRdm transposon DNA grown in the presence of increasing concentrations of MTX (0, 50, 100, and 200 nM) at 3 days (white bars), 5 days (horizontal stripes), 7 days (vertical stripes), and 10 days (black bars) was performed.
  • Panel A of Figure 3 shows the percent GFP+/PI- and
  • Panel B of Figure 3 shows the mean GFP relative fluorescence units (RFU).
  • Figure 4 shows a series of bar graphs that demonstrate the transgene persistence after MTX withdrawal. As shown is the flow cytometric analysis of H9 cell populations that were stably transfected with T3/GFP-T2 A-DHFRdm transposon grown in media supplemented with different concentrations of MTX (50, 100, and 200 nM) for 2 weeks (black bars), after which MTX selection was withdrawn and data collected at different time points afterwards: 1 week (horizontal stripes), 2 weeks (vertical stripes), 3 weeks (checked bars), and 4 weeks (white bars).
  • Panel A of Figure 4 shows the percent GFP+/PI-;
  • Panel B of Figure 4 shows the mean GFP relative fluorescence units (RFU).
  • Figure 5 A shows the transposon copy number per human haploid genome.
  • Genomic DNA was isolated from populations of H9 cells stably transfected with T3/GFP-T2A-DHFRdm transposon DNA before and after selection with different concentrations of MTX (50, 100, and 200 nM). The average transposon copy number was determined by quantitative PCR.
  • the "Gold standard” was generated by the limiting dilution method.
  • the "Sorted” population was created by sorting the original H9 population (8% of integrated transposon) to 100% GFP positive cells.
  • Figure 5B shows the distribution of transposon integration events.
  • Sixty clones were isolated by limited dilution method from an H9 population that was previously selected with 200 nM MTX to 100% cells with integrated T3/GFP-T2A-DHFRdm transposon.
  • Genomic DNA was isolated and transposon copy number determined by relative RT-qPCR. Numbers were rounded to the nearest integer value (e.g., 0.5-1.5 was rounded to 1).
  • Figure 6 shows a series of pie graphs representing the analysis of the multiplexing of transposons.
  • Panels A-C are the flow cytometric analysis of H9 cell populations nucleofected with 3 minicircles carrying transposons with different fluorescent proteins (FPs) (MC T3/GFP-T2 A-DHFRdm, MC T3/ BFP-T2A-DHFRdm, MC_T3/mCherry-T2A-DHFRdm), 2 ⁇ g each and 6 ⁇ g of MC SB100X DNA at different time points: (Panel A) 24 hours after transfection (transient expression), (Panel B) 1 week (stable integration), and (Panel C) 1 week of selection with 200 nM of MTX.
  • FPs fluorescent proteins
  • Figure 7 shows the bar graph analysis of step selection of the distribution of expression of single, double, and triple FPs.
  • H9 cell population stably transfected with three transposons was selected with 200 nM MTX for a week and then was exposed to higher MTX concentrations of 500 and 1000 nM.
  • FIG 8 shows an example of the flow analysis for the stable expression of transposon DNA with Sleeping Beauty in lymphocytes after MTX selection.
  • Freshly thawed PBMC cells were electroporated with minicircle GFP (mcGFP) DNA (MC T3/GFP- T2A-DHFRdm) and Sleeping Beauty transposase DNA (MC SB100X), then stimulated with Miltenyi Transact beads which selectively activate T-cells by binding to CD3 and CD28.
  • mcGFP minicircle GFP
  • MC T3/GFP- T2A-DHFRdm minicircle GFP
  • MC SB100X Sleeping Beauty transposase DNA
  • Panels A, B, and C show the sequential selection for lymphocytes (A), single cells (B), and live cells (C). Shown in Panel D are the high levels of GFP expression in both the CD8+ and CD8- populations. Note that for this donor, the majority of lymphocytes after stimulation are CD8+ T cells.
  • Figure 9 shows histograms of the initial expression of transposon DNA with Sleeping Beauty in lymphocytes.
  • PBMC were transfected with either mcGFP DNA alone (10 ug), mcGFP (10 ug) and MC SB100X DNA (5 ug) at a mcGFP:MC_SB100X ratio of 2: 1, mcGFP (10 ug) and MC SB100X DNA (10 ug) at a mcGFP:MC_SB100X ratio of 1 : 1, a pMAXGFP (10 ug) control, or a no DNA control.
  • Shown in Panel A are the results for cells in which Transact beads were not added, two days after transfection as an example of the initial electroporation efficiency. Shown in Panel B are the results in cells exposed to transact beads after five days. While by day 5 the levels of mcGFP DNA decline to near control levels, the expression of mcGFP in cells co-transfected with transposase remain elevated.
  • Figure 10 shows the expression of GFP transposon DNA and the levels of cell growth in transfected lymphocytes in the week before MTX addition.
  • PBMC peripheral blood cells
  • mcGFP and MC SB100X DNA at a mcGFP:MC_SB100X ratio of 2: 1
  • mcGFP and MC SB100X DNA at a mcGFP:MC_SB100X ratio of 1 : 1, a pMAXGFP control (10 ug), or a no DNA control.
  • Panel A shows the decreasing levels of GFP expression from day 2 to day 7.
  • Panel B shows the level of live cells from day 0 to day 7 of the transfected cell samples which had been treated with Miltenyi Transact beads on dO.
  • Panel C shows the level of live cells from day 0 to day 7 of the transfected cell samples in the absence of Transact beads. As shown, there is a slow growth of the cells transfected with mcGFP DNA in the presence of Miltenyi Transact beads.
  • Figure 11 shows the stable expression of transposon DNA with Sleeping Beauty in T-cells following 1 week of MTX selection. Shown are the flow cytometry scattergrams in which GFP production and proliferation of T-cells modified to express GFP after transfection with transposon DNA and Sleeping Beauty transposase DNA were investigated. Panels A, B, E, and F show the scatter profiles to identify lymphocytes, while Panels C, D, G, and H show CD8 and GFP expression. Panels A-D show the flow cytometry analysis of cells treated with 100 nM MTX. Panels E-H shows the flow cytometry analysis of cells that were not treated with MTX.
  • Panels A, C, E and G are samples transfected with mcGFP alone.
  • Panels B, D, F and H show the flow cytometry results of cells transfected with mcGFP and MC SB100X (Sleeping Beauty transposase) DNA at 2: 1.
  • Panel D in T-cells (both CD8+ and CD8-) co-transfected with mcGFP and SBIOOX such that the GFP gene is stably inserted into the cellular genome, about 95% of the cells stably express GFP in the presence of MTX at ⁇ while only about 23% express GFP in the absence of MTX.
  • Figure 12 shows the proliferation and the GFP/CD8 expression in transposon-transfected lymphocytes after 14 days of MTX selection.
  • Cell samples were transfected with no DNA (control), mcGFP alone, mcGFP and MC SB100X DNA at a mcGFP:MC_SB100X ratio of 2: 1 ratio, or mcGFP and MC SB100X DNA at a mcGFP:MC_SB100X ratio of 1 : 1.
  • the cells were selected using 0 nM MTX (control), 25 nM MTX, 50nM MTX, or 100 nM MTX.
  • the lymphocyte window shown in the first, third, fifth and seventh columns, demonstrates the survival of only stably transfected cells in the presence of higher concentrations of MTX.
  • the live, single lymphocytes were gated for GFP and CD8 detection in the second, fourth, sixth and eighth columns.
  • GFP expression is lost over time (second column).
  • cells transfected with both mcGFP and MC SB100X stably express GFP both with MTX selection (>90%) and without MTX selection (-20%) (columns four and six).
  • MTX was effective for selection at concentrations of 50 and 100 nM MTX and no significant difference was seen between the ratios 2: 1 or 1 :1. Note that the majority of lymphocytes are CD8+ T-cells.
  • Figure 13 shows both the lymphocyte window and GFP/CD8 expression in transposon-transfected cells after 19 days of MTX selection.
  • Cell samples were transfected with no DNA (control), mcGFP alone, mcGFP and MC SB100X DNA at a mcGFP:MC_SB100X ratio of 2: 1 ratio, or mcGFP and MC SB100X DNA at a mcGFP:MC_SB100X ratio of 1 : 1.
  • the cells were selected using 0 nM MTX (control), 25 nM MTX, 50nM MTX, or 100 nM MTX.
  • the lymphocyte window is shown in the first, third, fifth and seventh columns, showing the survival of only stably transfected cells in the presence of MTX.
  • the live, single lymphocytes were gated for GFP and CD8 detection in the second, fourth, sixth and eighth columns.
  • GFP expression is lost over time (second column).
  • cells transfected with both mcGFP and MC SB100X stably express GFP both with MTX selection (>90%) and without MTX selection (-20%) (columns four and six).
  • FIG. 14 shows the live cell counts of cells that stably express transposon DNA and undergoes MTX selection. Trypan blue cell counts were taken at 7, 14, and 19 days post transfection.
  • PBMC samples were transfected with no DNA (control), mcGFP alone, mcGFP and MC SB100X DNA at a mcGFP:MC_SB100X ratio of 2: 1 ratio, or mcGFP and MC SB100X DNA at a mcGFP:MC_SB100X ratio of 1 : 1.
  • the cells were selected on day 7 using 0 nM MTX (control), 25 nM MTX, 50nM MTX, or 100 nM MTX.
  • Panel A shows the level of live cells in the absence of MTX.
  • Panel B shows the levels of live cells after exposure to ⁇ MTX.
  • Panel C shows the levels of live cells after exposure to 50nM.
  • Panel D shows the levels of live cells after exposure to 25nM MTX.
  • MTX slows the growth of cells by inhibiting the metabolism of folic acid
  • DHFRdm mcGFP transposon co-expressing the MTX-resistance gene
  • MC SB100X plasmid encoding the Sleeping Beauty Transposase were able to proliferate in the presence of high MTX, due to stable expression of the integrated transposon DNA.
  • Figure 15 shows an analysis of GFP expression by lymphocytes stably expressing GFP transposon DNA with Sleeping Beauty transposase under MTX selection.
  • PBMC samples were transfected with mcGFP alone, mcGFP and MC SB100X at a mcGFP:MC_SB100X ratio of 2: 1, mcGFP and MC SB100X at a mcGFP:MC_SB100X ratio of 1 : 1, pMAXGFP (10 ug), and no DNA (control).
  • Cells were exposed to MTX on day 7 after transfection, and GFP expression was measured for live, single lymphocytes.
  • Panel A shows the level of GFP expression on days 2, 5, 7, 14, and 19 in the absence of MTX.
  • Panel B shows the level of GFP expression from days 7, 14, and 19 of lymphocytes transfected with mcGFP alone under MTX selection at MTX concentrations of 0 nM, 25 nM, 50 nM and 100 nM.
  • Panel C shows the GFP expression of T-cells transfected with mcGFP and MC SB100X at a mcGFP:MC_SB100X ratio of 2: 1 under MTX selection of OnM, 25nM, 50nM and ⁇ .
  • Panel D shows the GFP expression of T-cells transfected with mcGFP and MC SB100X at a mcGFP:MC_SB100X ratio of 1 : 1 under control of MTX selection concentrations of 0 nM, 25 nM, 50 nM and 100 nM.
  • the results from transfecting with mcGFP and MC SB100X with a 2: 1 and a 1 : 1 ratio were similar, with approximately 75% GFP expression at 25 nM and approximately 90% GFP expression at 50 and 100 nM after 1 week of MTX. Additionally, there was minimal difference in the GFP expression between the treatment with 50 nM MTX and 100 nM MTX.
  • FIG. 16 Sleeping Beauty Transposons: minicircle constructs. As shown in the figure are the schematics of several sleeping beauty constructs designed for several alternatives described herein.
  • Figure 17 As shown are several scattergrams of cells transfected with Sleeping Beauty transposons carrying a gene for expression of GFP. As shown are the cells fourteen days after transfection. Cells were electroporated with SB100X or transposons carrying genes for GFP.
  • FIG. Sleeping Beauty Transposons and MTX: GFP transposon. As shown, cells were transfected with different ratios of mcGFP plasmids and the Sleeping Beauty transposon carrying a gene for expression of GFP (McGFP: SB at a 1 : 1 and 2: 1 ratio). As shown, GFP expression was low with no MTX was added after 18 days. With the Sleeping Beauty transposon, it is shown that there is an increase in GFP expression in the presence of MTX.
  • FIG. Sleeping Beauty Transposons: minicircle constructs. As shown in the figure are the schematics of several sleeping beauty constructs designed for several alternatives described herein.
  • FIG. 20 Sleeping Beauty Transposons and MTX:GFP transposon— SB100X DNA and RNA. Cells were electroporated with SB100X (DNA or R A) or transposons carrying genes for GFP, CARs, or GFP/mCherry/BFP.
  • FIG. 21 Sleeping Beauty Transposons and MTX: GFP transposon— SB100X DNA and RNA. As shown in the figure are several scattergrams of the cells that are transfected with GFP gene carrying transposons. Several samples of cells are transfected with DNA comprising a gene for GFP expression (2.5ug and 5ug), mcGFP only, and RNA (lug and 3ug). The samples are split and grown under the influence of varying concentrations of MTX at 0 uM, 50uM and lOOuM.
  • FIG. 22 Sleeping Beauty Transposons and MTX: GFP transposon— SB100X DNA and RNA. Cells were transfected with Sleeping Beauty transposons carrying a gene for GFP expression at different concentrations as seen in the top left panel. MTX was then added at day 7 after transfection. As shown, cells trans fected with 50ug to lOOug can express GFP after day 7 to day 14.
  • FIG. 23 GFP expressing DNA and RNA in the presence of MTX.
  • cells transfected with mcGFP, GFP: SB, and GFP:SB RNA were grown and exposed to MTX seven days after transfection.
  • As a control cells were grown to fourteen days without exposure to MTX (top left panel).
  • FIG. 24 Expression of GFP in cells transfected with GFP: SB.
  • cells were transfected with varying concentrations of GFP: SB (2.5 ug, 5 ug) and exposed to different concentrations of MTX (50 uM and lOOuM).
  • MTX 50 uM and lOOuM
  • cells were able to express GFP in the presence of MTX optimally at 50 uM MTX when they were transfected with 5 ug of GFP: SB.
  • This experiment was also performed using RNA, however, DNA has a higher efficiency for leading to expression of the protein.
  • FIG. 25 Sleeping Beauty Transposons: minicircle constructs. As shown in the figure are the schematics of several sleeping beauty constructs designed for several alternatives described herein.
  • FIG. 26 Expression of CD19CAR.
  • a Sleeping Beauty construct carrying a gene for CD19CAR was constructed (SB: CD19CAR).
  • Cells were transfected with either DNA (2.5 ug or 5ug), or RNA (lug or 3ug). As shown, cells that were transfected with DNA or RNA at both concentrations were able to express the CD19CAR in the presence of 50 uM MTX. This was also shown for cells that were transfected with the RNA at lug in the presence of lOOuM MTX.
  • FIG. 27 Expression of CD19CAR.
  • a Sleeping Beauty construct carrying a gene for CD19CAR was constructed (SB: CD19CAR). Cells were transfected with either DNA (2.5 ug or 5ug), or RNA (lug or 3ug). Cells were grown and at day seven after transfection, were exposed to MTX.
  • the CD19CAR also included an EGFRt tag. As shown, detection of the tag correlates to the expression of the CD19CAR. After exposure to MTX, detection of the tag was seen in cells that were transfected with the DNA carrying the Sleeping Beauty construct carrying a gene for CAR19 as well as the cells transfected with the RNA carrying the Sleeping Beauty construct carrying a gene for CAR19.
  • FIG. 28 Sleeping Beauty Transposons and MTX: CD 19 CAR: CD8+ cell growth. Expression of CD19CAR.
  • a Sleeping Beauty construct carrying a gene for CD19CAR was constructed (SB: CD19CAR). Cells were transfected with either DNA (2.5 ug or 5ug), or RNA (lug or 3ug). Cells were grown and at day seven after transfection, were exposed to MTX. As shown, the CD8+ cells were able to grow when a lower concentration of DNA was transfected. However, with RNA , it was seen that a higher concentration led to better expression, but a lower concentration led to better initial growth of the cells.
  • FIG. 29 Sleeping Beauty Transposons: minicircle constructs. As shown in the figure are the schematics of several sleeping beauty constructs designed for several alternatives described herein.
  • FIG. 30 Sleeping Beauty Transposons and MTX: Multiplex 3 FP's. Cells were electroporated with DNA or mcFP and grown in the presence of MTX. Afterwards, cells were analyzed for expression of mCherry, BFP, and/or GFP as indicated by the scattergrams.
  • Figure 31 Sleeping Beauty Transposons and MTX: Multiplex 3 FP's.
  • FIG. 32 Sleeping Beauty Transposons: minicircle constructs. As shown in the figure are the schematics of several sleeping beauty constructs designed for several alternatives described herein.
  • FIG. 33 As shown, cells electroporated with DNA comprising Sleeping Beauty transposons were subjected to different concentrations of MTX at the second round of selection.
  • FIG. 34 Expression of Smarker proteins in cells electroporated with DNA comprising Sleeping Beauty transposons in the presence of different concentrations of MTX (2, ⁇ , 250nM, and 500nM).
  • FIG. 35 Sleeping Beauty Transposons: minicircle constructs. As shown in the figure are the schematics of several sleeping beauty constructs designed for several alternatives described herein.
  • a or “an” can mean one or more than one.
  • the term “about” indicates that a value includes the inherent variation of error for the method being employed to determine a value, or the variation that exists among experiments.
  • nucleic acid or “nucleic acid molecule” refers to polynucleotides, such as deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), oligonucleotides, fragments generated by the polymerase chain reaction (PCR), and fragments generated by any of ligation, scission, endonuclease action, and exonuclease action.
  • DNA deoxyribonucleic acid
  • RNA ribonucleic acid
  • PCR polymerase chain reaction
  • Nucleic acid molecules can be composed of monomers that are naturally-occurring nucleotides (such as DNA and RNA), or analogs of naturally-occurring nucleotides (e.g., enantiomeric forms of naturally-occurring nucleotides), or a combination of both.
  • Modified nucleotides can have alterations in sugar moieties and/or in pyrimidine or purine base moieties.
  • Sugar modifications include, for example, replacement of one or more hydroxyl groups with halogens, alkyl groups, amines, and azido groups, or sugars can be functionalized as ethers or esters.
  • the entire sugar moiety can be replaced with sterically and electronically similar structures, such as aza-sugars and carbocyclic sugar analogs.
  • modifications in a base moiety include alkylated purines and pyrimidines, acylated purines or pyrimidines, or other well-known heterocyclic substitutes.
  • Nucleic acid monomers can be linked by phosphodiester bonds or analogs of such linkages. Analogs of phosphodiester linkages include phosphorothioate, phosphorodithioate, phosphoroselenoate, phosphorodiselenoate, phosphoroanilothioate, phosphoranilidate, phosphoramidate, and the like.
  • nucleic acid molecule also includes so-called “peptide nucleic acids,” which comprise naturally-occurring or modified nucleic acid bases attached to a polyamide backbone. Nucleic acids can be either single stranded or double stranded. In some alternatives described herein, a gene delivery polynucleotide for stable insertion of a nucleic acid into a gene is provided. "Oligonucleotide” can be used interchangeable with nucleic acid and can refer to DNA or RNA, either double stranded or a single stranded piece or DNA or RNA.
  • a "gene” is the molecular unit of heredity of a living organism, describing some stretches of deoxyribonucleic acids (DNA) and ribonucleic acids (RNA) that code for a polypeptide or for an RNA chain that has a function in the organism, and can be a locatable region in the genome of an organism.
  • RNA ribonucleic acids
  • a gene delivery polynucleotide for stable insertion of a nucleic acid into a gene, wherein the nucleic acid for insertion is flanked by inverted terminal repeat gene sequences in the gene delivery polynucleotide and wherein the gene delivery polynucleotide is selectable is provided.
  • a "chromosome,” is a packaged and organized chromatin, a complex of macromolecules found in cells, consisting of DNA, protein and RNA.
  • a gene delivery polynucleotide for stable insertion of a nucleic acid into a gene wherein the nucleic acid for insertion is flanked by inverted terminal repeat gene sequences in the gene delivery polynucleotide and wherein the gene delivery polynucleotide is selectable, the gene delivery polynucleotide, is provided.
  • the nucleic acid is inserted into a gene of a chromosome.
  • a "promoter” is a nucleotide sequence that directs the transcription of a structural gene.
  • a promoter is located in the 5' non-coding region of a gene, proximal to the transcriptional start site of a structural gene. Sequence elements within promoters that function in the initiation of transcription are often characterized by consensus nucleotide sequences. These promoter elements include RNA polymerase binding sites, TATA sequences, CAAT sequences, differentiation-specific elements (DSEs; McGehee et al., Mol. Endocrinol.
  • CREs cyclic AMP response elements
  • SREs serum response elements
  • GREs glucocorticoid response elements
  • binding sites for other transcription factors such as CRE/ATF (O'Reilly et al, J. Biol. Chem. 267: 19938 (1992); incorporated by reference in its entirety), AP2 (Ye et al., J. Biol. Chem. 269:25728 (1994); incorporated by reference in its entirety), SP1, cAMP response element binding protein (CREB; Loeken, Gene Expr.
  • CREs cyclic AMP response elements
  • SREs serum response elements
  • GREs glucocorticoid response elements
  • binding sites for other transcription factors such as CRE/ATF (O'Reilly et al, J. Biol. Chem. 267: 19938 (1992); incorporated by reference in its entirety), AP2 (Ye et al., J. Biol. Chem. 269:25728 (1994); incorporated
  • a promoter can be constitutively active, repressible or inducible. If a promoter is an inducible promoter, then the rate of transcription increases in response to an inducing agent. In contrast, the rate of transcription is not regulated by an inducing agent if the promoter is a constitutive promoter. Repressible promoters are also known.
  • a gene delivery polynucleotide is provided. In some alternatives, the gene delivery polynucleotide comprises a promoter sequence.
  • Selectable marker cassette is a gene introduced into a vector or a cell that confers a trait for artificial selection.
  • a selectable marker cassette can be a screenable marker to allow a researcher to distinguish between wanted and unwanted cells, or to enrich for a specific cell type.
  • a gene delivery polynucleotide is provided.
  • the gene delivery polynucleotide comprises a selectable marker cassette.
  • DHFR dihydrofolate reductase
  • NADPH electron donor
  • a gene delivery polynucleotide is provided.
  • the gene delivery polynucleotide comprises at least one selectable marker cassette encoding for a double mutant of dihydrofolate reductase.
  • Methodhotrexate (MTX), as described herein, is an antimetabolite and antifolate drug. It acts by inhibiting the metabolism of folic acid.
  • MTX Metalhotrexate
  • a method of generating engineered multiplexed T-cells for adoptive T-cell immunotherapy is provided.
  • the method can comprise providing the gene delivery polynucleotide of any of the alternatives described herein, introducing the gene delivery polynucleotide into a T-cell, providing a vector encoding a Sleeping Beauty transposase, introducing the vector encoding the Sleeping Beauty transposase into the T-cell, selecting the cells comprising the gene delivery polynucleotide, wherein the selecting comprises a first round of selection and a second round of selection, wherein the first round of selection comprises adding a selection reagent at a first concentration range and the second round of selection comprises adding the same selection reagent at a second concentration range, wherein the second concentration range is greater than the first concentration range and, wherein the second concentration range is at least 1.5 fold higher than that of the first concentration range, and isolating the T-cells expressing a phenotype under this selective pressure.
  • the selection reagent comprises an agent for selection.
  • the selection reagent is MTX
  • An "inverted repeat" or IR is a sequence of nucleotides followed downstream by its reverse complement.
  • Inverted repeats can have a number of important biological functions. They can define the boundaries in transposons and indicate regions capable of self-complementary base pairing (regions within a single sequence which can base pair with each other). These properties play an important role in genome instability and contribute to cellular evolution, genetic diversity and also to mutation and disease.
  • a gene delivery polynucleotide is provided.
  • the gene delivery polynucleotide comprises a first inverted terminal repeat gene sequence and a second inverted terminal repeat gene sequence.
  • the gene delivery polynucleotide comprises a sleeping beauty transposon positioned between two inverted repeat sequences.
  • IR Inverted repeat
  • the sequence of IR is as follows : cagttgaagtcggaagtttacatacacttaagttggagtcattaaaactcgtttttcaactacTccacaaatttcttgttaacaacaatagt tttggcaagtcagttaggacatctactttgtgcatgacacaagtcattttttccaacaattgtttacagacagattatttcacttataattcactg tatcacaattccagtgggtcagaagtttacatacactaagttgactgtgcctttaaacagcttggaaaattccagaaatgatgtcatggct ttagaag
  • a "polypeptide” is a polymer of amino acid residues joined by peptide bonds, whether produced naturally or synthetically. Polypeptides of less than about 10 amino acid residues are commonly referred to as “peptides.”
  • a "protein” is a macromolecule comprising one or more polypeptide chains.
  • a protein can also comprise non-peptide components, such as carbohydrate groups. Carbohydrates and other non-peptide substituents can be added to a protein by the cell in which the protein is produced, and will vary with the type of cell. Proteins are defined herein in terms of their amino acid backbone structures; substituents such as carbohydrate groups are generally not specified, but can be present nonetheless.
  • a gene delivery polynucleotide for stable insertion of a nucleic acid into a gene wherein the nucleic acid for insertion is flanked by inverted terminal repeat gene sequences in the gene delivery polynucleotide and wherein the gene delivery polynucleotide is selectable, the gene delivery polynucleotide, is provided.
  • the gene delivery polynucleotide further comprises a sequence for at least one protein.
  • An "antibody” as described herein refers to a large Y-shape protein produced by plasma cells that is used by the immune system to identify and neutralize foreign objects such as bacteria and viruses.
  • the antibody protein can comprise four polypeptide chains; two identical heavy chains and two identical light chains connected by disulfide bonds. Each chain is composed of structural domains called immunoglobulin domains. These domains can contain about 70-110 amino acids and are classified into different categories according to their size and function.
  • a gene delivery polynucleotide for stable insertion of a nucleic acid into a gene wherein the nucleic acid for insertion is flanked by inverted terminal repeat gene sequences in the gene delivery polynucleotide and wherein the gene delivery polynucleotide is selectable, the gene delivery polynucleotide, is provided.
  • the gene delivery polynucleotide further comprises a sequence for at least one protein.
  • the gene delivery polynucleotide can comprise a sequence for an antibody or a portion thereof, which may be humanized.
  • a "chimeric antigen receptor” also known as chimeric T-cell receptors, refers to artificial T-cell receptors that are engineered receptors, which graft an arbitrary specificity onto an immune effector cell. These receptors can be used to graft the specificity of a monoclonal antibody onto a T-cell, for example; with transfer of their coding sequence facilitated by retroviral vectors.
  • the structure of the CAR can comprise single- chain variable fragments (scFv) derived from monoclonal antibodies, fused to CD3-zeta transmembrane and endodomain. Such molecules result in the transmission of a zeta signal in response to recognition by the scFv of its target.
  • Some alternatives utilize a gene delivery polynucleotide for stable insertion of a nucleic acid into a gene, wherein the nucleic acid for insertion is flanked by inverted terminal repeat gene sequences in the gene delivery polynucleotide, and wherein the gene delivery polynucleotide is selectable.
  • the gene delivery polynucleotide further comprises a sequence for at least one protein.
  • the protein is a chimeric antigen receptor. Chimeric receptor can also be referred to as artificial T cell receptors, chimeric T cell receptors, chimeric immunoreceptors, and chimeric antigen receptors (CARs).
  • CARs are engineered receptors that can graft an arbitrary specificity onto an immune receptor cell.
  • Chimeric antigen receptors or "CARs" are considered by some investigators in some contexts to include the antibody or antibody fragment, spacer, signaling domain, and transmembrane region.
  • the components of the CAR are described herein in some contexts to include these features as independent elements. The variation of the different elements of the CAR can, for example, lead to stronger binding affinity for a specific epitope.
  • T-cells can be used as a therapy for cancer or viral infection using a technique called adoptive cell transfer.
  • T-cells are removed from a patient and modified so that they express receptors specific for a molecule displayed on a cancer cell or virus, or virus-infected cell.
  • the genetically engineered T-cells which can then recognize and kill the cancer cells or the virus infected cells or promote clearance of the virus, are reintroduced into the patient.
  • the gene delivery polynucleotide can comprise a sequence for a chimeric antigen receptor.
  • a method of generating engineered multiplexed T-cells for adoptive T-cell immunotherapy is provided.
  • the method can comprise providing the gene delivery polynucleotide of any one of the alternatives described herein, introducing the gene delivery polynucleotide into a T-cell, providing a vector encoding a Sleeping Beauty transposase, introducing the vector encoding the Sleeping Beauty transposase into the T-cell, selecting the cells comprising the gene delivery polynucleotide, wherein selecting comprises a first round of selection and a second round of selection, wherein the first round of selection comprises adding a selection reagent at a first concentration range and the second round of selection comprises adding the selection reagent at a second concentration range, and wherein the second concentration range is at least 1.5 fold higher than that of the first concentration range and isolating the T-cells expressing a phenotype under selective pressure.
  • the selection reagent is MTX.
  • T-cell co-stimulation is desired for development of an effective immune response and this event occurs during the activation of lymphocytes.
  • a co-stimulatory signal is antigen non-specific and is provided by the interaction between co-stimulatory molecules expressed on the membrane of the antigen bearing cell and the T-cell.
  • Co-stimulatory molecules can include but are not limited to CD28, CD80, and CD86.
  • a method for generating engineered multiplexed T-cell for adoptive T-cell immunotherapy is provided.
  • the T-cell is a chimeric antigen receptor bearing T-cell.
  • the chimeric antigen receptor bearing T-cell is engineered to express co- stimulatory ligands.
  • methods are provided for treating, inhibiting, or ameliorating cancer or a viral infection in a subject.
  • the method can comprise administering to the subject a T-cell of any of the alternatives described herein.
  • genetically engineered T cells are used to treat, inhibit, or ameliorate a cancer or a viral disease, wherein the genetically engineered T cells are obtained by preferential amplification of T cells that are transformed to express multiple transgenes encoding receptors or chimeric receptors specific for a molecule presented by a virus or a cancer cell and selection pressure on the transformed T cells is applied in a two-stage MTX selection, utilizing increasing concentrations of MTX.
  • the subject is an animal, such as domestic livestock or a companion animal and on other alternatives, the subject is a human.
  • the chimeric antigen bearing T-cell is engineered to express a co-stimulatory molecule.
  • the gene delivery polynucleotide comprises a sequence for at least one co-stimulatory molecule.
  • the gene delivery polynucleotide is circular.
  • the gene delivery polynucleotide is at least lkB to 6kB.
  • the gene delivery polynucleotide is a minicircle.
  • T cell precursors refers to lymphoid precursor cells that can migrate to the thymus and become T cell precursors, which do not express a T cell receptor. All T cells originate from hematopoietic stem cells in the bone marrow. Hematopoietic progenitors (lymphoid progenitor cells) from hematopoietic stem cells populate the thymus and expand by cell division to generate a large population of immature thymocytes. The earliest thymocytes express neither CD4 nor CD8, and are therefore classed as double-negative (CD4 CD8 ) cells.
  • CD4 CD8 double-negative
  • thymocytes As they progress through their development, they become double-positive thymocytes (CD4 + CD8 + ), and finally mature to single-positive (CD4 CD8 or CD4 ⁇ CD8 + ) thymocytes that are then released from the thymus to peripheral tissues.
  • CD4 + CD8 + double-positive thymocytes
  • CD4 ⁇ CD8 + single-positive thymocytes that are then released from the thymus to peripheral tissues.
  • About 98% of thymocytes die during the development processes in the thymus by failing either positive selection or negative selection, whereas the other 2% survive and leave the thymus to become mature immunocompetent T cells.
  • the double negative (DN) stage of the precursor T cell is focused on producing a functional ⁇ -chain whereas the double positive (DP) stage is focused on producing a functional a-chain, ultimately producing a functional ⁇ T cell receptor.
  • the T cell expresses an invariant a-chain but rearranges the ⁇ -chain locus. If the rearranged ⁇ - chain successfully pairs with the invariant a-chain, signals are produced which cease rearrangement of the ⁇ -chain (and silence the alternate allele) and result in proliferation of the cell.
  • these signals require this pre-TCR at the cell surface, they are dependent on ligand binding to the pre-TCR.
  • These thymocytes will then express both CD4 and CD8 and progresses to the double positive (DP) stage where selection of the a-chain takes place. If a rearranged ⁇ -chain does not lead to any signaling (e.g. as a result of an inability to pair with the invariant a-chain), the cell may die by neglect (lack of signaling).
  • Hematopoietic stem cells are precursor cells that can give rise to myeloid cells such as, for example, macrophages, monocytes, macrophages, neutrophils, basophils, eosinophils, erythrocytes, megakaryocytes/platelets, dendritic cells and lymphoid lineages (such as, for example, T-cells, B-cells, NK-cells).
  • HSCs have a heterogeneous population in which three classes of stem cells exist, which are distinguished by their ratio of lymphoid to myeloid progeny in the blood (L/M).
  • a method of generating engineered multiplexed T- cells for adoptive T-cell immunotherapy comprises providing a gene delivery polynucleotide, introducing the gene delivery polynucleotide into a T-cell, providing a vector encoding a Sleeping Beauty transposase, introducing the vector encoding the Sleeping Beauty transposase into the T-cell, selecting the cells comprising the gene delivery polynucleotide wherein selecting comprises a first round of selection and a second round of selection, wherein the first round of selection comprises adding a selection reagent at a first concentration range and the second round of selection comprises adding the selection reagent at a second concentration range, wherein the second concentration range is higher than the first concentration range and, wherein the second concentration range is at least 1.5 fold higher than that of the first concentration range and isolating the T-cells expressing a phenotype under selective pressure.
  • the gene delivery polynucleotide comprises a first sequence, wherein the first sequence comprises a first inverted terminal repeat gene sequence, a second sequence, wherein the second sequence comprises a second inverted terminal repeat gene sequence, a third sequence, wherein the third sequence comprises a promoter region sequence, a fourth sequence, wherein the fourth sequence comprises at least one gene encoding a protein, and wherein the fourth sequence is optimized, a fifth sequence, wherein the fifth sequence comprises at least one selectable marker cassette encoding a double mutant of dihydrofolate reductase, wherein the double mutant of dihydrofolate reductase has a 15,000 fold or about 15,000 fold reduced affinity for methotrexate, wherein the methotrexate can be used as a selection mechanism to selectively amplify cells transduced with the gene delivery polynucleotide and wherein the fifth sequence is optimized, a sixth sequence, wherein the sixth sequence comprises a first attachment site (attP) and a seventh sequence, wherein
  • the gene encoding the double mutant of human dihydrofolate reductase comprises the DNA sequence: ATGGTTGGTTCGCTAAACTGCATCGTCGCTGTGTCCCAGAACATGGGCATCGGCA AGAACGGGGACTTCCCCTGGCCACCGCTCAGGAATGAATCCAGATATTTCCAGA GAATGACCACAACCTCTTCAGTAGAAGGTAAACAGAATCTGGTGATTATGGGTA AGAAGACCTGGTTCTCCATTCCTGAGAAGAATCGACCTTTAAAGGGTAGAATTA ATTTAGTTCTCAGCAGAGAACTCAAGGAACCTCCACAAGGAGCTCATTTTCTTTC CAGAAGTCTAGATGATGCCTTAAAACTTACTGAACAACCAGAATTAGCAAATAA AGTAGACATGGTCTGGATAGTTGGTGGCAGTTCTGTTTATAAGGAAGCCATGAAT CACCCAGGCCATCTTAAACTATTTGTGACAAGGATCATGCAAGACTTTGAAAGTG ACACGTTTTCCAGAAATTGATTTG
  • the double mutant of human dihydro folate reductase comprises the protein sequence: MVGSLNCIVA VSQNMGIGKN GDFPWPPLRN ESRYFQRMTT TSSVEGKQNL VIMGK TWFS IPEKNRPLKG RINLVLSREL KEPPQGAHFL SRSLDDALKL TEQPELANKV DMVWIVGGSS VYKEAMNHPG HLKLFVTRIM QDFESDTFFP EIDLEKYKLL PEYPGVLSDV QEEKGIKYKF EVYEKND (SEQ ID NO: 3).
  • the gene delivery polynucleotide is circular.
  • the gene delivery polynucleotide is at least lkB to 5kB. In some alternatives, the gene delivery polynucleotide is a minicircle. In some alternatives, the promoter region comprises an EF1 promoter sequence. In some alternatives, the fourth sequence comprises one, two, three, four, or five genes that encode proteins. In some alternatives, the fourth sequence is codon optimized to reduce the total GC/AT ratio of the fourth sequence. In some alternatives, the fourth sequence is optimized by codon optimization for expression in humans. In some alternatives, the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins.
  • the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins, such as a plurality of antibody binding domains, which are specific for the same epitope.
  • the plurality of related proteins comprise a plurality of antibody binding domains, wherein the plurality of antibody binding domains are specific for the same epitope.
  • the fifth sequence is codon optimized to reduce the total GC/AT ratio of the fifth sequence.
  • the fifth sequence is optimized by codon optimization for expression in humans.
  • the protein is a protein for therapy.
  • the codon optimization and/or consensus sequence is generated by comparing the variability of sequence and/or nucleobases utilized in a plurality of related sequences.
  • the protein comprises an antibody or a portion thereof, which may be humanized.
  • the double mutant of dihydrofolate reductase comprises amino acid mutations of L22F and F31S.
  • the double mutant of dihydrofolate reductase comprises amino acid mutations of L22F and F3 IS.
  • the introducing is performed by electroporation.
  • the selecting is performed by increasing selective pressure through the selective marker cassette.
  • the selection reagent comprises an agent for selection.
  • the agent for selection is methotrexate.
  • the first concentration range is at least 50nM - lOOnM and the second concentration range is at least 75 to 150nM.
  • the first concentration is 50 nM, 60 nM, 70 nM, 80 nM, 90 nM, or lOOnM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 75 nM, 80 nM, 90 nM, 100 nM, 110 nM, 120 nM, 130 nM, 140 nM, or 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 75 nM - 150 nM and the second concentration range is at least 112.5 nM to 225 nM.
  • the first concentration is 75 nM, 85 nM, 95 nM, 105 nM, 115 nM, 125 nM, 135 nM, 145 nM, or 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 112 nM, 122 nM, 132 nM, 142 nM, 152 nM, 162 nM, 172 nM, 182 nM, 192 nM, 202 nM, 212 nM, or 225 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 300 nM - 675 nM and the first concentration range is at least 450 nM to 1012 nM.
  • the first concentration is 300 nM, 350 nM, 400 nM, 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, or 675 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, 700 nM, 750 nM, 800 nM, 850 nM, 900 nM, 1000 nM, or 1012 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first round of selection comprises exposing the T-cells to the selection agent for 2, 3, 4, 5, 6 or 7 days before the second round of selection.
  • the second round of selection comprises exposing the T-cells to the selection agent for at least 2, 3, 4, 5, 6,7, 8, 9, 10, 11, 12, 13, or 14 days or any time that is between a range of times defined by any two of the aforementioned time points before isolation.
  • the T cells comprise precursor T cells.
  • the precursor T cells are hematopoietic stem cells.
  • a method of generating engineered cells for adoptive T-cell immunotherapy comprising, providing a gene delivery polynucleotide, introducing the gene delivery polynucleotide into a precursor T cell, providing a vector encoding a Sleeping Beauty transposase, introducing the vector encoding the Sleeping Beauty transposase into the precursor T cell, selecting the precursor T cells comprising the gene delivery polynucleotide; wherein selecting comprises a first round of selection and a second round of selection, wherein the first round of selection comprises adding a selection reagent at a first concentration range and the second round of selection comprises adding the selection reagent at a second concentration range, wherein the second concentration range is higher than the first concentration range and, wherein the second concentration range is at least 1.5 fold higher than that of the first concentration range and isolating the precursor T-cells expressing a phenotype under selective pressure.
  • the gene delivery polynucleotide is for stable insertion of a nucleic acid into an oligonucleotide wherein the nucleic acid for insertion is flanked by inverted terminal repeat gene sequences in the gene delivery polynucleotide and wherein the gene delivery polynucleotide is selectable, wherein the gene delivery polynucleotide comprises a first sequence, wherein the first sequence comprises a first inverted terminal repeat gene sequence, a second sequence, wherein the second sequence comprises a second inverted terminal repeat gene sequence, a third sequence, wherein the third sequence comprises a promoter region sequence, a fourth sequence, wherein the fourth sequence comprises at least one gene, wherein the at least one gene encodes a protein or encodes a sequence for mR A transcription, and wherein the fourth sequence is optimized, a fifth sequence, wherein the fifth sequence comprises at least one selectable marker cassette encoding a double mutant of dihydrofolate reductase, wherein the double mutant of dihydrof
  • the gene delivery polynucleotide is circular. In some alternatives, the gene delivery polynucleotide is at least lkB to 5kB. In some alternatives, the promoter region comprises an EF1 promoter sequence. In some alternatives, the fourth sequence comprises one, two, three, four, or five genes that encode proteins. In some alternatives, the fourth sequence is codon optimized to reduce the total GC/AT ratio of the fourth sequence. In some alternatives, the fourth sequence is optimized by codon optimization for expression in humans. In some alternatives, the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins.
  • the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins, such as a plurality of antibody binding domains, which are specific for the same epitope.
  • the plurality of related proteins comprise a plurality of antibody binding domains, wherein the plurality of antibody binding domains are specific for the same epitope.
  • the fifth sequence is codon optimized to reduce the total GC/AT ratio of the fifth sequence.
  • the fifth sequence is optimized by codon optimization for expression in humans.
  • the codon optimization and/or consensus sequence is generated by comparing the variability of sequence and/or nucleobases utilized in a plurality of related sequences.
  • the protein is a protein for therapy.
  • the protein comprises an antibody or a portion thereof, which may be humanized.
  • the double mutant of dihydro folate reductase comprises amino acid mutations of L22F and F31 S.
  • the gene delivery polynucleotide is a minicircle.
  • the introducing is performed by electroporation.
  • the selecting is performed by increasing selective pressure through the selective marker cassette.
  • the selection reagent comprises an agent for selection.
  • the agent for selection is methotrexate.
  • the first concentration range is at least 50nM - lOOnM and the second concentration range is at least 75 to 150nM.
  • the first concentration range is at least 75 nM - 150 nM and the second concentration range is at least 112.5 nM to 225 nM. In some alternatives, the first concentration range is at least 300 nM - 675 nM and the first concentration range is at least 450 nM to 1012 nM. In some alternatives, the first round of selection comprises exposing the T-cells to the selection agent for 2, 3, 4, 5, 6 or 7 days before the second round of selection. In some alternatives, the second round of selection comprises exposing the T-cells to the selection agent for at least 2, 3, 4, 5, 6,7, 8, 9, 10, 11, 12, 13, or 14 days or any time that is between a range of times defined by any two of the aforementioned time points before isolation. In some alternatives, the T cell precursor is a hematopoietic stem cell.
  • a method of increasing protein production in a precursor T-cell comprising providing a polynucleotide, introducing the polynucleotide into a cell, providing a vector encoding a Sleeping Beauty transposase; introducing the vector encoding the Sleeping Beauty transposase into the precursor T-cell, selecting the precursor T cells comprising the gene delivery polynucleotide, wherein selecting comprises a first round of selection and a second round of selection, wherein the first round of selection comprises adding a selection reagent at a first concentration range and the second round of selection comprises adding the selection reagent at a second concentration range, wherein the second concentration range is higher than the first concentration range and, wherein the second concentration range is at least 1.5 fold higher than that of the first concentration range and isolating the precursor T cells expressing a phenotype under selective pressure.
  • the gene delivery polynucleotide is for stable insertion of a nucleic acid into an oligonucleotide wherein the nucleic acid for insertion is flanked by inverted terminal repeat gene sequences in the gene delivery polynucleotide and wherein the gene delivery polynucleotide is selectable, wherein the gene delivery polynucleotide comprises a first sequence, wherein the first sequence comprises a first inverted terminal repeat gene sequence, a second sequence, wherein the second sequence comprises a second inverted terminal repeat gene sequence, a third sequence, wherein the third sequence comprises a promoter region sequence, a fourth sequence, wherein the fourth sequence comprises at least one gene, wherein the at least one gene encodes a protein or encodes a sequence for mR A transcription, and wherein the fourth sequence is optimized, a fifth sequence, wherein the fifth sequence comprises at least one selectable marker cassette encoding a double mutant of dihydrofolate reductase, wherein the double mutant of dihydrof
  • the gene delivery polynucleotide is circular. In some alternatives, the gene delivery polynucleotide is at least lkB to 5kB. In some alternatives, the promoter region comprises an EF1 promoter sequence. In some alternatives, the fourth sequence comprises one, two, three, four, or five genes that encode proteins. In some alternatives, the fourth sequence is codon optimized to reduce the total GC/AT ratio of the fourth sequence. In some alternatives, the fourth sequence is optimized by codon optimization for expression in humans. In some alternatives, the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins.
  • the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins, such as a plurality of antibody binding domains, which are specific for the same epitope.
  • the plurality of related proteins comprise a plurality of antibody binding domains, wherein the plurality of antibody binding domains are specific for the same epitope.
  • the fifth sequence is codon optimized to reduce the total GC/AT ratio of the fifth sequence.
  • the fifth sequence is optimized by codon optimization for expression in humans.
  • the codon optimization and/or consensus sequence is generated by comparing the variability of sequence and/or nucleobases utilized in a plurality of related sequences.
  • the protein is a protein for therapy.
  • the protein comprises an antibody or a portion thereof, which may be humanized.
  • the double mutant of dihydro folate reductase comprises amino acid mutations of L22F and F31 S.
  • the gene delivery polynucleotide is a minicircle.
  • the introducing is performed by electroporation.
  • the selecting is performed by increasing selective pressure through the selective marker cassette.
  • the selection reagent comprises an agent for selection.
  • the agent for selection is methotrexate.
  • the first concentration range is at least 50nM - 100 nM and the second concentration range is at least 75 to 150 nM. In some alternatives, the first concentration range is at least 75nM - 150nM and the second concentration range is at least 112.5 nM to 225 nM. In some alternatives, the first concentration range is at least 300 nM - 675 nM and the second concentration range is at least 450 nM to 1012 nM. In some alternatives, the first round of selection comprises exposing the cells to the selection agent for 2, 3, 4, 5, 6 or 7 days before the second round of selection. In some alternatives, the second round of selection comprises exposing the cells to the selection agent for at least 2, 3, 4, 5, 6, or 7 days before isolation. In some alternatives, the precursor T cells are hematopoietic stem cells.
  • a peptide or polypeptide encoded by a non-host DNA molecule is a "heterologous" peptide or polypeptide.
  • An "integrated genetic element” is a segment of DNA that has been incorporated into a chromosome of a host cell after that element is introduced into the cell through human manipulation.
  • integrated genetic elements can be derived from minicircles that are introduced into the cells by electroporation or other techniques. Integrated genetic elements are passed from the original host cell to its progeny.
  • an integrated genetic element is incorporated into a chromosome of a host cell by a gene delivery polynucleotide is circular.
  • the gene delivery polynucleotide is at least lkB to 6kB.
  • the gene delivery polynucleotide is a minicircle.
  • a "cloning vector” or vector is a nucleic acid molecule, such as a minicircle, plasmid, cosmid, plastome, or bacteriophage that has the capability of replicating autonomously in a host cell.
  • Cloning vectors typically contain one or a small number of restriction endonuclease recognition sites that allow insertion of a nucleic acid molecule in a determinable fashion without loss of an essential biological function of the vector, as well as nucleotide sequences encoding a marker gene that is suitable for use in the identification and selection of cells transduced with the cloning vector.
  • Marker genes typically include genes that provide tetracycline resistance or ampicillin resistance but in some alternatives can include a methotrexate resistance gene.
  • an "expression vector” is a nucleic acid molecule encoding a gene that is expressed in a host cell.
  • an expression vector comprises a transcription promoter, a gene, and a transcription terminator. Gene expression is usually placed under the control of a promoter, and such a gene is said to be “operably linked to" the promoter. Similarly, a regulatory element and a core promoter are operably linked if the regulatory element modulates the activity of the core promoter.
  • an expression vector is provided.
  • the expression vector encodes a transposase.
  • the transposase is a Sleeping Beauty transposase.
  • expression vector is circular.
  • the expression vector is at least lkB to 6kB. In some alternatives, the expression vector is a minicircle.
  • minicircles are small circular plasmid derivatives that have been freed from all prokaryotic vector parts. Minicircles can serve as an expression vector, where they have been applied as transgene carriers for the genetic modification of mammalian cells, with the advantage that, since they contain no bacterial DNA sequences, they are less likely to be perceived as foreign and destroyed. As such, typical transgene delivery methods involve plasmids, which contain foreign DNA. The smaller size of minicircles also extends their cloning capacity and facilitates their delivery into cells. Without being limiting, the preparation of minicircles can follow a two-step procedure, which can involve production of a parental plasmid (bacterial plasmid with eukaryotic inserts) in E.
  • a parental plasmid bacterial plasmid with eukaryotic inserts
  • the purified minicircle can be transferred into the recipient cell by transfection, by electroporation, or by other methods known to those skilled in the art.
  • minicircles can lack an origin of replication, so they cannot replicate within the target cells and the encoded genes will disappear as the cell divides (which can be either an advantage or disadvantage depending on whether the application demands persistent or transient expression).
  • Some alternatives utilize a gene delivery polynucleotide for stable insertion of a nucleic acid into a gene, wherein the nucleic acid for insertion is flanked by inverted terminal repeat gene sequences in the gene delivery polynucleotide, and wherein the gene delivery polynucleotide is selectable.
  • the gene delivery polynucleotide is a minicircle.
  • nucleofection refers to a transfection method of exogenous nucleic acid(s) into a host cell and is performed by electroporation.
  • a method of generating engineered multiplexed T-cells for adoptive T-cell immunotherapy is provided.
  • the method can comprise providing the gene delivery polynucleotide of any of the alternatives described herein, introducing the gene delivery polynucleotide into a T-cell, selecting the cells comprising the gene delivery polynucleotide, wherein selecting comprises a first round of selection and a second round of selection, wherein the first round of selection comprises adding a selection reagent at a first concentration range and the second round of selection comprises adding the selection reagent at a second concentration range, wherein the second concentration range is higher than the first concentration range and, wherein the second concentration range is at least 1.5 fold higher than that of the first concentration range and isolating the T-cells expressing a phenotype under selective pressure.
  • the selection reagent is MTX.
  • introducing the gene delivery polynucleotide into a T-cell can be performed by electroporation.
  • Host cell is a cell that contains one or more nucleases, for example endonucleases, end-processing enzymes, and/or endonuclease/end- processing enzyme fusion proteins encompassed by the present alternatives or a vector encoding the same that supports the replication, and/or transcription or transcription and translation (expression) of one or more nucleases, for example endonucleases, end- processing enzymes, and/or endonuclease/end-processing enzyme fusion proteins.
  • host cells for use in the present alternatives can be eukaryotic cells.
  • Host cells of the immune system can include T-cells.
  • a method of generating engineered multiplexed T-cells for adoptive T-cell immunotherapy can comprise providing the gene delivery polynucleotide of any one of the alternatives described herein, introducing the gene delivery polynucleotide into a T- cell, providing a vector encoding a Sleeping Beauty transposase, introducing the vector encoding the Sleeping Beauty transposase into the T-cell, selecting the cells comprising the gene delivery polynucleotide, wherein the selecting comprises a first round of selection and a second round of selection, wherein the first round of selection comprises adding a selection reagent at a first concentration range and the second round of selection comprises adding the selection reagent at a second concentration range, wherein the second concentration range is higher than the first concentration range and, wherein the second concentration range is at least 1.5 fold higher than that of the first concentration range and isolating the T-cells expressing a phenotype under selective pressure.
  • the method can comprise providing the gene delivery polynucleot
  • transposable element can be referred to as a DNA sequence that can change its position within the genome, sometimes creating or reversing mutations and altering the cell's genome size. Transposition often results in duplication of the TE.
  • TEs can make up a large fraction of the C-value of eukaryotic cells.
  • C-values refers to amount, in picograms, of DNA contained within a haploid nucleus of one half the amount in a diploid somatic cells of a eukaryotic organism.
  • the terms C-value and genome size are used interchangeably, however in polyploids the C-value can represent two or more genomes contained within the same nucleus.
  • Oxytricha which has a unique genetic system, they play a critical role in development. They are also very useful to researchers as a means to alter DNA inside a living organism.
  • a gene delivery polynucleotide for stable insertion of a nucleic acid into a gene, wherein the nucleic acid for insertion is flanked by inverted terminal repeat gene sequences in the gene delivery polynucleotide and wherein the gene delivery polynucleotide is selectable, the gene delivery polynucleotide is provided.
  • the gene delivery polynucleotide comprises a transposon.
  • the "Sleeping Beauty transposon system” as described herein, is composed of a Sleeping Beauty (SB) transposase and a transposon that was designed in 1997 to insert specific sequences of DNA into genomes of vertebrate animals.
  • SB Sleeping Beauty
  • DNA transposons can translocate from one DNA site to another in a simple, cut-and-paste manner. Transposition is a precise process in which a defined DNA segment is excised from one DNA molecule and moved to another site in the same or different DNA molecule or genome.
  • An SB transposase can insert a transposon into a TA dinucleotide base pair in a recipient DNA sequence.
  • the insertion site can be elsewhere in the same DNA molecule, or in another DNA molecule (or chromosome). In mammalian genomes, including humans, there are approximately 200 million TA sites.
  • the TA insertion site is duplicated in the process of transposon integration. This duplication of the TA sequence is a hallmark of transposition and used to ascertain the mechanism in some experiments.
  • the transposase can be encoded either within the transposon or the transposase can be supplied by another source, in which case the transposon becomes a non-autonomous element.
  • a gene delivery polynucleotide for stable insertion of a nucleic acid into a gene wherein the nucleic acid for insertion is flanked by inverted terminal repeat gene sequences in the gene delivery polynucleotide and wherein the gene delivery polynucleotide is selectable, the gene delivery polynucleotide, is provided.
  • the gene delivery polynucleotide comprises a transposon.
  • the transposon is a Sleeping Beauty transposon.
  • the nucleic acid to be inserted is a Sleeping Beauty transposon flanked by inverted terminal repeat gene sequences.
  • the gene delivery polynucleotide for stable insertion of nucleic acid is a minicircle. In some alternatives, the gene delivery polynucleotide for stable insertion of nucleic acid comprises a Sleeping Beauty transposon. In some alternatives, methods of generating engineered multiplexed T-cells are provided. In some alternatives, the method comprises delivering a Sleeping Beauty transposase to a cell. In some alternatives, methods of increasing protein production in a T-cell are provided. In some alternatives, the method comprises providing a vector encoding a Sleeping Beauty transposase. In some alternatives, the method comprises delivering a vector encoding a Sleeping Beauty transposase to a cell.
  • Codon optimization refers to the design process of altering codons to codons known to increase maximum protein expression efficiency in a desired cell.
  • codon optimization is described, wherein codon optimization can be performed by using algorithms that are known to those skilled in the art to create synthetic genetic transcripts optimized for high protein yield.
  • Programs containing alogorithms for codon optimization are known to those skilled in the art.
  • Programs can include, for example, OptimumGeneTM, GeneGPS® algorithms, etc.
  • synthetic codon optimized sequences can be obtained commercially for example from Integrated DNA Technologies and other commercially available DNA sequencing services.
  • a gene delivery polynucleotide for stable insertion of a nucleic acid into a gene wherein the nucleic acid for insertion is flanked by inverted terminal repeat gene sequences in the gene delivery polynucleotide and wherein the gene delivery polynucleotide is selectable, is provided.
  • the gene delivery polynucleotides are described, wherein the genes for the complete gene transcript are codon optimized for expression in humans.
  • the genes are optimized to have selected codons specifically for maximal protein expression in human cells, which can increase the concentration of proteins or CARs of a T-cell.
  • Codon optimization can be performed to reduce the occurrence of secondary structure in a polynucleotide, as well.
  • codon optimization can also be performed to reduce the total GC/AT ratio.
  • Strict codon optimization can also lead to unwanted secondary structure or an undesirable GC content that leads to secondary structure.
  • the secondary structures affect transcriptional efficiency.
  • Programs such as GeneOptimizer can be used after codon usage optimization, for secondary structure avoidance and GC content optimization. These additional programs can be used for further optimization and troubleshooting after an initial codon optimization to limit secondary structures that may occur after the first round of optimization.
  • Alternative programs for optimization are known to those skilled in the art.
  • a gene delivery polynucleotide for stable insertion of a nucleic acid into a gene, wherein the nucleic acid for insertion is flanked by inverted terminal repeat gene sequences in the gene delivery polynucleotide and wherein the gene delivery polynucleotide is selectable provided.
  • the gene delivery polynucleotide comprises sequences that are codon optimized for expression in humans and/or to remove secondary structure and/or to reduce the total GC/AT ratio.
  • the sequences are optimized for secondary structure avoidance.
  • the sequences are optimized to reduce the total GC/AT ratio.
  • a method of generating engineered multiplexed T- cells for adoptive T-cell immunotherapy can comprise providing the gene delivery polynucleotide of any one of the alternatives described herein, introducing the gene delivery polynucleotide into a T-cell, providing a vector encoding a Sleeping Beauty transposase, introducing the vector encoding the Sleeping Beauty transposase into the T-cell, selecting the cells comprising the gene delivery polynucleotide, wherein selecting comprises a first round of selection and a second round of selection, wherein the first round of selection comprises adding a selection reagent at a first concentration range and the second round of selection comprises adding the selection reagent at a second concentration range, wherein the second concentration range is higher than the first concentration range and, wherein the second concentration range is at least 1.5 fold higher than that of the first concentration range, and isolating the T-cells expressing a phenotype under selective pressure
  • Adoptive immunotherapy for cancer or a viral disease Adoptive immunotherapy for cancer or a viral disease.
  • the premise of adoptive immunotherapy for cancer is transferring a patient's own tumor-specific T-cells into patients to facilitate the destruction of malignant cells.
  • T-cells can be genetically-engineered to recognize tumor- specific antigens and exert cytotoxic activity against cancer cells.
  • a method of adoptive immunotherapy for cancer is to isolate patient T-cells and introduce tumor recognition capability by expressing chimeric antigen receptors (CARs), membrane proteins that contain an extracellular tumor-binding domain linked to an intracellular signaling domain via a transmembrane segment.
  • CARs chimeric antigen receptors
  • "Adoptive immunotherapy” or "T-cell adoptive transfer” refers to use of T-cell based cytotoxic response to attack cancer cells or specific cell targets.
  • T-cells that have a natural or genetically engineered reactivity to a patient's cancer can be generated in vitro and then transferred back into the subject in need.
  • an example of adoptive transfer can be achieved by removing T-cells from a subject that has cancer or a viral disease and these T cells can be genetically engineered to express receptors specific for biomarkers found on a cancer cell or virus such that the genetically engineered T cells attack the cancer cells or virus or virus infected cells once the genetically engineered T-cells are transferred back into the subject.
  • a method of generating engineered multiplexed T- cells for adoptive T-cell immunotherapy is provided.
  • methods of targeting malignant cells for destruction are provided.
  • a method of treating, inhibiting, or ameliorating a cancer or a viral disease in a subject comprises administering to the subject an engineered multiplexed T-cells for adoptive T-cell immunotherapy.
  • the subject is human.
  • CAR-expressing T-cells can further increase the anti-tumor or antiviral activity of CAR-expressing T-cells.
  • Comprehensive T-cell activation requires, in addition to initial tumor or viral recognition and signal initiation by CAR, engagement of costimulatory and cytokine receptors, which may not be present within the immunosuppressive environment of the tumor or the viral infected subject.
  • expression of co-stimulatory ligands such as CD80 and 4-1BBL in engineered, CAR-expressing T-cells can result in greater T-cell expansion due to auto-co-stimulation compared to expression of co-stimulatory ligands on tumor cells.
  • T-cell immunotherapy Another challenge in T-cell immunotherapy is cell survival after infusion into patients. Induced expression of anti-apoptotic proteins has been shown to improve in vivo survival of T-cells. Tumor homing and infiltration can be increased by introduction of chemokine receptors in engineered T-cells and this approach can be especially useful for tumors that express chemokines that are not normally recognized by T- cells. Finally, T-cells can be engineered to better resist the immunosuppressive tumor microenvironment or the immunocompromised virally infected subject through, for example, induced cytokine expression. Thus, methods to rapidly generate engineered T-cells expressing multiple transgenes are important and advantageous for clinical translation of T- cell immunotherapy.
  • methods of generating engineered multiplexed T- cells for adoptive T-cell immunotherapy are provided.
  • the T-cells express chimeric antigen receptors.
  • T-cells expressing chimeric antigen receptors are engineered to express co-stimulatory ligands.
  • the T-cells expressing chimeric antigen receptors express co-stimulatory ligands.
  • the co-stimulatory ligands are CD80.
  • the co-stimulatory ligands are 4- 1BBL.
  • Adoptive cell transfer can refer to the transfer of cells, immune-derived cells, back into the same patient or into a different recipient host.
  • blood can be drawn into tubes containing anticoagulant and the PBM (buffy coat) cells are isolated, typically by density barrier centrifugation.
  • PBM denffy coat
  • the cells can be expanded in vitro using cell culture methods relying heavily on the immunomodulatory action of interleukin-2 and returned to the patient in large numbers intravenously in an activated state.
  • Anti-CD3 antibody can be used to promote the proliferation of T-cells in culture. Research into interleukin-21 indicates that it can also play an important role in enhancing the efficacy of T-cell based therapies prepared in vitro.
  • Cells used in adoptive cell transfer can be used to deliver genetically modified lymphocytes, using recombinant DNA technology to achieve any number of goals.
  • adoptive cell transfer is used to transfer cells into a subject, wherein the cells are CAR expressing lymphocytes.
  • CAR expressing lymphocytes are host cells in methods for generating engineered multiplexed T-cells for adoptive T-cell immunotherapy.
  • the method comprises providing the gene delivery polynucleotide of the alternatives described herein, introducing the gene delivery polynucleotide into a T-cell, providing a vector encoding a Sleeping Beauty transposase, introducing the vector encoding the Sleeping Beauty transposase into the T-cell, selecting the cells comprising the gene delivery polynucleotide, wherein selecting comprises a first round of selection and a second round of selection, wherein the first round of selection comprises adding a selection reagent at a first concentration range and the second round of selection comprises adding the selection reagent at a second concentration range, wherein the second concentration range is higher than the first concentration range and, wherein the second concentration range is at least 1.5 fold higher than that of the first concentration range, and isolating the T-cells expressing a phenotype under selective pressure.
  • the gene delivery polynucleotide comprises a sequence for a co-stimulatory ligand. In some alternatives, the gene delivery polynucleotide comprises a sequence for a chimeric antigen receptor. In some alternatives, the T-cell expresses a CAR. In alternatives described herein, the CAR expressing lymphocytes are genetically modified by minicircles wherein the minicircles comprise Sleeping Beauty transposons. In some alternatives, the selection reagent is MTX.
  • genetically engineered T-cells can be created by infecting patient's cells with a transferring virus that contain a copy of a T- cell receptor (TCR) gene that is specialized to recognize, for example, tumor or viral antigens. It is important that the transferring virus is not able to reproduce within the cell however, but should integrate into the human genome. This is beneficial as new TCR gene remains stable in the T-cell.
  • a patient's own T-cells are exposed to these transferring viruses and then are expanded non-specifically or stimulated using the genetically engineered TCR. The cells are then transferred back into the patient and are ready to mount an immune response against the tumor, virus, or viral infected cell.
  • adoptive cell transfer with genetically engineered T-cells is a promising new approach for the treatment of a variety of cancers or viral infections.
  • methods of adoptive immunotherapy for cancer are provided.
  • methods of adoptive immunotherapy for viral infections are provided.
  • the method of making genetically engineered T-cells by using a viral vector can have several drawbacks. Genetic modification of T-cells is typically accomplished using ⁇ -retroviral or lentiviral vectors. While effective, drawbacks include cost of production, limited gene packaging capacity, and potential safety issues. Plasmids containing transposon systems such as Sleeping Beauty (SB) or piggyBac offer a non-viral approach for stably introducing genes into T-cells. Recently, the piggyBac system was used to produce stably- transfected mammalian cells expressing multiple transgenes of interest by delivery of multiple transposons.
  • SB Sleeping Beauty
  • piggyBac offer a non-viral approach for stably introducing genes into T-cells. Recently, the piggyBac system was used to produce stably- transfected mammalian cells expressing multiple transgenes of interest by delivery of multiple transposons.
  • the SB system first reactivated for mammalian cell use by Ivies and coworkers, has been used as the gene delivery modality in clinical trials of T-cell immunotherapy.
  • Gene integration by SB has weaker preference for transcriptional units and their regulatory sequences compared to the ⁇ -retroviral and lentiviral vectors and is therefore considered to be safer.
  • genetic modification by minicircles comprising the Sleeping Beauty system are contemplated.
  • genetic modification by minicircles comprising the piggyBac system are contemplated.
  • genetic modification by minicircles comprising the Sleeping Beauty system are contemplated. [0098]
  • Minicircles are particularly attractive as transfection platforms for three reasons.
  • the transfection efficiency of minicircles by electroporation is superior to that of their plasmid analogues.
  • transposition efficiency is higher in minicircles due to the shorter distance between the two transposon ends, which has been shown to affect transposase efficiency.
  • minicircles are more advantageous given their smaller size compared to their analogous plasmids.
  • the optimized SB100X hyperactive transposase developed by Izsvak et al. ⁇ Nature Genet. 2009, 41, 753-761; incorporated by reference in its entirety can be used in combination with the T3 generation of SB previously by Yant et al (Mol. Cell.
  • methods for making a genetically modified T-cell for adoptive cell transfer are contemplated.
  • the methods comprise introducing a minicircle into a T-cell.
  • the introduction comprises electroporation delivery.
  • T-cell immunotherapy Another challenge in T-cell immunotherapy is cell survival after infusion into patients. Induced expression of anti-apoptotic proteins has been shown to improve in vivo survival of T-cells. Tumor homing and infiltration has been increased by introduction of chemokine receptors in engineered T-cells; this approach can be especially useful for tumors that express chemokines that are not normally recognized by T-cells. Finally, T-cells can be engineered to better resist the immunosuppressive tumor microenvironment through, for example, induced cytokine expression. Thus, methods to rapidly generate engineered T-cells expressing multiple transgenes are important and advantageous for clinical translation of T- cell immunotherapy.
  • the additional genes encode co-stimulatory ligands.
  • the co-stimulatory ligand is CD80.
  • the co-stimulatory ligand is 4-1BBL.
  • the additional genes encode anti-apoptotic proteins.
  • the additional genes encode chemokine receptors.
  • the method can comprise providing the gene delivery polynucleotide of any of the alternatives described herein, introducing the gene delivery polynucleotide into a T-cell, providing a vector encoding a Sleeping Beauty transposase, introducing the vector encoding the Sleeping Beauty transposase into the T-cell, selecting the cells comprising the gene delivery polynucleotide, wherein selecting comprises a first round of selection and a second round of selection, wherein the first round of selection comprises adding a selection reagent at a first concentration range and the second round of selection comprises adding the selection reagent at a second concentration range, wherein the second concentration range is higher than the first concentration range and, wherein the second concentration range is at least 1.5 fold higher than that of the first concentration range, and isolating the T-cells expressing a phenotype under selective pressure.
  • the first round of selection comprises adding a selection reagent at a first concentration range
  • the second round of selection comprises adding the selection reagent at a second
  • the method can comprise providing the gene delivery polynucleotide of any of the alternatives described herein, introducing the gene delivery polynucleotide into a T-cell, providing a vector encoding a Sleeping Beauty transposase, introducing the vector encoding the Sleeping Beauty transposase into the T-cell, selecting the cells comprising the gene delivery polynucleotide, wherein selecting comprises a first round of selection and a second round of selection, wherein the first round of selection comprises adding a selection reagent at a first concentration range and the second round of selection comprises adding the selection reagent at a second concentration range, wherein the second concentration range is higher than the first concentration range and, wherein the second concentration range is at least 1.5 fold higher than that of the first concentration range, and isolating the T-cells expressing a phenotype under selective pressure.
  • the selection reagent is MT
  • an alternative of the system comprises an engineered, non- viral gene delivery system comprising three key features: (1) Sleeping Beauty transposon system for stable gene expression, (2) minicircles for enhanced transfection, and (3) a double mutant of human dihydrofolate reductase (DHFRdm) as a selection mechanism ( Figure 1).
  • Minicircles are particularly attractive as transfection platforms for three reasons. First, the transfection efficiency of minicircles by electroporation is superior to that of their plasmid analogues. Second, transposition efficiency is higher in minicircles due to the shorter distance between the two transposon ends, which has been shown to affect transposase efficiency.
  • minicircles are more desirable given their smaller size compared to their analogous plasmids.
  • the optimized SB100X hyperactive transposase developed by Izsvak et al. ⁇ Nature Genet. 2009, 41, 753-761; incorporated herein by reference in its entirety) was used in combination with the T3 generation of SB transposon previously by Yant et al (Mol. Cell. Biol. 2004, 24, 9239-9247; incorporated herein by reference in its entirety).
  • genetic modification of T-cells is performed using minicircles.
  • the minicircles comprise transposons.
  • the transposons comprise Sleeping Beauty transposons.
  • an optimized SB100X hyperactive transposase is used in combination with a T3 generation of SB transposon.
  • a selection mechanism for rapid selection of engineered T-cells can also be employed.
  • the double mutant of human dihydrofolate reductase (DHFRdm, with amino acid mutations L22F and F31S) exhibits a 15,000-fold reduced affinity for methotrexate, a potent inhibitor of DHFR that results in blockade of thymidylate and purine synthesis.
  • Expression of DHFRdm in T-cells imparts MTX resistance without compromising proliferative ability, expression of T-cell markers, or cytolytic ability. Additional advantages of this selection system include availability of clinical grade MTX, the use of a non- genotoxic drug, and the small gene size of DHFRdm (561 bp).
  • the minicircles comprise a genetic sequence encoding a double mutant of human dihydrofolate reductase.
  • a selection method for rapid selection of engineered T-cells is provided.
  • the selection method comprises contacting engineered T-cells with clinical grade methotrexate.
  • the T- cells comprise a minicircle wherein the minicircle comprises a sequence for a double mutant of human dihydrofolate reductase.
  • the double mutant of human dihydrofolate reductase exhibits a 15,000 fold or about 15,000 fold reduced specificity for methotrexate.
  • methotrexate can be used to contact the T-cells for selectively amplifying cells transduced with minicircles, wherein the minicircles comprise a sequence for the double mutant of human dihydro folate reductase.
  • the gene encoding the double mutant of human dihydrofolate reductase comprises the DNA sequence:
  • the double mutant of human dihydrofolate reductase comprises the protein sequence: MVGSLNCIVA VSQNMGIGKN GDFPWPPLRN ESRYFQRMTT TSSVEGKQNL VIMGK TWFS IPEKNRPLKG RINLVLSREL KEPPQGAHFL SRSLDDALKL TEQPELANKV DMVWIVGGSS VYKEAMNHPG HLKLFVTRIM QDFESDTFFP EIDLEKYKLL PEYPGVLSDV QEEKGIKYKF EVYEKND (SEQ ID NO: 3).
  • Stable transfer of up to three transgenes into the H9 T-cell line using multiplexed delivery of minicircles containing SB transposons followed by methotrexate (MTX) selection can be performed.
  • Cells with higher number of gene integrations can be preferentially obtained by increasing selection pressure with MTX.
  • MTX methotrexate
  • a method of stably transferring transgenes into a cell line is provided.
  • a method of introducing minicircles into a cell line is provided.
  • the minicircles comprise Sleeping Beauty transposons.
  • the method further comprises increasing selection pressure with methotrexate, wherein increasing the selection pressure comprises contacting the cell line with increasing concentrations of methotrexate.
  • the two rounds of methotrexate selection are performed.
  • a gene delivery polynucleotide for stable insertion of a nucleic acid into a gene wherein the nucleic acid for insertion is flanked by inverted terminal repeat gene sequences in the gene delivery polynucleotide and wherein the gene delivery polynucleotide is selectable, the gene delivery polynucleotide, is provided.
  • the gene delivery polynucleotide comprises a first sequence, wherein the first sequence comprises a first inverted terminal repeat gene sequence, a second sequence, wherein the second sequence comprises a second inverted terminal repeat gene sequence, a third sequence, wherein the third sequence comprises a promoter region sequence, a fourth sequence, wherein the fourth sequence comprises at least one gene encoding a protein, and wherein the fourth sequence is optimized, a fifth sequence, wherein the fifth sequence comprises at least one selectable marker cassette encoding a double mutant of dihydrofolate reductase, wherein the double mutant of dihydrofolate reductase has a 15,000 fold or about
  • methotrexate can be used as a selection mechanism to selectively amplify cells transduced with the gene delivery polynucleotide and wherein the fifth sequence is optimized, a sixth sequence, wherein the sixth sequence comprises a first attachment site (attP), and a seventh sequence, wherein the seventh sequence comprises a second attachment site (attB); wherein each of the first sequence, second sequence, third sequence, fourth sequence, fifth sequence, sixth sequence, and seventh sequence have a 5 ' terminus and a 3 ' terminus, and wherein the 3 ' terminus of the first sequence comprising the first inverted terminal repeat gene sequence is adjacent to the 5' terminus of the third sequence, the 3' terminus of the third sequence is adjacent to the
  • the gene encoding the double mutant of human dihydrofolate reductase comprises the DNA sequence:
  • the double mutant of human dihydro folate reductase comprises the protein sequence: MVGSLNCIVA VSQNMGIGKN GDFPWPPLRN ESRYFQRMTT TSSVEGKQNL VIMGK TWFS IPEKNRPLKG RINLVLSREL KEPPQGAHFL SRSLDDALKL TEQPELANKV DMVWIVGGSS VYKEAMNHPG HLKLFVTRIM QDFESDTFFP EIDLEKYKLL PEYPGVLSDV QEEKGIKYKF EVYEKND (SEQ ID NO: 3).
  • the gene delivery polynucleotide is circular.
  • the gene delivery polynucleotide is at least IkB to 6kB. In some alternatives, the gene delivery polynucleotide is a minicircle. In some alternatives, the promoter region comprises an EF1 promoter sequence. In some alternatives, the fourth sequence comprises one, two, three, four, or five genes that encode proteins. In some alternatives, the fourth sequence is codon optimized to reduce the total GC/AT ratio of the fourth sequence. In some alternatives, the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins, such as a plurality of antibody binding domains, which are specific for the same epitope. In some alternatives, the fifth sequence is codon optimized to reduce the total GC/AT ratio of the fourth sequence.
  • the codon optimization and/or consensus sequence is generated by comparing the variability of sequence and/or nucleobases utilized in a plurality of related sequences.
  • the protein is a protein for therapy.
  • the protein comprises an antibody or a portion thereof.
  • the double mutant of dihydrofolate reductase comprises amino acid mutations of L22F and F31S.
  • the minicircle comprises a sequence for the double mutant of dihydrofolate reductase, the sequence comprising the DNA sequence :
  • the double mutant of dihydrofolate reductase comprises the protein sequence: MVGSLNCIVA VSQNMGIGKN
  • a method of generating engineered multiplexed T- cells for adoptive T-cell immunotherapy can comprise providing the gene delivery polynucleotide of any of the alternatives described herein, introducing the gene delivery polynucleotide into a T-cell, providing a vector encoding a Sleeping Beauty transposase, introducing the vector encoding the Sleeping Beauty transposase into the T-cell, selecting the cells comprising the gene delivery polynucleotide, wherein selecting comprises a first round of selection and a second round of selection, wherein the first round of selection comprises adding a selection reagent at a first concentration range and the second round of selection comprises adding the selection reagent at a second concentration range, wherein the second concentration range is higher than the first concentration range and, wherein the second concentration range is at least 1.5 fold higher than that of the first concentration range, and isolating the T-cells expressing a phenotype under selective pressure.
  • introducing is performed by electroporation.
  • the selecting is performed by increasing selective pressure through the selective marker cassette.
  • the selection reagent comprises an agent for selection.
  • the agent for selection is methotrexate.
  • the first concentration range is at least 50nM - lOOnM and the second concentration range is at least 75 to 150nM.
  • the first concentration is 50 nM, 60 nM, 70 nM, 80 nM, 90 nM, or lOOnM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 75 nM, 80 nM, 90 nM, 100 nM, 110 nM, 120 nM, 130 nM, 140 nM, or 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 75 nM - 150 nM and the second concentration range is at least 112.5 nM to 225 nM.
  • the first concentration is 75 nM, 85 nM, 95 nM, 105 nM, 115 nM, 125 nM, 135 nM, 145 nM, or 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 112 nM, 122 nM, 132 nM, 142 nM, 152 nM, 162 nM, 172 nM, 182 nM, 192 nM, 202 nM, 212 nM, or 225 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 300 nM - 675 nM and the first concentration range is at least 450 nM to 1012 nM.
  • the first concentration is 300 nM, 350 nM, 400 nM, 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, or 675 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, 700 nM, 750 nM, 800 nM, 850 nM, 900 nM, 1000 nM, or 1012 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first round of selection comprises exposing the T-cells to the selection agent for 2, 3, 4, 5, 6 or 7 days before the second round of selection.
  • the second round of selection comprises exposing the T- cells to the selection agent for at least 2, 3, 4, 5, 6 or 7 days before isolation.
  • a method of increasing protein production in a cell can comprise providing the gene delivery polynucleotide of any one of the alternatives described herein, introducing the gene delivery polynucleotide into a T-cell, providing a vector encoding a Sleeping Beauty transposase, introducing the vector encoding the Sleeping Beauty transposase into the T-cell, selecting the cells comprising the gene delivery polynucleotide, wherein selecting comprises a first round of selection and a second round of selection, wherein the first round of selection comprises adding a selection reagent at a first concentration range and the second round of selection comprises adding the selection reagent at a second concentration range, wherein the second concentration range is higher than the first concentration range and, wherein the second concentration range is at least 1.5 fold higher than that of the first concentration range, and isolating the T-cells expressing a phenotype under selective pressure.
  • introducing is performed by electroporation. In some alternatives, selecting is performed by increasing selective pressure through the selective marker cassette. In some alternatives, the selection reagent comprises an agent for selection. In some alternatives, the agent for selection is methotrexate. In some alternatives, the low or first concentration range is at least 50 nM - 100 nM and the higher or second concentration range is at least 75 to 150 nM. In some alternatives, the low or first concentration range is at least 75 nM - 150 nM and the higher or second concentration range is at least 112.5 nM to 225 nM. In some alternatives, the low or first concentration range is at least 300 nM - 675 nM and the higher or second concentration range is at least 450 nM to 1012 nM.
  • the first round of selection comprises exposing the T-cells to the selection agent for 2, 3, 4, 5, 6 or 7 days before the second round of selection.
  • the second round of selection comprises exposing the T-cells to the selection agent for at least 2, 3, 4, 5, 6 or 7 days before isolation.
  • an engineered multiplexed T-cell for adoptive T-cell immunotherapy generated by any one of the methods of is provided.
  • the engineered multiplexed T-cells for adoptive T-cell immunotherapy is generated by a method, wherein the method comprises providing a gene delivery polynucleotide, introducing the gene delivery polynucleotide into a T-cell, providing a vector encoding a Sleeping Beauty transposase, introducing the vector encoding the Sleeping Beauty transposase into the T-cell, selecting the cells comprising the gene delivery polynucleotide wherein selecting comprises a first round of selection and a second round of selection, wherein the first round of selection comprises adding a selection reagent at a first concentration range and the second round of selection comprises adding the selection reagent at a second concentration range, wherein the second concentration range is higher than the first concentration range and, wherein the second concentration range is at least 1.5 fold higher than that of the first concentration range and iso
  • the gene delivery polynucleotide comprises a first sequence, wherein the first sequence comprises a first inverted terminal repeat gene sequence, a second sequence, wherein the second sequence comprises a second inverted terminal repeat gene sequence, a third sequence, wherein the third sequence comprises a promoter region sequence, a fourth sequence, wherein the fourth sequence comprises at least one gene encoding a protein, and wherein the fourth sequence is optimized, a fifth sequence, wherein the fifth sequence comprises at least one selectable marker cassette encoding a double mutant of dihydrofolate reductase, wherein the double mutant of dihydrofolate reductase has a 15,000 fold or about 15,000 fold reduced affinity for methotrexate, wherein the methotrexate can be used as a selection mechanism to selectively amplify cells transduced with the gene delivery polynucleotide and wherein the fifth sequence is optimized, a sixth sequence, wherein the sixth sequence comprises a first attachment site (attP) and a seventh sequence, wherein
  • the double mutant of human dihydro folate reductase comprises the protein sequence: MVGSLNCIVA VSQNMGIGKN GDFPWPPLRN ESRYFQRMTT TSSVEGKQNL VIMGK TWFS IPEKNRPLKG RINLVLSREL KEPPQGAHFL SRSLDDALKL TEQPELANKV DMVWIVGGSS VYKEAMNHPG HLKLFVTRIM QDFESDTFFP EIDLEKYKLL PEYPGVLSDV QEEKGIKYKF EVYEKND (SEQ ID NO: 3).
  • the gene delivery polynucleotide is circular.
  • the gene delivery polynucleotide is at least lkB to 5kB. In some alternatives, the gene delivery polynucleotide is a minicircle. In some alternatives, the promoter region comprises an EF1 promoter sequence. In some alternatives, the fourth sequence comprises one, two, three, four, or five genes that encode proteins. In some alternatives, the fourth sequence is codon optimized to reduce the total GC/AT ratio of the fourth sequence. In some alternatives, the fourth sequence is optimized by codon optimization for expression in humans. In some alternatives, the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins.
  • the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins, such as a plurality of antibody binding domains, which are specific for the same epitope.
  • the plurality of related proteins comprise a plurality of antibody binding domains, wherein the plurality of antibody binding domains are specific for the same epitope.
  • the fifth sequence is codon optimized to reduce the total GC/AT ratio of the fifth sequence.
  • the fifth sequence is optimized by codon optimization for expression in humans.
  • the protein is a protein for therapy.
  • the codon optimization and/or consensus sequence is generated by comparing the variability of sequence and/or nucleobases utilized in a plurality of related sequences.
  • the protein comprises an antibody or a portion thereof, which may be humanized.
  • the double mutant of dihydrofolate reductase comprises amino acid mutations of L22F and F31S.
  • the double mutant of dihydro folate reductase comprises amino acid mutations of L22F and F31S.
  • the introducing is performed by electroporation.
  • the selecting is performed by increasing selective pressure through the selective marker cassette.
  • the selection reagent comprises an agent for selection.
  • the agent for selection is methotrexate.
  • the first concentration range is at least 50nM - lOOnM and the second concentration range is at least 75 to 150nM.
  • the first concentration is 50 nM, 60 nM, 70 nM, 80 nM, 90 nM, or lOOnM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 75 nM, 80 nM, 90 nM, 100 nM, 110 nM, 120 nM, 130 nM, 140 nM, or 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 75 nM - 150 nM and the second concentration range is at least 112.5 nM to 225 nM.
  • the first concentration is 75 nM, 85 nM, 95 nM, 105 nM, 115 nM, 125 nM, 135 nM, 145 nM, or 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 112 nM, 122 nM, 132 nM, 142 nM, 152 nM, 162 nM, 172 nM, 182 nM, 192 nM, 202 nM, 212 nM, or 225 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 300 nM - 675 nM and the first concentration range is at least 450 nM to 1012 nM.
  • the first concentration is 300 nM, 350 nM, 400 nM, 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, or 675 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, 700 nM, 750 nM, 800 nM, 850 nM, 900 nM, 1000 nM, or 1012 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first round of selection comprises exposing the T-cells to the selection agent for 2, 3, 4, 5, 6 or 7 days before the second round of selection.
  • the second round of selection comprises exposing the T-cells to the selection agent for at least 2, 3, 4, 5, 6,7, 8, 9, 10, 11, 12, 13, or 14 days or any time that is between a range of times defined by any two of the aforementioned time points before isolation.
  • the gene delivery polynucleotide comprises a first sequence, wherein the first sequence comprises a first inverted terminal repeat gene sequence, a second sequence, wherein the second sequence comprises a second inverted terminal repeat gene sequence, a third sequence, wherein the third sequence comprises a promoter region sequence, a fourth sequence, wherein the fourth sequence comprises at least one gene encoding a protein, and wherein the fourth sequence is optimized, a fifth sequence, wherein the fifth sequence comprises at least one selectable marker cassette encoding a double mutant of dihydrofolate reductase, wherein the double mutant of dihydrofolate reductase has a 15,000 fold or about 15,000 fold reduced affinity for methotrexate, wherein the methotrexate can be used as a selection mechanism to selectively amplify cells transduced with the gene delivery polynucleotide and wherein the fifth sequence is optimized, a sixth sequence, wherein the sixth sequence comprises a first attachment site (attP) and a seventh sequence, wherein
  • the gene encoding the double mutant of human dihydrofolate reductase comprises the DNA sequence: ATGGTTGGTTCGCTAAACTGCATCGTCGCTGTGTCCCAGAACATGGGCATCGGCA AGAACGGGGACTTCCCCTGGCCACCGCTCAGGAATGAATCCAGATATTTCCAGA GAATGACCACAACCTCTTCAGTAGAAGGTAAACAGAATCTGGTGATTATGGGTA AGAAGACCTGGTTCTCCATTCCTGAGAAGAATCGACCTTTAAAGGGTAGAATTA ATTTAGTTCTCAGCAGAGAACTCAAGGAACCTCCACAAGGAGCTCATTTTCTTTC CAGAAGTCTAGATGATGCCTTAAAACTTACTGAACAACCAGAATTAGCAAATAA AGTAGACATGGTCTGGATAGTTGGTGGCAGTTCTGTTTATAAGGAAGCCATGAAT CACCCAGGCCATCTTAAACTATTTGTGACAAGGATCATGCAAGACTTTGAAAGTG ACACGTTTTCCAGAAATTGATTTG
  • the double mutant of human dihydro folate reductase comprises the protein sequence: MVGSLNCIVA VSQNMGIGKN GDFPWPPLRN ESRYFQRMTT TSSVEGKQNL VIMGK TWFS IPEKNRPLKG RINLVLSREL KEPPQGAHFL SRSLDDALKL TEQPELANKV DMVWIVGGSS VYKEAMNHPG HLKLFVTRIM QDFESDTFFP EIDLEKYKLL PEYPGVLSDV QEEKGIKYKF EVYEKND (SEQ ID NO: 3).
  • the gene delivery polynucleotide is circular.
  • the gene delivery polynucleotide is at least lkB to 5kB. In some alternatives, the gene delivery polynucleotide is a minicircle. In some alternatives, the promoter region comprises an EF1 promoter sequence. In some alternatives, the fourth sequence comprises one, two, three, four, or five genes that encode proteins. In some alternatives, the fourth sequence is codon optimized to reduce the total GC/AT ratio of the fourth sequence. In some alternatives, the fourth sequence is optimized by codon optimization for expression in humans. In some alternatives, the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins.
  • the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins, such as a plurality of antibody binding domains, which are specific for the same epitope.
  • the plurality of related proteins comprise a plurality of antibody binding domains, wherein the plurality of antibody binding domains are specific for the same epitope.
  • the fifth sequence is codon optimized to reduce the total GC/AT ratio of the fifth sequence.
  • the fifth sequence is optimized by codon optimization for expression in humans.
  • the protein is a protein for therapy.
  • the codon optimization and/or consensus sequence is generated by comparing the variability of sequence and/or nucleobases utilized in a plurality of related sequences.
  • the protein comprises an antibody or a portion thereof, which may be humanized.
  • the double mutant of dihydrofolate reductase comprises amino acid mutations of L22F and F31S.
  • the introducing is performed by electroporation.
  • the selecting is performed by increasing selective pressure through the selective marker cassette.
  • the selection reagent comprises an agent for selection.
  • the agent for selection is methotrexate.
  • the first concentration range is at least 50nM - lOOnM and the second concentration range is at least 75 to 150nM.
  • the first concentration is 50 nM, 60 nM, 70 nM, 80 nM, 90 nM, or ⁇ or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 75 nM, 80 nM, 90 nM, 100 nM, 110 nM, 120 nM, 130 nM, 140 nM, or 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 75 nM - 150 nM and the second concentration range is at least 112.5 nM to 225 nM.
  • the first concentration is 75 nM, 85 nM, 95 nM, 105 nM, 115 nM, 125 nM, 135 nM, 145 nM, or 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 112 nM, 122 nM, 132 nM, 142 nM, 152 nM, 162 nM, 172 nM, 182 nM, 192 nM, 202 nM, 212 nM, or 225 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 300 nM - 675 nM and the first concentration range is at least 450 nM to 1012 nM.
  • the first concentration is 300 nM, 350 nM, 400 nM, 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, or 675 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, 700 nM, 750 nM, 800 nM, 850 nM, 900 nM, 1000 nM, or 1012 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first round of selection comprises exposing the T-cells to the selection agent for 2, 3, 4, 5, 6 or 7 days before the second round of selection.
  • the second round of selection comprises exposing the T- cells to the selection agent for at least 2, 3, 4, 5, 6,7, 8, 9, 10, 11, 12, 13, or 14 days or any time that is between a range of times defined by any two of the aforementioned time points before isolation.
  • a method of treating, inhibiting, or ameliorating cancer or a disease in a subject comprises administering to the subject the modified or engineered multiplexed T-cell as described below.
  • the engineered multiplexed T-cells for adoptive T-cell immunotherapy is generated by a method, wherein the method comprises providing a gene delivery polynucleotide, introducing the gene delivery polynucleotide into a T-cell, providing a vector encoding a Sleeping Beauty transposase, introducing the vector encoding the Sleeping Beauty transposase into the T-cell, selecting the cells comprising the gene delivery polynucleotide wherein selecting comprises a first round of selection and a second round of selection, wherein the first round of selection comprises adding a selection reagent at a first concentration range and the second round of selection comprises adding the selection reagent at a second concentration range, wherein the second concentration range is higher than the first concentration range and, where
  • the gene delivery polynucleotide comprises a first sequence, wherein the first sequence comprises a first inverted terminal repeat gene sequence, a second sequence, wherein the second sequence comprises a second inverted terminal repeat gene sequence, a third sequence, wherein the third sequence comprises a promoter region sequence, a fourth sequence, wherein the fourth sequence comprises at least one gene encoding a protein, and wherein the fourth sequence is codon optimized for expression in humans, a fifth sequence, wherein the fifth sequence comprises at least one selectable marker cassette encoding a double mutant of dihydrofolate reductase, wherein the double mutant of dihydrofolate reductase has a 15,000 fold or about 15,000 fold reduced affinity for methotrexate, wherein the methotrexate can be used as a selection mechanism to selectively amplify cells transduced with the gene delivery polynucleotide and wherein the fifth sequence is codon optimized for expression in humans, a sixth sequence, wherein the sixth sequence comprises a first attachment site (
  • the double mutant of human dihydro folate reductase comprises the protein sequence: MVGSLNCIVA VSQNMGIGKN GDFPWPPLRN ESRYFQRMTT TSSVEGKQNL VIMGK TWFS IPEKNRPLKG RINLVLSREL KEPPQGAHFL SRSLDDALKL TEQPELANKV DMVWIVGGSS VYKEAMNHPG HLKLFVTRIM QDFESDTFFP EIDLEKYKLL PEYPGVLSDV QEEKGIKYKF EVYEKND (SEQ ID NO: 3).
  • the gene delivery polynucleotide is circular.
  • the gene delivery polynucleotide is a minicircle. In some alternatives, the gene delivery polynucleotide is at least lkB to 5kB. In some alternatives, the promoter region comprises an EF1 promoter sequence. In some alternatives, the fourth sequence comprises one, two, three, four, or five genes that encode proteins. In some alternatives, the fourth sequence is codon optimized to reduce the total GC/AT ratio of the fourth sequence. In some alternatives, the fourth sequence is optimized by codon optimization for expression in humans. In some alternatives, the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins.
  • the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins, such as a plurality of antibody binding domains, which are specific for the same epitope.
  • the plurality of related proteins comprise a plurality of antibody binding domains, wherein the plurality of antibody binding domains are specific for the same epitope.
  • the fifth sequence is codon optimized to reduce the total GC/AT ratio of the fifth sequence.
  • the fifth sequence is optimized by codon optimization for expression in humans.
  • the protein is a protein for therapy.
  • the codon optimization and/or consensus sequence is generated by comparing the variability of sequence and/or nucleobases utilized in a plurality of related sequences.
  • the protein comprises an antibody or a portion thereof, which may be humanized.
  • the double mutant of dihydrofolate reductase comprises amino acid mutations of L22F and F31S.
  • the double mutant of dihydrofolate reductase comprises amino acid mutations of L22F and F31S.
  • the introducing is performed by electroporation.
  • the selecting is performed by increasing selective pressure through the selective marker cassette.
  • the selection reagent comprises an agent for selection.
  • the agent for selection is methotrexate.
  • the first concentration range is at least 50nM - lOOnM and the second concentration range is at least 75 to 150nM.
  • the first concentration is 50 nM, 60 nM, 70 nM, 80 nM, 90 nM, or lOOnM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 75 nM, 80 nM, 90 nM, 100 nM, 110 nM, 120 nM, 130 nM, 140 nM, or 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 75 nM - 150 nM and the second concentration range is at least 112.5 nM to 225 nM.
  • the first concentration is 75 nM, 85 nM, 95 nM, 105 nM, 115 nM, 125 nM, 135 nM, 145 nM, or 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 112 nM, 122 nM, 132 nM, 142 nM, 152 nM, 162 nM, 172 nM, 182 nM, 192 nM, 202 nM, 212 nM, or 225 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 300 nM - 675 nM and the first concentration range is at least 450 nM to 1012 nM.
  • the first concentration is 300 nM, 350 nM, 400 nM, 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, or 675 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, 700 nM, 750 nM, 800 nM, 850 nM, 900 nM, 1000 nM, or 1012 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first round of selection comprises exposing the T-cells to the selection agent for 2, 3, 4, 5, 6 or 7 days before the second round of selection.
  • the second round of selection comprises exposing the T-cells to the selection agent for at least 2, 3, 4, 5, 6,7, 8, 9, 10, 11, 12, 13, or 14 days or any time that is between a range of times defined by any two of the aforementioned time points before isolation.
  • the subject is human.
  • pMC_T3/GFP-T2 A-DHFRdm mini-circle (MC) plasmid that carries the T3 SB transposon cassette containing an EFla promoter, maxGFP gene, Thoseaasigna virus 2A peptide (T2A) and a double mutant of dihydrofolate reductase (DHFRdm) insensitive to methotrexate (MTX) was constructed using pMC_T3/eGFP_IRES_FGFR (Nucleic Acids Research, 2012, 1-10 doi: 10.1093/nar/gks213, incorporated in its entirety herein) as a backbone, implementing the cloning strategy described previously (Cold Spring Harbor Protoc; 2012; doi: 10.1101/pdb.ip067876 ) to create the GFP-T2A-DHFRdm cassette.
  • MaxGFP Longza
  • pEGFRt-T2A-IMPDHdm-T2A-DHFRdm Generously provided by Michael Jensen
  • Plasmid MC SB100X was described previously (Nucleic Acids Research, 2012, 1-10 doi: 10.1093/nar/gks213, incorporated in its entirety herein). Minicircles were produced and purified according to the System Biosciences user manual for minicircle DNA vector technology. All plasmids were amplified under endotoxin free conditions using an Endofree Plasmid Kit (Qiagen).
  • H9 cells were cultured in DMEM with 10% FBS.
  • the optimized nucleofection protocol forH9 cells (Lonza) was followed (program X-001, Nucleofector Kit V). Per nucleofection, lxlO 6 cells were used with varying amounts of MC DNA. Cells were grown for a week after nucleofection to achieve stable transfection. For MTX selection, cells were cultured in DMEM with 10% FBS supplemented with different concentrations of MTX. Flow cytometry analysis.
  • Live cells were selected based on propidium iodide exclusion by adding propidium iodide in the flow cytometry buffer to 2 ⁇ g/ml.
  • Flow cytometry analysis was carried out on a MACSQuant Analyzer (Miltenyi Biotec) and LSRII (BD Biosciences). Collected data was analyzed with FlowJo software. Appropriate negative controls (untransfected H9 cells with and without propidium iodide staining, as well as cells transfected with single genes for GFP, BFP, and mCherry) were used for compensation and gating. A Becton Dickinson FACSAria II was used for cell sorting. Part of flow cytometry work was conducted at the UW Immunology Flow Cytometry Facility.
  • Genomic DNA was extracted with Puregene Kit A according to the manufacturer's instructions (Qiagen), and qPCR was performed using a 7300 Real-Time PCR System (Applied Biosystems) using Universal SYBR Green Supermix (BioRad).
  • Primer3 software maxGFP forward primer: 5'- ACAAGATCATCCGCAGCAAC-3 ' (SEQ ID NO: 4); reverse primer: 5'- TTGAAGTGCATGTGGCTGTC-3 ' (SEQ ID NO: 5); GAPDH forward primer: 5'- AC AACTTTGGTATCGTGGAAGG-3 ' (SEQ ID NO: 6); GAPDH reverse primer: 5'- GCCATCACGCCACAGTTTC-3 ' (SEQ ID NO: 7).
  • MaxGFP primers are specific for the maxGFP gene in the transposon.
  • Standard curves were generated using genomic DNA of a H9 clone with a single insertion of transposon ("gold standard") obtained by limiting dilution method. Copy number was calculated using the AACT method (Schmittgen,T.D. and Livak,K.J. (2008), incorporated in its entirety herein).
  • a population of T3/GFP-T2A-DHFRdm transfected-H9 cells selected with 200 nM MTX was plated in 96 well plates at a concentration of 0.5 cells/well in DMEM 10%FBS along with irradiated (5000 R) H9 feeder cells at 5,000 cells/well. Plates were incubated for 2-3 weeks, after which clonal populations were moved to larger plates and expanded. GFP expression was confirmed by flow cytometry. Relative RT-qPCR analysis was performed using DNA of 60 individual clones in order to determine transposon copy number. Optimization of stable gene transfer to H9 cells.
  • Minicircle constructs which have bacterial plasmid sequences removed, were used for all gene transfer studies. Minicircles can be generated as described previously by Kay et al. and colleagues (Chen, Z. Y.; He, C. Y.; Ehrhardt, A.; Kay, M. A. Molecular Therapy 2003, 8, 495-500 and Kay, M. A.; He, C. Y.; Chen, Z. Y. Nat. Biotechnol. 2010, 28, 1287-U96; incorporated herein by reference in their entirety). Three reporter minicircles containing transposons expressing different fluorescent proteins (maxGFP, mCherry, or BFP) under the EFl alpha promoter were constructed.
  • the selection gene a double mutant of dihydrofolate reductase (DHFRdm) that confers metabolic resistance to MTX, was cloned in frame after the T2A sequence.
  • the SB100X transposase gene was also prepared in a separate minicircle construct for co-delivery with transposon minicircles.
  • transposase binding sites there are four transposase binding sites in a transposon (two per inverted terminal repeat). Bound transposase were proposed to interact with each other to promote juxtaposition of the two transposon ends. Overexpression of transposase has been hypothesized to lead to inhibition of transposition due to interaction of free transposase with bound transposase, thus preventing the juxtaposition step. Therefore, the optimal transposon/transposase ratio needed to be determined whether these genes are delivered on separate constructs. Reports of the inhibition phenomenon have been varied.
  • the percentage of GFP + cells increased with the transposon/transposase ratio, reaching 39.2% ⁇ 3.0% at 1 :4 ratio, which reflects 58.6% integration efficiency of the initial transiently-integrated population. Higher ratios were not tested due to reduced cell viability. The overexpression inhibition effect was not observed in this tested range of transposon/transposase ratios. Therefore, from the results, the transduction experiments were carried out using this optimized transposon/transposase ratio of 1 :4.
  • the mean GFP fluorescence in GFP + cells increased with selection pressure (Figure 3, panel B); the mean fluorescence in cells selected with 200 nM MTX was 6.4-fold higher than unselected cells and 3.3-fold higher than cells selected with 50 nM MTX.
  • Figure 3, panel B The mean GFP fluorescence in GFP + cells increased with selection pressure
  • the mean fluorescence in cells selected with 200 nM MTX was 6.4-fold higher than unselected cells and 3.3-fold higher than cells selected with 50 nM MTX.
  • the positive correlation between mean GFP expression in GFP+ cells and MTX concentration suggests that increasing MTX concentration selects for cells with increased DHFRdm expression and therefore, multiple integration events.
  • the average integration events in cells selected with 200 nM MTX was 2.1 ⁇ 0.45 compared to an average of 1.1 ⁇ 0.02 integration events in GFP+ cells before MTX selection.
  • RT-qPCR was performed in triplicates and data represents a single biological replica for the sorted population and 3 biological replicas for MTX selection. Statistical difference was assessed by Student's t-test.
  • H9 cells were nucleofected with three minicircles containing three different reporter genes (maxGFP, mCherry, and BFP) in transposon cassettes and the SB100X transposase minicircle. Stably-transduced cells were then selected for 7 days with 200 nM and cell population assessed by flow cytometry analysis.
  • Figure 6 shows the flow cytometric analysis of H9 cell populations nucleofected with 3 minicircles carrying transposons with different fluorescent proteins (MC_T3/GFP-T2A-DHFRdm, MC T3/ BFP-T2A-DHFRdm, MC_T3/mCherry-T2A-DHFRdm), 2 ⁇ g each and 6 ⁇ g of MC SB100X DNA at different time points after transfection.
  • the stably transduced population was 37 ⁇ 1.4%, reflecting 54%> integration efficiency. Of this population, 19 ⁇ 0.6%) expressed two or three different fluorescent proteins.
  • PBMCs peripheral blood mononuclear cells
  • PBMCs peripheral blood mononuclear cells
  • the cells were transfected with l( ⁇ g of minicircle GFP (MC_T3/GFP-T2A-DHFRdm) and different amounts of SB100X hyperactive transposase (0, 5, or 10 ⁇ g).
  • Control cells were transfected with either the non- minicircle pMAXGFP vector (10 ug) or with no DNA. The cells were then stimulated with Miltenyi Transact beads 4 to 6 hours after transfection in the presence of IL-2 and IL-15.
  • FIG. 8 shows an example of the flow analysis of the lymphocytes expressing GFP after minicircle transfection.
  • Single cells panel B) from the lymphocyte window (panel A) were analyzed for viability with the Invitrogen LIVE/DEAD red stain (panel C).
  • Live lymphocytes were then analyzed for CD8 and GFP expression (panel D).
  • panel D after selecting with 50 nM methotrexate, the majority of lymphocytes were CD8+ and expressed GFP.
  • Figure 10 shows graphs of the levels of GFP expression and cell growth from days 2 to 7.
  • the amounts of percent GFP expression decreases over time (pMAXGFP (10 ug), mcGFP: MC SB100X 1 : 1, and mcGFP: MC SB100X 2: 1).
  • pMAXGFP 10 ug
  • mcGFP MC SB100X 1 : 1
  • mcGFP MC SB100X 2: 1
  • 100 nM MTX selection was effective with GFP expression at both ratios of mcGFP to SB at a 2: 1 mcGFP: MC SB100X ratio and at a 1 : 1 mcGFP: MC SB100X ratio after cell selection with MTX for seven days.
  • Figure 12 and Figure 13 show the results of a FACS assay of the transfected cells after treatment with methotrexate for 7 and 12 days, respectively. Scatter plots and CD8+/GFP expression for live lymphocytes are shown for each condition. Percent GFP expression in lymphocytes is given in boxes in Figure 12.
  • a gene delivery polynucleotide for stable insertion of a nucleic acid into a gene, wherein the nucleic acid for insertion is flanked by inverted terminal repeat gene sequences in the gene delivery polynucleotide and wherein the gene delivery polynucleotide is selectable wherein the gene delivery polynucleotide comprises a first sequence, wherein the first sequence comprises a first inverted terminal repeat gene sequence, a second sequence, wherein the second sequence comprises a second inverted terminal repeat gene sequence, a third sequence, wherein the third sequence comprises a promoter region sequence, a fourth sequence, wherein the fourth sequence comprises at least one gene encoding a protein, and wherein the fourth sequence is optimized, a fifth sequence, wherein the fifth sequence comprises at least one selectable marker cassette encoding a double mutant of dihydrofolate reductase, wherein the double mutant of dihydrofolate reductase has a 15,000 fold or about 15,000 fold
  • the gene encoding the double mutant of human dihydrofolate reductase comprises the DNA sequence: ATGGTTGGTTCGCTAAACTGCATCGTCGCTGTGTCCCAGAACATGGGCATCGGCA AGAACGGGGACTTCCCCTGGCCACCGCTCAGGAATGAATCCAGATATTTCCAGA GAATGACCACAACCTCTTCAGTAGAAGGTAAACAGAATCTGGTGATTATGGGTA AGAAGACCTGGTTCTCCATTCCTGAGAAGAATCGACCTTTAAAGGGTAGAATTA ATTTAGTTCTCAGCAGAGAACTCAAGGAACCTCCACAAGGAGCTCATTTTCTTTC CAGAAGTCTAGATGATGCCTTAAAACTTACTGAACAACCAGAATTAGCAAATAA AGTAGACATGGTCTGGATAGTTGGTGGCAGTTCTGTTTATAAGGAAGCCATGAAT CACCCAGGCCATCTTAAACTATTTGTGACAAGGATCATGCAAGACTTTGAAAGTG ACACGTTTTCCAGAAATTGATTTG
  • the double mutant of human dihydrofolate reductase comprises the protein sequence: MVGSLNCIVA VSQNMGIGKN GDFPWPPLRN ESRYFQRMTT TSSVEGKQNL VIMGK TWFS IPEKNRPLKG RINLVLSREL KEPPQGAHFL SRSLDDALKL TEQPELANKV DMVWIVGGSS VYKEAMNHPG HLKLFVTRIM QDFESDTFFP EIDLEKYKLL PEYPGVLSDV QEEKGIKYKF EVYEKND (SEQ ID NO: 3).
  • the gene delivery polynucleotide is circular.
  • the gene delivery polynucleotide is at least lkB to 5kB. In some alternatives, the gene delivery polynucleotide is a minicircle. In some alternatives, the gene delivery polynucleotide is a minicircle. In some alternatives, the promoter region comprises an EFl promoter sequence. In some alternatives, the fourth sequence comprises one, two, three, four, or five genes that encode proteins. In some alternatives, the fourth sequence is codon optimized to reduce the total GC/AT ratio of the fourth sequence. In some alternatives, the fourth sequence is optimized by codon optimization for expression in humans. In some alternatives, the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins.
  • the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins, such as a plurality of antibody binding domains, which are specific for the same epitope.
  • the plurality of related proteins comprise a plurality of antibody binding domains, wherein the plurality of antibody binding domains are specific for the same epitope.
  • the fifth sequence is codon optimized to reduce the total GC/AT ratio of the fifth sequence.
  • the fifth sequence is optimized by codon optimization for expression in humans.
  • the protein is a protein for therapy.
  • the codon optimization and/or consensus sequence is generated by comparing the variability of sequence and/or nucleobases utilized in a plurality of related sequences.
  • the protein comprises an antibody or a portion thereof, which may be humanized.
  • the double mutant of dihydrofolate reductase comprises amino acid mutations of L22F and F31S.
  • a method of generating engineered multiplexed T- cells for adoptive T-cell immunotherapy comprises providing a gene delivery polynucleotide as described herein, introducing the gene delivery polynucleotide into a T-cell, providing a vector encoding a Sleeping Beauty transposase, introducing the vector encoding the Sleeping Beauty transposase into the T-cell, selecting the cells comprising the gene delivery polynucleotide wherein selecting comprises a first round of selection and a second round of selection, wherein the first round of selection comprises adding a selection reagent at a first concentration range and the second round of selection comprises adding the selection reagent at a second concentration range, wherein the second concentration range is higher than the first concentration range and, wherein the second concentration range is at least 1.5 fold higher than that of the first concentration range and isolating the T-cells expressing a phenotype under selective pressure.
  • the gene delivery polynucleotide comprises a first sequence, wherein the first sequence comprises a first inverted terminal repeat gene sequence, a second sequence, wherein the second sequence comprises a second inverted terminal repeat gene sequence, a third sequence, wherein the third sequence comprises a promoter region sequence, a fourth sequence, wherein the fourth sequence comprises at least one gene encoding a protein, and wherein the fourth sequence is optimized, a fifth sequence, wherein the fifth sequence comprises at least one selectable marker cassette encoding a double mutant of dihydrofolate reductase, wherein the double mutant of dihydrofolate reductase has a 15,000 fold or about 15,000 fold reduced affinity for methotrexate, wherein the methotrexate can be used as a selection mechanism to selectively amplify cells transduced with the gene delivery polynucleotide and wherein the fifth sequence is optimized, a sixth sequence, wherein the sixth sequence comprises a first attachment site (attP) and a seventh sequence, wherein
  • the double mutant of human dihydrofolate reductase comprises the protein sequence: MVGSLNCIVA VSQNMGIGKN GDFPWPPLRN ESRYFQRMTT TSSVEGKQNL VIMGK TWFS IPEKNRPLKG RINLVLSREL KEPPQGAHFL SRSLDDALKL TEQPELANKV DMVWIVGGSS VYKEAMNHPG HLKLFVTRIM QDFESDTFFP EIDLEKYKLL PEYPGVLSDV QEEKGIKYKF EVYEK D (SEQ ID NO: 3).
  • the gene delivery polynucleotide is circular.
  • the gene delivery polynucleotide is at least lkB to 5kB. In some alternatives, the gene delivery polynucleotide is a minicircle. In some alternatives, the promoter region comprises an EF1 promoter sequence. In some alternatives, the fourth sequence comprises one, two, three, four, or five genes that encode proteins. In some alternatives, the fourth sequence is codon optimized to reduce the total GC/AT ratio of the fourth sequence. In some alternatives, the fourth sequence is optimized by codon optimization for expression in humans. In some alternatives, the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins.
  • the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins, such as a plurality of antibody binding domains, which are specific for the same epitope.
  • the plurality of related proteins comprise a plurality of antibody binding domains, wherein the plurality of antibody binding domains are specific for the same epitope.
  • the fifth sequence is codon optimized to reduce the total GC/AT ratio of the fifth sequence.
  • the fifth sequence is optimized by codon optimization for expression in humans.
  • the protein is a protein for therapy.
  • the codon optimization and/or consensus sequence is generated by comparing the variability of sequence and/or nucleobases utilized in a plurality of related sequences.
  • the protein comprises an antibody or a portion thereof, which may be humanized.
  • the double mutant of dihydrofolate reductase comprises amino acid mutations of L22F and F31S.
  • the introducing is performed by electroporation.
  • the selecting is performed by increasing selective pressure through the selective marker cassette.
  • the selection reagent comprises an agent for selection.
  • the agent for selection is methotrexate.
  • the first concentration range is at least 50nM - lOOnM and the second concentration range is at least 75 to 150nM.
  • the first concentration is 50 nM, 60 nM, 70 nM, 80 nM, 90 nM, or lOOnM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 75 nM, 80 nM, 90 nM, 100 nM, 110 nM, 120 nM, 130 nM, 140 nM, or 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 75 nM - 150 nM and the second concentration range is at least 112.5 nM to 225 nM.
  • the first concentration is 75 nM, 85 nM, 95 nM, 105 nM, 115 nM, 125 nM, 135 nM, 145 nM, or 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 112 nM, 122 nM, 132 nM, 142 nM, 152 nM, 162 nM, 172 nM, 182 nM, 192 nM, 202 nM, 212 nM, or 225 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 300 nM - 675 nM and the first concentration range is at least 450 nM to 1012 nM.
  • the first concentration is 300 nM, 350 nM, 400 nM, 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, or 675 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, 700 nM, 750 nM, 800 nM, 850 nM, 900 nM, 1000 nM, or 1012 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first round of selection comprises exposing the T-cells to the selection agent for 2, 3, 4, 5, 6 or 7 days before the second round of selection.
  • the second round of selection comprises exposing the T- cells to the selection agent for at least 2, 3, 4, 5, 6,7, 8, 9, 10, 11, 12, 13, or 14 days or any time that is between a range of times defined by any two of the aforementioned time points before isolation.
  • a method of increasing protein production in a T-cell comprises providing a polynucleotide described herein, introducing the polynucleotide into a cell, providing a vector encoding a Sleeping Beauty transposase, introducing the vector encoding the Sleeping Beauty transposase into the T-cell, selecting the cells comprising the gene delivery polynucleotide wherein selecting comprises a first round of selection and a second round of selection, wherein the first round of selection comprises adding a selection reagent at a first concentration range and the second round of selection comprises adding the selection reagent at a second concentration range, wherein the second concentration range is higher than the first concentration range and, wherein the second concentration range is at least 1.5 fold higher than that of the first concentration range and isolating the cells expressing a phenotype under selective pressure.
  • the introducing is performed by electroporation. In some alternatives, the selecting is performed by increasing selective pressure through the selective marker cassette. In some alternatives, the selection reagent comprises an agent for selection. In some alternatives, the agent for selection is methotrexate. In some alternatives, the first concentration range is at least 50nM - lOOnM and the second concentration range is at least 75 to 150nM.
  • the first concentration is 50 nM, 60 nM, 70 nM, 80 nM, 90 nM, or lOOnM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 75 nM, 80 nM, 90 nM, 100 nM, 110 nM, 120 nM, 130 nM, 140 nM, or 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 75 nM - 150 nM and the second concentration range is at least 112.5 nM to 225 nM.
  • the first concentration is 75 nM, 85 nM, 95 nM, 105 nM, 115 nM, 125 nM, 135 nM, 145 nM, or 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 112 nM, 122 nM, 132 nM, 142 nM, 152 nM, 162 nM, 172 nM, 182 nM, 192 nM, 202 nM, 212 nM, or 225 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 300 nM - 675 nM and the first concentration range is at least 450 nM to 1012 nM.
  • the first concentration is 300 nM, 350 nM, 400 nM, 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, or 675 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, 700 nM, 750 nM, 800 nM, 850 nM, 900 nM, 1000 nM, or 1012 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first round of selection comprises exposing the T-cells to the selection agent for 2, 3, 4, 5, 6 or 7 days before the second round of selection.
  • the second round of selection comprises exposing the T-cells to the selection agent for at least 2, 3, 4, 5, 6,7, 8, 9, 10, 11, 12, 13, or 14 days or any time that is between a range of times defined by any two of the aforementioned time points before isolation.
  • the gene delivery polynucleotide comprises a first sequence, wherein the first sequence comprises a first inverted terminal repeat gene sequence, a second sequence, wherein the second sequence comprises a second inverted terminal repeat gene sequence, a third sequence, wherein the third sequence comprises a promoter region sequence, a fourth sequence, wherein the fourth sequence comprises at least one gene encoding a protein, and wherein the fourth sequence is optimized, a fifth sequence, wherein the fifth sequence comprises at least one selectable marker cassette encoding a double mutant of dihydrofolate reductase, wherein the double mutant of dihydrofolate reductase has a 15,000 fold or about 15,000 fold reduced affinity for methotrexate, wherein the methotrexate can be used as a selection mechanism to selectively amplify cells transduced with the gene delivery polynucleotide and wherein the fifth sequence is optimized, a sixth sequence, wherein the sixth sequence comprises a first attachment site (attP) and a seventh
  • the gene encoding the double mutant of human dihydrofolate reductase comprises the DNA sequence: ATGGTTGGTTCGCTAAACTGCATCGTCGCTGTGTCCCAGAACATGGGCATCGGCA AGAACGGGGACTTCCCCTGGCCACCGCTCAGGAATGAATCCAGATATTTCCAGA GAATGACCACAACCTCTTCAGTAGAAGGTAAACAGAATCTGGTGATTATGGGTA AGAAGACCTGGTTCTCCATTCCTGAGAAGAATCGACCTTTAAAGGGTAGAATTA ATTTAGTTCTCAGCAGAGAACTCAAGGAACCTCCACAAGGAGCTCATTTTCTTTC CAGAAGTCTAGATGATGCCTTAAAACTTACTGAACAACCAGAATTAGCAAATAA AGTAGACATGGTCTGGATAGTTGGTGGCAGTTCTGTTTATAAGGAAGCCATGAAT CACCCAGGCCATCTTAAACTATTTGTGACAAGGATCATGCAAGACTTTGAAAGTG ACACGTTTTCCAGAAATTGATTTG
  • the double mutant of human dihydro folate reductase comprises the protein sequence: MVGSLNCIVA VSQNMGIGKN GDFPWPPLRN ESRYFQRMTT TSSVEGKQNL VIMGK TWFS IPEKNRPLKG RINLVLSREL KEPPQGAHFL SRSLDDALKL TEQPELANKV DMVWIVGGSS VYKEAMNHPG HLKLFVTRIM QDFESDTFFP EIDLEKYKLL PEYPGVLSDV QEEKGIKYKF EVYEKND (SEQ ID NO: 3).
  • the gene delivery polynucleotide is circular.
  • the gene delivery polynucleotide is at least lkB to 5kB. In some alternatives, the gene delivery polynucleotide is a minicircle. In some alternatives, the gene delivery polynucleotide is a minicircle. In some alternatives, the promoter region comprises an EFl promoter sequence. In some alternatives, the fourth sequence comprises one, two, three, four, or five genes that encode proteins. In some alternatives, the fourth sequence is codon optimized to reduce the total GC/AT ratio of the fourth sequence. In some alternatives, the fourth sequence is optimized by codon optimization for expression in humans. In some alternatives, the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins.
  • the fourth sequence is a consensus sequence generated from a plurality of nucleic acids that encode a plurality of related proteins, such as a plurality of antibody binding domains, which are specific for the same epitope.
  • the plurality of related proteins comprise a plurality of antibody binding domains, wherein the plurality of antibody binding domains are specific for the same epitope.
  • the fifth sequence is codon optimized to reduce the total GC/AT ratio of the fifth sequence.
  • the fifth sequence is optimized by codon optimization for expression in humans.
  • the codon optimization and/or consensus sequence is generated by comparing the variability of sequence and/or nucleobases utilized in a plurality of related sequences.
  • the protein comprises an antibody or a portion thereof, which may be humanized.
  • the double mutant of dihydro folate reductase comprises amino acid mutations of L22F and F31S.
  • the introducing is performed by electroporation.
  • the selecting is performed by increasing selective pressure through the selective marker cassette.
  • the selection reagent comprises an agent for selection.
  • the agent for selection is methotrexate.
  • the first concentration range is at least 50nM - lOOnM and the second concentration range is at least 75 to 150nM.
  • the first concentration is 50 nM, 60 nM, 70 nM, 80 nM, 90 nM, or lOOnM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 75 nM, 80 nM, 90 nM, 100 nM, 110 nM, 120 nM, 130 nM, 140 nM, or 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 75 nM - 150 nM and the second concentration range is at least 112.5 nM to 225 nM.
  • the first concentration is 75 nM, 85 nM, 95 nM, 105 nM, 115 nM, 125 nM, 135 nM, 145 nM, or 150 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 112 nM, 122 nM, 132 nM, 142 nM, 152 nM, 162 nM, 172 nM, 182 nM, 192 nM, 202 nM, 212 nM, or 225 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first concentration range is at least 300 nM - 675 nM and the first concentration range is at least 450 nM to 1012 nM.
  • the first concentration is 300 nM, 350 nM, 400 nM, 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, or 675 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations
  • the second concentration range is 450 nM, 500 nM, 550 nM, 600 nM, 650 nM, 700 nM, 750 nM, 800 nM, 850 nM, 900 nM, 1000 nM, or 1012 nM or any concentration that is between a range of concentrations defined by any two of the aforementioned concentrations.
  • the first round of selection comprises exposing the T-cells to the selection agent for 2, 3, 4, 5, 6 or 7 days before the second round of selection.
  • the second round of selection comprises exposing the T-cells to the selection agent for at least 2, 3, 4, 5, 6,7, 8, 9, 10, 11, 12, 13, or 14 days or any time that is between a range of times defined by any two of the aforementioned time points before isolation.
  • a method of treating, inhibiting, or ameliorating cancer or a disease in a subject comprising administering to the subject a modified T-cell as described herein.
  • the subject is human.

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MX2016013149A MX2016013149A (es) 2014-04-10 2015-04-08 Produccion de celulas t modificadas, mediante transposon bella durmiente, acoplada con seleccion por metotrexato.
JP2017504604A JP6788573B6 (ja) 2014-04-10 2015-04-08 メトトレキサートによる選択と組み合わせたＳｌｅｅｐｉｎｇ Ｂｅａｕｔｙトランスポゾンによる遺伝子改変Ｔ細胞の製造
RU2016143389A RU2016143389A (ru) 2014-04-10 2015-04-08 Получение генно-инженерных т-клеток посредством транспозона "спящая красавица" в сочетании с отбором метотрексатом
EP15776501.7A EP3129480A4 (en) 2014-04-10 2015-04-08 Production of engineered t-cells by sleeping beauty transposon coupled with methotrexate selection
CN201580030815.7A CN106661570B (zh) 2014-04-10 2015-04-08 通过与氨甲蝶呤选择偶联的睡美人转座子制备工程化t细胞
CA2945303A CA2945303C (en) 2014-04-10 2015-04-08 Production of engineered t-cells by sleeping beauty transposon coupled with methotrexate selection
US15/302,449 US20170029774A1 (en) 2014-04-10 2015-04-08 Production of engineered t-cells by sleeping beauty transposon coupled with methotrexate selection
KR1020167031069A KR20160144431A (ko) 2014-04-10 2015-04-08 메토트렉세이트 선택과 연결된 슬리핑 뷰티 트랜스포존에 의한 조작된 t-세포의 생산
AU2015243922A AU2015243922B2 (en) 2014-04-10 2015-04-08 Production of engineered T-cells by sleeping beauty transposon coupled with methotrexate selection
BR112016023517A BR112016023517A2 (pt) 2014-04-10 2015-04-08 produção de células t projetadas por transpóson sleeping beauty acoplado com seleção de metotrexato
NZ725081A NZ725081A (en) 2014-04-10 2015-04-08 Production of engineered t-cells by sleeping beauty transposon coupled with methotrexate selection
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US201462088363P 2014-12-05 2014-12-05
US62/088,363 2014-12-05
US201462089730P 2014-12-09 2014-12-09
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PCT/US2015/024947 Ceased WO2015157432A1 (en) 2014-04-10 2015-04-08 Drug related transgene expression
PCT/US2015/024895 Ceased WO2015157399A1 (en) 2014-04-10 2015-04-08 Transgene genetic tags and methods of use
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