IP Library › Granted Patent US 12,742,171
Granted Patent B2
US 12,742,171 · App. 17/832,409 · Granted Sep 22, 2026

Integration of nucleic acid constructs into eukaryotic cells with a transposase from oryzias

Inventors: Jeremy Minshull (Los Altos, CA); Sridhar Govindarajan (Los Altos, CA); Maggie Lee (San Jose, CA)
Assignee: DNA TWOPOINTO INC.
C12N15/67C12N15/1082C12N15/52C12N15/625C12N15/8509C12N2830/007C12N2830/42C12N2840/203
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Quick Facts
Patent No.
US 12,742,171
App. No.
17/832,409
Granted
Sep 22, 2026
Kind
B2
Abstract

The present invention provides polynucleotide vectors for high expression of heterologous genes. Some vectors further comprise novel transposons and transposases that further improve expression. Further disclosed are vectors that can be used in a gene transfer system for stably introducing nucleic acids into the DNA of a cell. The gene transfer systems can be used in methods, for example, gene expression, bioprocessing, gene therapy, insertional mutagenesis, or gene discovery.

Claims (15)

1 . A method of integrating a transposon into a eukaryotic cell, the method comprising (a) introducing into the cell a transposon comprising SEQ ID NO: 7 and SEQ ID NO: 8 as left and right ends respectively flanking a heterologous polynucleotide encoding a polypeptide; (b) introducing into the cell a transposase, the sequence of which is at least 90% identical to SEQ ID NO:782, wherein the transposase transposes the transposon to produce a genome comprising SEQ ID NO:7 and SEQ ID NO:8 flanking the heterologous polynucleotide at left and right ends respectively; and (c) expressing the polypeptide from the heterologous polynucleotide within the genome.

2 . The method of claim 1 , wherein the polypeptide is a chimeric antigen receptor.

3 . The method of claim 1 , wherein the polypeptide comprises a chain of an antibody.

4 . The method of claim 1 , further comprising purifying the polypeptide.

5 . The method of claim 1 , further comprising incorporating the purified polypeptide into a pharmaceutical composition.

6 . The method of claim 1 , wherein the cell is a mammalian cell.

7 . The method of claim 1 , wherein the cell is a human cell.

8 . The method of claim 1 , wherein the cell is a rodent cell.

9 . The method of claim 1 , wherein the transposase is introduced as a polynucleotide encoding the transposase.

10 . The method of claim 9 , wherein the polynucleotide is an mRNA.

11 . The method of claim 1 , wherein the transposase is introduced as a protein.

12 . The method of claim 1 , wherein the transposase has a sequence which comprises any of SEQ ID NOS:782 or 805-908.

13 . The method of claim 1 , wherein the transposon further comprises a sequence at least 90% identical to SEQ ID NO:12 immediately adjacent to the left transposon end and between the left transposon end and the heterologous polynucleotide and a sequence at least 90% identical to SEQ ID NO:15 immediately adjacent to the right transposon end and between the right transposon end and the heterologous polynucleotide.

14 . The method of claim 1 , wherein the heterologous polynucleotide encodes two open reading frames, each operably linked to a separate promoter, one encoding the polypeptide, and the other a second polypeptide.

15 . The method of claim 14 , wherein the open reading frames encode heavy and light chains of an antibody.

Assignments (1)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Jun 9, 2022
From: MINSHULL, JEREMY; GOVINDARAJAN, SRIDHAR; LEE, MAGGIE
To: DNA TWOPOINTO INC.
Reel/Frame 060149/0994 →
Continuity (6)
Continuation 17339617 · Jun 4, 2021
Continuation 16842719 · Apr 7, 2020
Provisional Application 62982186 · Feb 27, 2020
Provisional Application 62873338 · Jul 12, 2019
Provisional Application 62831092 · Apr 8, 2019
Related Publication 20230103199A1 · Mar 30, 2023
References Cited (111)
US 7932088B1 · Adams et al. · 2011 [cited by applicant]
US 9670503B2 · Craig · 2017 [cited by applicant]
US 11060086B2 · Minshull et al. · 2021 [cited by applicant]
US 11060098B2 · Minshull et al. · 2021 [cited by applicant]
US 11060109B2 · Minshull et al. · 2021 [cited by applicant]
US 11401521B2 · Govindarajan et al. · 2022 [cited by applicant]
US 20080263730A1 · Anderson · 2008 [cited by applicant]
US 20100129914A1 · Koga et al. · 2010 [cited by applicant]
US 20110045532A1 · Kawakami et al. · 2011 [cited by applicant]
US 20120027847A1 · Kusk · 2012 [cited by applicant]
US 20170101629A1 · Minshull et al. · 2017 [cited by applicant]
US 20200318107A1 · Minshull et al. · 2020 [cited by applicant]
US 20200318121A1 · Minshull et al. · 2020 [cited by applicant]
US 20200318135A1 · Minshull et al. · 2020 [cited by applicant]
US 20210292719A1 · Minshull et al. · 2021 [cited by applicant]
US 20210292773A1 · Minshull et al. · 2021 [cited by applicant]
US 20210324408A1 · Minshull et al. · 2021 [cited by applicant]
WO WO2010143698A1 · 2010 [cited by applicant]
WO WO2013155572A1 · 2013 [cited by applicant]
WO WO2017062668A2 · 2017 [cited by applicant]
WO WO2020210236A1 · 2020 [cited by applicant]
WO WO2020210237A1 · 2020 [cited by applicant]
WO WO2020210239A1 · 2020 [cited by applicant]
Ley et al., “MAR Elements and Transposons for Improved Transgene Integration and Expression” 8(4) PLOS ONE e62784, 1-11 (Year: 2013). [cited by examiner]
Morita et al., “Enhanced Expression of Anti-CD19 Chimeric Antigen Receptor in piggyBac Transposon-Engineered T Cells” 8 Molecular Therapy: Methods & Clinical Development 131-140 (Year: 2018). [cited by examiner]
Databse RefSeq XP 013190765, online, NCBI, “Predicted: piggyBac transposable element-derived protein 4-like {Amyelois transittela},” Aug. 6, 2015. [cited by applicant]
Fritz et al., “Contemporary evolution of a Lepidopteran species, [cited by applicant]
Guilliam, et al., “Molecular basis for PrimPol recruitment to repliation forks by RPA,” Nature Communications, vol. 8, No. 551, pp. 1014, (2017). [cited by applicant]
Johnson et al., “A non-autonomous insect piggyBac transposable element is mobile in tobacco,” Mol Genet Genomics, 289: 895-902, (2014). [cited by applicant]
Kasahara, et al., “The medaka draft genome and instights into vertebrate genome evolution,” Nature, vol. 447, pp. 714-719, (2007). [cited by applicant]
Kawakami, et al., “Identificatio of a functional transposase of the Tol2 element, an Ac-llike element from the Japanese medaka fish, and its transposition in the zebrafish germ lineage,” PNAS, vol. 97, No. 21, pp. 11403… [cited by applicant]
Skipper et al., “DNA transposon-based gene vehicles—scenes from an evolutionary drive,” Journal of Biomedical Science, 20:92, (2013). [cited by applicant]
Yusa, piggyBac Transposon, Microbiology Spectrum, 3: 1-16, (2014). [cited by applicant]
EP 20787187.0 Extended European Search Report mailed Dec. 13, 2022. [cited by applicant]
EP 20788191.5 Extended European Search Report mailed Dec. 9, 2022. [cited by applicant]
EP20788172.3 Extended European Search Report mailed Dec. 22, 2022. [cited by applicant]
MY P12021003499 Search Report mailed May 13, 2024. [cited by applicant]
MY P12021003506 Search Report mailed Apr. 30, 2024. [cited by applicant]
U.S. Appl. No. 17/339,607, Advisory Action mailed Nov. 20, 2024. [cited by applicant]
U.S. Appl. No. 17/339,607, Final Office Action mailed Sep. 20, 2024. [cited by applicant]
U.S. Appl. No. 17/339,607, Non-Final Office Action mailed Apr. 22, 2024. [cited by applicant]
U.S. Appl. No. 17/339,607, Non-Final Office Action mailed Nov. 22, 2023. [cited by applicant]
U.S. Appl. No. 17/339,607, Requirement for Restriction/Election mailed Jun. 6, 2023. [cited by applicant]
Belancio et al., “Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health,” Genome Research, 18;343-358, (2008). [cited by applicant]
Bonizzoni et al., “Highly similar piggyBactransposase-like sequences from various [cited by applicant]
Bouallegue, et al., “Molecular Evolution of piggyBac Superfamily: From Selfishness to Domestication,” Genome Biol. Evol. 9(2):323-339, (Jan. 12, 2017). [cited by applicant]
Daimon et al., “Recent transposition of yabusame, a novel piggyBac-like transposable element in the genome of the silkworm, [cited by applicant]
Deininger et al., Alu Repeats and Human Disease, Molecular Genetics and Metabolism, 67, 183-193, (1999). [cited by applicant]
Doherty et al., “Hyperactive piggyBac Gene Transfer in Human Cells and In Vivo,” Human Gene Therapy, 23:311-320, (2012). [cited by applicant]
Genbank Accession No. NW_0133535463.1, Anyelois transitella strain UIUC subculture of SPIRL-1966 unplaced genomic scaffold, ASM118610v1 Atra_scaffold_0159, whole genome shotgun sequence, 1 page, (Aug. 2015). [cited by applicant]
Genbank Accession No. XM_133335311, Predicted: Amyelois transitella piggyBac transposable element-derived protein 4-like (LOC106135111), mRNA, 2 pages, (Aug. 2015). [cited by applicant]
GenBank: : Accession No. ABD76335.1, “transposase [Heliothis virescens],” Direct Submission on Feb. 19, 2006, Entomology, Kansas State Univ, retrieved @: www.ncbi.nlm.nih.gov/protein/abd76335.1. [cited by applicant]
GenBank: : Accession No. PCG77621.1, “hypothetical protein B5V51_6758 [Heliothis virescens],” Direct Submission on Sep. 2, 2017, Department of Entomology, Univ. of Maryland; Retrieved on Dec. 8, 2020 @: www.ncbi.nlm.nih… [cited by applicant]
GenBank: BAF64515.1, Transposase [ [cited by applicant]
Handler et al., “The piggyBac transposon mediates germ-line transformation in the Oriental fruit fly and closely related elements exist in its genome,” Insect Molecular Biology, 9(6):605-612, (2000). [cited by applicant]
Hikosaka et al., “Evolution of the Xenopus piggyBac Transposon Family TxpB: Domesticated and Untamed Strategies of Transposon Subfamilies,” Mol. Biol. Evol., 24(12):2648-2656, (2007). [Retrieved from the Internet Apr. 1… [cited by applicant]
Le Rouzic et al., “Reversible introduction of transgene in natural populations of insects,” Insect Molecular Biology, 15(2), 227-234, (2006). [cited by applicant]
Li, et al., “piggyBac internal sequences are necessary for efficient transformation of target genomes,” Insect Molecular Biology, 14(1), pp. 17-30, (2005). [cited by applicant]
Luo et al., “A new active piggyBac-like element in Aphis gossypii,” Insect Science, 18:652-662, (2011). [cited by applicant]
Luo et al., “Molecular characterization of the piggyBac-like element, a candidate marker for phylogenetic research of Chilo suppressalis (Walker) in China,” BMC Molecular Biology, 15:28, 12 pages, (2014). [cited by applicant]
Mitra, et al., “Functional characterization of piggyBat from the bat [cited by applicant]
Muñoz-López et al., “DNA Transposons: Nature and Applications in Genomics,” Current Genomics, 11:115-128, (2010). [cited by applicant]
NCBI Reference Sequence: XP_023815209.1, piggyBac transposable element-dirived protein 4-like [Oryzias latipes], BioProject: PRJNA193868, Feb. 15, 2018, retrieved @: www.ncbi.nlm.nih.gov/protein/XP_023815209.1. [cited by applicant]
NCBI Reference Sequence: XP_030017403.1, piggyBac transposable element-dirived protein 4-like [Sphaeramia orbicularis], BioProject: PRJNA556027, Aug. 2, 2019, retrieved @: www.ncbi.nlm.nih.gov/protein/XP_030017403.1. [cited by applicant]
NCBI References Sequence: XP_026724774.1, piggyBac transposable element-dirived protein 4-like [Trichoplusia ni], BioProject: PRJNA497582, Oct. 25, 2018, retrieved @: www.ncbi.nlm.nih.gov/protein/XP_026724774.1. [cited by applicant]
Sarkar et al., “Molecular evolutionary analysis of widespread piggyBac transposon family and related ‘domesticated’ sequences,” Mol Gen Genomics, 270(2):173-180, (2003). [cited by applicant]
Sequence Alignment of SDQ ID No. 108 from U.S. Patent Application 2020-0318121; Seq ID 15 Sequence Search Conducted on Dec. 26, 2020, 1 page. [cited by applicant]
Sequence Alignment of SDQ ID No. 108 from U.S. Patent Application 2020-0318121; Seq ID 16, Sequence Search Conducted on Dec. 26, 2020, 1 page. [cited by applicant]
Sequence Alignment of SDQ ID No. 256 from U.S. Patent Application 2020-0318135; Seq ID 15, Sequence Search Conducted on Dec. 26, 2020, 1 page. [cited by applicant]
Sequence Alignment of SDQ ID No. 256 from U.S. Patent Application 2020-0318135; Sequence Search Conducted on Dec. 26, 2020, 1 page. [cited by applicant]
Sequence Alignment of SEQ ID No. 781 with CP020674s3, Sequence search conducted Sep. 28, 2021, 6 pages, (2021). [cited by applicant]
Sequence Alignment of SEQ ID No. 782 with A0A3Q2ZEU4 Kryma, search conducted Dec, 14, 2021; submitted to UniProtKB on (Jan. 2019). [cited by applicant]
Sequence Alignment of SEQ ID No. 7 with SEQ ID No. 55960 of U.S. Patent Application 2008/0263730; Sequence Search Conducted on Sep. 18, 2020, 1 page. [cited by applicant]
Sequence Alignment of SEQ ID No. 8 with SEQ ID No. 55960 of U.S. Patent Application 2008/0263730; Sequence Search Conducted on Sep. 18, 2020, 1 page. [cited by applicant]
UnitProt Submission A0A2A4JOM2_Helvi, Uncharacterized protein from [cited by applicant]
UnitProt Submission A0A2A4K028_HELVI, [cited by applicant]
UnitProt Submission A0A3B3INT3_ORYLA [cited by applicant]
Wang et al., “Large diversity of the piggyBac-like elements in the genome of Tribolium castaneum,” Insect Biochem Mol Biol, 38(4):490-498, doi: 10.1016/j.ibmb.2007.04.012, (2008). [cited by applicant]
Wang et al., “piggyBac -like elements in the tobacco budworm, [cited by applicant]
Wu et al., “An active piggyBac-like element in Macdunnoughia crassisigna,” Insect Science, 15:521-528, (2008). [cited by applicant]
WU et.al., “Cloning and characterization of piggyBac-like elements in lepidopteran insects,” Genetica, 139:149-154, (Jan. 6, 2011). [cited by applicant]
Xu et al., “Identification and characterization of piggyBac-like elements in the genome of domesticated silkworm, [cited by applicant]
Zimowska et al., “Highly conserved piggyBac elements in noctuid species of [cited by applicant]
NCBI References Sequence: XP 013190765.1, Predicted: piggyBac transposable element-derived protein 4-like [Amyelois transitella], BioProject: PRJNA292025, Aug. 6, 2015, retrieved @: www.ncbi.nlm.nih.gov/protein/XP_01319… [cited by applicant]
NCBI References Sequence: XP 013197997.1; Predicted: piggyBac transposable element-derived protein 4-like [Amyelois transitella], BioProject: PRJNA292025, Aug. 6, 2015, retrieved @: www.ncbi.nlm.nih.gov/protein/XP_03139… [cited by applicant]
U.S. Appl. No. 16/842,707, Non-Final Office Action mailed Dec. 31, 2020. [cited by applicant]
U.S. Appl. No. 16/842,707, Notice of Allowance mailed Mar. 22, 2021. [cited by applicant]
U.S. Appl. No. 16/842,707, Requirement for Restriction/Election mailed Oct. 9, 2020. [cited by applicant]
U.S. Appl. No. 16/842,709, Non-Final Office Action mailed Jan. 6, 2021. [cited by applicant]
U.S. Appl. No. 16/842,709, Notice of Allowance mailed Apr. 13, 2021. [cited by applicant]
U.S. Appl. No. 16/842,709, Requirement for Restriction/Election mailed Sep. 28, 2020. [cited by applicant]
U.S. Appl. No. 16/842,719, Non-Final Office Action mailed Dec. 22, 2020. [cited by applicant]
U.S. Appl. No. 16/842,719, Notice of Allowance mailed Apr. 6, 2021. [cited by applicant]
U.S. Appl. No. 17/339,597, Non-Final Office Action mailed Dec. 21, 2021. [cited by applicant]
U.S. Appl. No. 17/339,597, Notice of Allowance mailed Mar. 23, 2022. [cited by applicant]
U.S. Appl. No. 17/339,597, Requirement for Restriction/Election mailed Oct. 1, 2021. [cited by applicant]
U.S. Appl. No. 17/339,617, Non-Final Office Action mailed Jan. 5, 2022. [cited by applicant]
U.S. Appl. No. 17/339,617, Notice of Allowance mailed Mar. 2, 2022. [cited by applicant]
U.S. Appl. No. 17/339,617, Requirement for Restriction/Election mailed Oct. 7, 2021. [cited by applicant]
U.S. Appl. No. 16/842,719, Requirement for Restriction/Election mailed Jul. 17, 2020. [cited by applicant]
WIPO Application No. PCT/US2020/027077, Invitation To Pay Additional Fees mailed Jul. 9, 2020. [cited by applicant]
WIPO Application No. PCT/US2020/027077, PCT International Preliminary Report on Patentability mailed Sep. 28, 2021. [cited by applicant]
WIPO Application No. PCT/US2020/027077, PCT International Search Report and Written Opinion of the International Searching Authority mailed Sep. 4, 2020. [cited by applicant]
WIPO Application No. PCT/US2020/027078, Invitation To Pay Additional Fees mailed Jul. 9, 2020. [cited by applicant]
WIPO Application No. PCT/US2020/027078, PCT International Preliminary Report on Patentability mailed Sep. 28, 2021. [cited by applicant]
WIPO Application No. PCT/US2020/027078, PCT International Search Report and Written Opinion of the International Searching Authority mailed Sep. 4, 2020. [cited by applicant]
WIPO Application No. PCT/US2020/027080, Invitation To Pay Additional Fees mailed Jul. 14, 2020. [cited by applicant]
WIPO Application No. PCT/US2020/027080, PCT International Preliminary Report on Patentability mailed Sep. 28, 2021. [cited by applicant]
WIPO Application No. PCT/US2020/027080, PCT International Search Report and Written Opinion of the International Searching Authority mailed Sep. 4, 2020. [cited by applicant]
U.S. Appl. No. 17/339,617, filed Jun. 4, 2021, U.S. Pat. No. 11,401,521, Issued. [cited by applicant]
U.S. Appl. No. 16/842,719, filed Apr. 7, 2020, U.S. Pat. No. 11,060,098, Issued. [cited by applicant]