Granted Patent
B2
US 12,297,465 · App. 17/150,533 · Granted May 13, 2025
CBLB endonuclease variants, compositions, and methods of use
Inventors:
Jordan Jarjour (Seattle, WA); Kyle Havens (Seattle, WA); Anne-Rachel Krostag (Lake Forest Park, WA)
Assignee:
REGENERON PHARMACEUTICALS, INC.
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Abstract
The present disclosure provides improved genome editing compositions and methods for editing a CBLB gene. The disclosure further provides genome edited cells for the prevention, treatment, or amelioration of at least one symptom of, a cancer, an infectious disease, an autoimmune disease, an inflammatory disease, or an immunodeficiency.
Claims (7)
1. A polynucleotide encoding a fusion polypeptide comprising the amino acid sequence set forth in SEQ ID NO: 13, wherein the polypeptide binds to and cleaves a target site in a human Cbl lymphoma proto-oncogene B (CBLB) gene set forth in SEQ ID NO: 22.
2. The polynucleotide of claim 1 , wherein the polynucleotide is a cDNA.
3. The polynucleotide of claim 1 wherein the polynucleotide is an mRNA.
4. The polynucleotide of claim 1 , wherein the polynucleotide comprises the sequence set forth in SEQ ID NO: 31.
5. A polynucleotide encoding a fusion polypeptide comprising an amino acid sequence selected from the amino acid sequence set forth in SEQ ID NO: 14, SEQ ID NO:15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, and SEQ ID NO:19, wherein the polypeptide binds to and cleaves a target site in a human Cbl lymphoma proto-oncogene B (CBLB) gene set forth in SEQ ID NO: 22.
6. The polynucleotide of claim 5 , wherein the polynucleotide is a cDNA.
7. The polynucleotide of claim 5 , wherein the polynucleotide is an mRNA.
Assignments (3)
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Jun 26, 2024
From: 2SEVENTY BIO, INC.
To: REGENERON PHARMACEUTICALS, INC.
Reel/Frame 067839/0242 →
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Sep 14, 2021
From: BLUEBIRD BIO, INC.
To: 2SEVENTY BIO, INC.
Reel/Frame 057683/0099 →
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Mar 31, 2021
From: JARJOUR, JORDAN; HAVENS, KYLE; KROSTAG, ANNE-RACHEL
To: BLUEBIRD BIO, INC.
Reel/Frame 055777/0551 →
Continuity (2)
Continuation
PCTUS2018054347
· Oct 4, 2018
References Cited (150)
US 4751180A
· Cousens et al.
· 1988
[cited by applicant]
US 4873192A
· Kunkel
· 1989
[cited by applicant]
US 4935233A
· Bell et al.
· 1990
[cited by applicant]
US 5804413A
· DeLuca
· 1998
[cited by applicant]
US 5837532A
· Preston et al.
· 1998
[cited by applicant]
US 5846782A
· Wickham et al.
· 1998
[cited by applicant]
US 5994136A
· Naldini et al.
· 1999
[cited by applicant]
US 6013516A
· Verma et al.
· 2000
[cited by applicant]
US 6682907B1
· Charneau et al.
· 2004
[cited by applicant]
US 6692736B2
· Yu et al.
· 2004
[cited by applicant]
US 8614092B2
· Zhang et al.
· 2013
[cited by applicant]
US 8784799B2
· Samulski et al.
· 2014
[cited by applicant]
US 8809058B2
· Ferrari et al.
· 2014
[cited by applicant]
US 8889641B2
· Asokan et al.
· 2014
[cited by applicant]
US 9012224B2
· Bowles et al.
· 2015
[cited by applicant]
US 9017967B2
· Bonas et al.
· 2015
[cited by applicant]
US 9169492B2
· Monahan et al.
· 2015
[cited by applicant]
US 9169494B2
· Hewitt et al.
· 2015
[cited by applicant]
US 20110294217A1
· McConnell-Smith et al.
· 2011
[cited by applicant]
US 20120159659A1
· Arnould et al.
· 2012
[cited by applicant]
US 20130337454A1
· Duchateau et al.
· 2013
[cited by applicant]
US 20140148361A1
· Stoddard et al.
· 2014
[cited by applicant]
US 20170175128A1
· Welstead
· 2017
[cited by examiner]
US 20180171298A1
· Duchateau et al.
· 2018
[cited by applicant]
WO WO9102788
· 1991
[cited by applicant]
WO WO9604394
· 1996
[cited by applicant]
WO WO9815637
· 1998
[cited by applicant]
WO WO9906583
· 1999
[cited by applicant]
WO WO2006010834
· 2006
[cited by applicant]
WO WO2011064750
· 2011
[cited by applicant]
WO WO2011156430
· 2011
[cited by applicant]
WO 2012118717A2
· 2012
[cited by applicant]
WO 2014191527A1
· 2014
[cited by applicant]
WO WO2014191525
· 2014
[cited by applicant]
WO WO2017001572
· 2017
[cited by applicant]
WO 2018022619A1
· 2018
[cited by applicant]
WO 2018035141A1
· 2018
[cited by applicant]
WO 2018039333A1
· 2018
[cited by applicant]
WO WO2018049226A1
· 2018
[cited by examiner]
WO WO2018218194
· 2018
[cited by applicant]
Baxter et al., Engineering domain fusion chimeras from I-Onul family Laglidadg homing endonucleases, Nucleic Acids Res. 40, 2012, 7985-8000. (Year: 2012).
[cited by examiner]
Laforet et al., Modifying a covarying protein-DNA interaction changes substrate preference of a site-specific endonuclease, Nucleic Acids Res., 47, 2019, 10830-41. (Year: 2019).
[cited by examiner]
Ashworth et al., “Computational redesign of endonuclease DNA binding and cleavage specificity,” Nature, vol. 441, No. 7093, pp. 656-659 (2006).
[cited by applicant]
Bennardo et al., “Limiting the Persistence of a Chromosome Break Diminishes Its Mutagenic Potential,” PLoS Genetics, vol. 5, No. 10, e1000683, pp. 1-14 (2009).
[cited by applicant]
Brunner et al., “Cytotoxic T cells: Double-barreled shot guns,” Nature Medicine, vol. 5, No. 1, p. 20 (1999).
[cited by applicant]
Chevalier et al., “Design, Activity, and Structure of a Highly Specific Artificial Endonuclease,” Molecular Cell, vol. 10, pp. 895-905 (2002).
[cited by applicant]
Coico et al., “Immunogens and Antigens,” Immunology: A Short Course, Sixth Edition, pp. 29-39 (2009).
[cited by applicant]
Epinat et al., “A novel engineered meganuclease induces homologous recombination in yeast and mammalian cells,” Nucleic Acids Research, vol. 31, No. 11, pp. 2952-2962 (2003).
[cited by applicant]
Keskin et al., “A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications,” Protein Science, vol. 13, pp. 1043-1055 (2004).
[cited by applicant]
Pakula et al., “Genetic Analysis of Protein Stability and Function,” Annual Review of Genetics, vol. 23, pp. 289-310 (1989).
[cited by applicant]
Paques et al., “Meganucleases and DNA Double-Strand Break-Induced Recombination: Perspectives for Gene Therapy,” Current Gene Therapy, vol. 7, pp. 49-66 (2007).
[cited by applicant]
Roitt et al., “Immunology,” Mosby, Fifth Edition, pp. 107-119 (15 pages) (1998).
[cited by applicant]
Stoddard, B., “Homing Endonucleases: From Microbial Genetic Invaders to Reagents for Targeted DNA Modification,” Structure 19, pp. 7-15 (2011).
[cited by applicant]
Zhong et al., “Chimeric Antigen Receptors Combining 4-1BB and CD28 Signaling Domains Augment PI3kinase/AKT/Bcl-XL Activation and CD8+ T Cell-mediated Tumor Eradication,” Molecular Therapy, vol. 18, No. 2, pp. 413-420 (2…
[cited by applicant]
Balazs et al., “Liposomes for use in gene delivery,” Journal of Drug Delivery 2011, 1-12.
[cited by applicant]
Baxter et al., “Engineering domain fusion chimeras from I-Onul family LAGLIDADG homing endonucleases,” Nucleic Acids Research, 2012, vol. 40, No. 16, 7985-8000.
[cited by applicant]
Bird, Robert E., et al. “Single-chain antigen-binding proteins.” Science (1988); 242.4877: 423-427.
[cited by applicant]
Boissel et al., “megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering,” Nucleic Acids Research, 2013, 42(4):2591-2601.
[cited by applicant]
Brinkman et al., “Easy quantitative assessment of genome editing by sequence trace decomposition” Nucleic Acids Res. Dec. 16, 2014;42(22).
[cited by applicant]
Certo et al., “Tracking genome engineering outcome at individual DNA breakpoints,” Nat Methods. Jul. 10, 2011;8(8):671-6.
[cited by applicant]
Certo et al., “Coupling endonucleases with DNA end-processing enzymes to drive gene disruption” Nat Methods. Oct. 2012; 9(10): 973-975.
[cited by applicant]
Challita, P. et al., “Multiple modifications in cis elements of the long terminal repeat of retroviral vectors lead to increased expression and decreased DNA methylation in embryonic carcinoma cells.” J Virol. (1995); 6…
[cited by applicant]
Chaudhary, Vuay K., et al. “A rapid method of cloning functional variable-region antibody genes in
[cited by applicant]
Clever, J. et al., “RNA Secondary Structure and Binding Sites for gag Gene Products in the 5′ Packaging Signal of Human Immunodeficiency Virus Type 1.” J. of Virology (1995); 69(4):2101-2109.
[cited by applicant]
Cullen et al., “Regulatory Pathways Governing HIV-1 Replication”, Cell (1989); 58: 423-426.
[cited by applicant]
Cullen, B.R., “Human Immunodeficiency Virus as a Prototypic Complex Retrovirus”, Journal of Virology (1991); 65(3): 1053-1056.
[cited by applicant]
Dayhoff et al., (1978) Atlas of Protein Sequence and Structure (Natl. Biomed. Res. Found., Washington, D.C., 8 pages.
[cited by applicant]
De Felipe et al., “Targeting of proteins derived from self-processing polyproteins containing multiple signal sequences.” Traffic (2004); 5.8: 616-626.
[cited by applicant]
Desjarlais et al., “Use of a zinc-finger consensus sequence framework and specificity rules todesign specific DNA binding proteins.” Proceedings of the National Academy of Sciences (1993); 90.6: 2256-2260.
[cited by applicant]
Desjarlais et al., “Length-encoded multiplex binding site determination: application to zinc finger proteins,” Proceedings of the National Academy of Sciences (1994); 91.23: 11099-11103.
[cited by applicant]
Donnelly, M. et al., “The ‘cleavage’ activities of foot-and-mouth disease virus 2A site-directed mutants and naturally occurring ‘2A-like’ sequences.” J Gen Virol. (2001); 82 (Pt 5): 1027-1041.
[cited by applicant]
Duke et al., Sequence and structural elements that contribute to efficient encephalomyocarditis virus RNA translation, J Virol. Mar. 1992;66(3):1602-9.
[cited by applicant]
Dull et al., “A third-generation lentivirus vector with a conditional packaging system”, Journal of Virology (1998); 72(11): 8463-8671.
[cited by applicant]
Extended European Search Report mailed on Dec. 23, 2020, for European Application No. 18806825.8, 12 pages.
[cited by applicant]
Gomez-Foix et al., “Adenovirus-mediated Transfer of the Muscle Glycogen Phosphorylase Gene into Hepatocytes Confers Altered Regulation of Glycogen Metabolism,” J Biol Chem. Dec. 15, 1992;267(35):25129-34.
[cited by applicant]
Graham et al., “Characteristics of a Human Cell Line Transformed by DNA from Human Adenovirus Type 5,” J. gen. Virol. 1977, 36, 59-72.
[cited by applicant]
Graham & Preveck, “Chapter 11, Manipulation of Adenovirus Vectors,” Methods in Molecular Biology, vol. 7: Gene transfer and Expression Protocols, 1991.
[cited by applicant]
Graham & Preveck, “Adenovirus-Based Expression Vectors and Recombinant Vaccines” Vaccines: New Approaches to Immunological Problems, 1992.
[cited by applicant]
Grunhaus, A., and Horwitz, M. S. “Adenoviruses as cloning vectors,” Semin. Virol. 1992; 3, 237-252.
[cited by applicant]
Hensgens et al., “Two Intron Sequences in Yeast Mitochondrial COX1 Gene: Homology among URF-Containing Introns and Strain-Dependent Variation in Flanking Exons,” Cell, vol. 32, 379-389, Feb. 1983.
[cited by applicant]
Herz & Gerard, “Adenovirus-mediated transfer of low density lipoprotein receptor gene acutely accelerates cholesterol clearance in normal mice,” PNAS, 1993, vol. 90, 2812-2816.
[cited by applicant]
Huang et al., “Role of the hepatitis B virus posttranscriptional regulatory element in export of intronless transcripts,” Molecular and Cellular Biology (1995); 15(7): 3864-3869.
[cited by applicant]
Huez et al., “Two independent internal ribosome entry sites are involved in translation initiation of vascular endothelial growth factor mRNA,” Mol Cell Biol. Nov. 1998;18(11):6178-90.
[cited by applicant]
International Search Report and Written Opinion mailed on Aug. 22, 2018, for International Application No. PCT/US2018/034726, 9 pages.
[cited by applicant]
International Search Report and Written Opinion mailed on Dec. 31, 2018, for International Application No. PCT/US2018/054347, 14 pages.
[cited by applicant]
Irion, S. et al., “Identification and targeting of the ROSA26 locus in human embryonic stem cells”, Nat Biotechnol. (2007); 25(12):1477-1482.
[cited by applicant]
Jackson, et al., “The novel mechanism of initiation of picornavirus RNA translation”, Trends Biochem Sci. (1990); 15(12): 477-483.
[cited by applicant]
Jackson, et al., “Internal initiation of translation in eukaryotes: the picornavirus paradigm and beyond”, RNA. (1995); 1(10): 985-1000.
[cited by applicant]
Jarjour et al., “High-resolution profiling of homing endonuclease binding and catalytic specificity using yeast surface display,” 2009. Nuc. Acids Res. 37(20): 6871-6880.
[cited by applicant]
Jones & Shenk, Isolation of Deletion and Substitution Mutants of Adenovirus Type 5, Cell 1978, vol. 13, 181-188.
[cited by applicant]
Katzav et al. “Mutations of c-Cbl in myeloid malignancies,” Oncotarget, May 4, 2015 (May 4, 2015), vol. 6, No. 13, pp. 10689-10696.
[cited by applicant]
Kay et al., “A bacterial effector acts as a plant transcription factor and induces a cell size regulator,” Science. Oct. 26, 2007;318(5850):648-51.
[cited by applicant]
Kim, Yang-Gyun, et al. “Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain.” Proceedings of the National Academy of Sciences (1996); 93.3: 1156-1160.
[cited by applicant]
Kunkel, TA. “Rapid and efficient site-specific mutagenesis without phenotypic selection”, Proc Natl Acad Sci U S A. (1985); 82(2): 488-492.
[cited by applicant]
Kunkel, et al.“Rapid and efficient site-specific mutagenesis without phenotypic selection”, Methods in Enzymol. (1987); 154: 367-382.
[cited by applicant]
Kurokawa et al., “Adaptation of intronic homing endonuclease for successful horizontal transmission,” FEBS Journal 272 (2005) 2487-2496.
[cited by applicant]
Kutner, et al., “Simplified production andconcentration of HIV-1-based lentiviral vectors using HYPERFlask vessels and anion exchange membrane chromatography”, BMC Biotechnol. (2009); 9:10. p. 1-7.
[cited by applicant]
Kutner et al., “Production, concentration and titration of pseudotyped HIV-1-based lentiviral vectors”, Nature Protocols (2009); 4: 495-505.
[cited by applicant]
Le Gal La Salle et al., “An Adenovirus Vector for Gene Transfer into Neurons and Glia in the Brain,” Science Feb. 12, 1993, vol. 259, 988-990.
[cited by applicant]
Levrero et al., “Defective and nondefective adenovirus vectors for expressing foreign genes in vitro and in vivo,” Gene 1991; 101:195-202.
[cited by applicant]
Liu et al., “HnRNP L binds a cis-acting RNA sequence element that enables intron-dependent gene expression,” Genes & Dev. (1995); 9: 1766-1780.
[cited by applicant]
Liu et al., “Design of polydactyl zinc-finger proteins for unique addressing within complex genomes,” Proceedings of the National Academy of Sciences (1997); 94.11: 5525-5530.
[cited by applicant]
Liu et al., “Poly(cationic lipid)-mediated in vivo gene delivery to mouse liver,” Gene Ther. Jan. 2003; 10(2):180-7.
[cited by applicant]
Lo et al. “An E3 ubiquitin ligase c-Cbl: a new therapeutic target of lung cancer in cell and animal models,” Cancer, May 23, 2011 (May 23, 2011), vol. 117, No. 23, pp. 5344-5350.
[cited by applicant]
Maratea et al., “Deletion and fusion analysis of the phage phi X174 lysis gene E,” Gene. 1985;40(1):39-46.
[cited by applicant]
Murphy et al., “Genetic construction, expression, and melanoma-selective cytotoxicity of a diphtheria toxin-related alpha-melanocyte-stimulating hormone fusion protein,” Proc Natl Acad Sci USA. Nov. 1986;83(21):8258-62.
[cited by applicant]
Naldini L. et al., “Efficient transfer, integration, and sustained long-term expression of thetransgene in adult rat brains injected with a lentiviral vector”, Proc Natl Acad Sci USA (1996); 93(21): 11382-11388.
[cited by applicant]
Naldini, L. et al., “In vivo gene delivery and stable transduction of nondividing cells by a lentiviral vector”, Science (1996); 272(5259): 263-267.
[cited by applicant]
Naldini, L., “Lentiviruses as gene transfer agents for delivery to non-dividing cells”, Curr Opin Biotechnol. (1998); 5: 457-463.
[cited by applicant]
Pomerantz, et al., “Structure-based design of transcription factors.” Science (1995); 267.5194: 93-96.
[cited by applicant]
Pomerantz, et al., “Analysis of homeodomain function by structure-based design of a transcription factor,” Proc Natl Acad Sci U S A. Oct. 10, 1995;92(21):9752-6.
[cited by applicant]
Ragot et al., “Efficient adenovirus-mediated transfer of a human minidystrophin gene to skeletal muscle of mdx mice,” Nature Feb. 18, 1993; vol. 361: 647-650.
[cited by applicant]
Rosenfeld et al., “Adenovirus-Mediated Transfer of a Recombinant α1-Antitrypsin Gene to the Lung Epithelium in Vivo,” Science Apr. 19, 1991; vol. 252: 431-434.
[cited by applicant]
Rosenfeld et al., “In vivo transfer of the human cystic fibrosis transmembrane conductance regulator gene to the airway epithelium,” Cell, Jan. 10, 1992; vol. 68: 143-155.
[cited by applicant]
Ryan, M. et al., “Virus-encoded proteinases of the picornavirus super-group.” J Gen Virol. (1997); 78 (Pt 4): 699-723.
[cited by applicant]
Sather et al., “Efficient modification of CCR5 in primary human hematopoietic cells using a megaTAL nuclease and AAV donor template,” www.ScienceTranslationalMedicine.org, Sep. 30, 2015, vol. 7, Issue 307, 14 pages.
[cited by applicant]
Sterman et al., “Adenovirus-mediated herpes simplex virus thymidine kinase/ganciclovir genetherapy in patients with localized malignancy: results of a phase I clinical trial in malignant mesothelioma,” Hum Gene Ther. Ma…
[cited by applicant]
Stoddard, “Homing endonuclease structure and function,” Quarterly Reviews of Biophysics 2005; 38(1): pp. 49-95.
[cited by applicant]
Szeto et al., “Mining Endonuclease Cleavage Determinants in Genomic Sequence Data,” The Journal of Biological Chemistry, vol. 286, No. 37, pp. 32617-32627, Sep. 16, 2011.
[cited by applicant]
Szymczak, Andrea L., et al. “Correction of multi-gene deficiency in vivo using a single‘self-cleaving’2A peptide-based retroviral vector.” Nature Biotechnology (2004); 22.5: 589-594.
[cited by applicant]
Takeuchi et al:“Tapping natural reservoirs of homing endonucleases for targeted genemodification”, Proceedings of the National Academy of Sciences, National Academy of Sciences, vol. 108, o. 32, Aug. 1, 2011 {Aug. 1, 20…
[cited by applicant]
Takeuchi et al., “Redesign of extensive protein-DNA interfaces of meganucleases using iterative cycles of in vitro compartmentalization,” PNAS, Mar. 18, 2014, vol. 111, No. 11, 4061-4066.
[cited by applicant]
Takeuchi et al., “Engineering of customized meganucleases via in vitro compartmentalization and in cellulo optimization,” Methods Mol Biol. 2015; 1239: 105-132.
[cited by applicant]
Zennou et al., “HIV-1 genome nuclear import is mediated by a central DNA flap,” Cell. Apr. 14, 2000;101(2):173-85.
[cited by applicant]
Zufferey et al., “Multiply attenuated lentiviral vector achieves efficient gene delivery in vivo”, Nat Biotechnol. (1997), 15(9): 871-875.
[cited by applicant]
Zufferey, R. et al., “Woodchuck hepatitis virus posttranscriptional regulatory element enhances expression of transgenes delivered by retroviral vectors.” J Virol. (1999); 73(4): 2886-2892.
[cited by applicant]
Lambert et al., Indirect DNA sequence recognition and Its impact on nuclease cleavage activity, 24(6) Structure 862-873 (2016).
[cited by applicant]
Morbitzer et al., Assembly of custom TALE-type DNA binding domains by modular cloning, 39(13) Nucleic Acids Research 5790-5799 (2011).
[cited by applicant]
Rogers et al., Context influences on TALE-DNA binding revealed by quantitative profiling, 6(7440) Nature 1-10 (2015).
[cited by applicant]
Sakuma et al., Repeating pattern of non-RVD variations in DNA-binding modules enhances TALEN activity, 3(3379) Nature 1-8 (2013).
[cited by applicant]
Sun et al., Transcription Activator-Like Effector Nucleases (TALENs): A Highly Efficient and Versatile Tool for Genome Editing, 110(7) Biotechnology and Bioengineering 1811-1821 (Jul. 2013).
[cited by applicant]
Wei et al., TALEN or Cas9-Rapid, Efficient and Specific Choices for Genome Modifications, 40 Journal of Genetics and Genomics 281-289 (2013).
[cited by applicant]
www.calculatorsoup.com/calculators/discretemathematics/combinations.php; last visited Dec. 11, 2023.
[cited by applicant]
Guha et al., “Programmable Genome Editing Tools and their Regulation for Efficient Genome Engineering,” Computational and Structural Biotechnology Journal, (2017), vol. 15, pp. 146-160.
[cited by applicant]