Granted Patent
B2
US 12,419,970 · App. 17/048,236 · Granted Sep 23, 2025
Gene therapy for diseases caused by unbalanced nucleotide pools including mitochondrial DNA depletion syndromes
Inventors:
Michio Hirano (New York, NY); Hasan O. Akman (Haworth, NJ); Carlos Lopez-Gomez (Fuengirola, ES)
View Patent ↗
Loading inventors, assignments & file history…
Abstract
The invention relates generally to a method of treatment for a human genetic disease, such as diseases characterized by unbalanced nucleotide pools, e.g., mitochondrial DNA depletion syndromes, and more specifically, thymidine kinase 2 (TK2) deficiency, using gene therapy. The gene therapy may involve administration of one or more constructs, such as a viral vector, containing a nucleic acid encoding a functional protein. The functional protein may correspond to a nuclear gene. For treatment of TK2 deficiency, the gene therapy may involve administration of one or more constructs, such as a viral vector, containing a nucleic acid encoding a functional TK2 enzyme. The treatment may also involve the administration of pharmacological therapy in conjunction with the gene therapy. The treatment protocols of the disclosure, such as those involving gene therapy alone or in combination with pharmacological therapy, can be used to treat, prevent, and/or cure various other disorders of unbalanced nucleoside pools, especially those found in mitochondrial DNA depletion syndrome.
Claims (6)
1. A method of increasing weight gain in a subject suffering from myopathic MDS characterized by one or more mutations in an endogenous gene encoding TK2, the method comprising administering to the subject a therapeutically effective amount of a composition comprising a vector of adeno-associated virus (AAV) and comprising a transgene encoding thymidine kinase 2 (TK2).
2. The method of claim 1 wherein the TK2 has the amino acid sequence of SEQ ID NO: 1.
3. The method of claim 1 wherein the composition comprises an AAV and is an AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAVrh74, AAVrh.8, or AAVrh.10.
4. The method of claim 1 wherein the AAV is AAV2/9 or AAV2/8.
5. The method of claim 1 , further comprising administering one or more of dT, dC, TMP and dCMP to the subject.
6. The method of claim 3 , wherein the AAV is AAV9.
Assignments (1)
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Jul 11, 2022
From: HIRANO, MICHIO; AKMAN, HASAN O.; LOPEZ-GOMEZ, CARLOS
To: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
Reel/Frame 060471/0001 →
Continuity (2)
Provisional Application
62659281
· Apr 18, 2018
References Cited (57)
US 5658785A
· Johnson
· 1997
[cited by applicant]
US 5843742A
· Natsoulis et al.
· 1998
[cited by applicant]
US 6632670B1
· Wadsworth et al.
· 2003
[cited by applicant]
WO WO2007118245
· 2007
[cited by applicant]
WO WO2016205671
· 2016
[cited by applicant]
WO WO2017191274A2
· 2017
[cited by examiner]
Bottani, E et al., “AAV-mediated Liver-specific MPV17 Expression Restores mtDNA Levels and Prevents Diet-induced Liver Failure”. Molecular Therapy. Nov. 19, 2013; vol. 22, No. 1; pp. 1-8; abstract; p. 4, col. 1, paragra…
[cited by applicant]
Hosseini, SH et al., “Targeted Transgenic Overexpression of Mitochondrial Thymidine Kinase (TK2) Alters Mitochondrial DNA (mtDNA) and Mitochondrial. Polypeptide Abundance: Transgenic TK2, mtDNA, and Antiretrovirals”. Th…
[cited by applicant]
El-Hattab, AW et al., “Mitochondrial DNA Depletion Syndromes: Review and Updates of Genetic Basis, Manifestations, and Therapeutic Options”. Neurotherapeutics. Apr. 2013; vol. 10, No. 2; pp. 186-198; abstract; p. 187, c…
[cited by applicant]
Sun, R et al., “Thymidine Kinase 2 Enzyme Kinetics Elucidate the Mechanism of Thymidine-Induced Mitochondrial DNA Depletion”. Biochemistry. Sep. 23, 2014; vol. 53, No. 39; abstract; Genbank Supplemental pp. 1-5; DOI: 10…
[cited by applicant]
Krishnan, Shuba, et al. “Long term expression of
[cited by applicant]
Van Poecke, Sara, et al. “Synthesis, modeling and evaluation of 3′-(1-aryl-1 H-tetrazol-5-ylamino)-substituted 3′-deoxythymidine derivatives as potent and selective human mitochondrial thymidine kinase inhibitors.” Orga…
[cited by applicant]
Sara Van Poecke et al., “Synthesis, modeling and evaluation of 3′ -(1-aryl-1 H-tetrazol-5-ylamino )substituted 3′-dcoxythymidinc derivatives as potent and selective human mitochondrial thymidine kinase inhibitorst”, Org…
[cited by applicant]
Krishnan et al., “Long Term Expression of Drosophila melanogaster Nucleoside Kinase in Thymidine Kinase 2-deficient Mice with No Lethal Effects Caused by Nucleotide Pool Imbalances”, J Biol Chem Nov. 21, 2014;289(47):32…
[cited by applicant]
Akman, et al. (May 6, 2008) Thymidine kinase 2 (H126N) knock in mice show the essential role of balanced deoxynucleotide pools for mitochondrial DNA maintenance. Hum Mol Genet 17:2433-2440.
[cited by applicant]
Bourdon, et al. (May 7, 2007) Mutation of RRM2B, encoding p53-controlled ribonucleotide reductase (p53R2), causes severe mitochondrial DNA depletion. Nat Genet 39: 776-780.
[cited by applicant]
Chanprasert, et al. (Dec. 6, 2012) TK2-Related Mitochondrial DNA Depletion Syndrome, Myopathic Form. GeneReviews® Internet.
[cited by applicant]
Copeland (Mar. 21, 2008) Inherited mitochondrial diseases of DNA replication. Ann. Rev. Med. 59:131-146.
[cited by applicant]
DiMauro, et al. (Feb. 20, 1987) Cytochrome c oxidase deficiency in Leigh syndrome. Ann Neurol 22: 498-506.
[cited by applicant]
DiMauro, Schon. (Jul. 1, 2003) Mitochondrial respiratory-chain diseases. N Engl J Med 348:2656-2668.
[cited by applicant]
DiMauro, Hirano. (2005) Mitochondrial encephalomyopathies: an update. Neuromuscul Disord 15:276-286. Accepted Dec. 10, 2004.
[cited by applicant]
Dorado, et al. (2011) Onset and organ specificity of Tk2 deficiency depends on Tk1 down-regulation and transcriptional compensation. Hum Mol Genet. 20:155-64. Accepted Oct. 6, 2010.
[cited by applicant]
Elpeleg, et al. (Apr. 7, 2005) Deficiency of the ADP-forming succinyl-CoA synthase activity is associated with encephalomyopathy and mitochondrial DNA depletion. Am J Hum Genet 76: 1081-1086.
[cited by applicant]
Galbiati, et al. (2006) New mutations in TK2 gene associated with mitochondrial DNA depletion. Pediatr Neurol 34: 177-185. Accepted Jul. 11, 2005.
[cited by applicant]
Garone, et al. (Sep. 10, 2012). MPV17 Mutations Causing Adult-Onset Multisystemic Disorder With Multiple Mitochondrial DNA Deletions. Arch Neurol 69:1648-1651.
[cited by applicant]
Gotz, et al. (Sep. 3, 2008) Thymidine kinase 2 defects can cause multi-tissue mtDNA depletion syndrome. Brain 131:2841-2850.
[cited by applicant]
Hirano, et al. (Dec. 2001) Defects of intergenomic communication: autosomal disorders that cause multiple deletions and depletion of mitochondrial DNA. Semin Cell Develop Biol 12:417-427.
[cited by applicant]
Mandel, et al. (Nov. 2001) The deoxyguanosine kinase gene is mutated in individuals with depleted hepatocerebral mitochondrial DNA. Nat Genet 29: 337-341.
[cited by applicant]
Naviaux, Nguyen. (Feb. 4, 2004) POLG mutations associated with Alpers' syndrome and mitochondrial DNA depletion. Ann Neurol 55: 706-712.
[cited by applicant]
Ostergaard, et al. (Apr. 26, 2007) Deficiency of the alpha subunit of succinate-coenzyme A ligase causes fatal infantile lactic acidosis with mitochondrial DNA depletion. Am J Hum Genet 81: 383-387.
[cited by applicant]
Paradas, et al. (2012) TK2 mutation presenting as indolent myopathy. Neurology 29:504-506. Jan. 9, 2013.
[cited by applicant]
Saada, et al. (Aug. 7, 2003) Mitochondrial deoxyribonucleoside triphosphate pools in thymidine kinase 2 deficiency. Biochem Biophys Res Commun 310:963-966.
[cited by applicant]
Spinazzola, et al. (Apr. 2, 2006) MPV17 encodes an inner mitochondrial membrane protein and is mutated in infantile hepatic mitochondrial DNA depletion. Nat Genet 38: 570-575.
[cited by applicant]
Tyynismaa, et al. (2012) Thymidine kinase 2 mutations in autosomal recessive progressive external ophthalmoplegia with multiple mitochondrial DNA deletions. Hum Mol Genet 21:66-75. Accepted Sep. 19, 2011.
[cited by applicant]
Garone et al., “Deoxypyrimidine monophosphate bypass therapy for thymidine kinase 2 deficiency”. EMBO Mol Med Jun. 26, 2014 vol. 6 No. 8 pp. 1016-1027. Especially abstract, p. 1016 col. 2, p. 1017 col. 1 para 2, para 2,…
[cited by applicant]
Van Goethem, et al. (Jul. 2001) Mutation of POLG is associated with progressive external ophthalmoplegia characterized by mtDNA deletions. Nature Genet. 28:211-212.
[cited by applicant]
Spelbrink, et al. (Jul. 2001). Human mitochondrial DNA deletions associated with mutations in the gene encoding Twinkle, a phage T7 gene 4-like protein localized in mitochondria. Nature Genet. 28:223-231.
[cited by applicant]
Franzolin, et al. (Mar. 23, 2006) Bromovinyl-deoxyuridine: a selective substrate for mitochondrial thymidine kinase in cell extracts. Biochem. Biophy. Res. Commun. 344(1):30-6.
[cited by applicant]
Sarzi, et al. (Dec. 2007) Twinkle helicase (PEO1) gene mutation causes mitochondrial DNA depletion. Ann. Neurol. 62: 579-587.
[cited by applicant]
Ronchi, et al. (Jun. 28, 2012). Next-generation sequencing reveals DGUOK mutations in adult atients with mitochondrial DNA multiple deletions. Brain 135:3404-3415.
[cited by applicant]
Quinzii, et al. (Feb. 2013) Tissue-specific oxidative stress and loss of mitochondria in CoQ-deficient Pdss2 mutant mice. FASEB J. 27:612-621.
[cited by applicant]
Nishino, et al. (Jan. 29, 1999). Thymidine phosphorylase gene mutations in MNGIE, a human mitochondrial disorder. Science 283:689-692.
[cited by applicant]
Longley, et al. (Jun. 2006). Mutant POLG2 disrupts DNA polymerase gamma subunits and causes progressive external ophthalmoplegia. Am J Hum Genet. 78:1026-1034.
[cited by applicant]
Garone, et al. (2018) Retrospective Natural History of Thymidine Kinase 2 Deficiency. J. Med. Genetics 55:515-21. Received Oct. 3, 2017.
[cited by applicant]
Birch-Machin, et al. (Feb. 1994) An evaluation of the measurement of the activities of complexes I-IV in the respiratory chain of human skeletal muscle mitochondria. Biochem Med Metab Biol 51:35-42.
[cited by applicant]
Béhin, et al. (Feb. 2012) Adult cases of mitochondrial DNA depletion due to TKZ defect an expanding spectrum. Neurology 78:644-648.
[cited by applicant]
Sandmair et al., “Thymidine kinase gene therapy for human malignant glioma, using replication-deficient retroviruses or adenoviruses”, Hum Gen Ther, vol. 11 / Issue 16 pp. 2197-2205, Nov. 1, 2000.
[cited by applicant]
Sangro et al., “A phase I clinical trial of thymidine kinase-based gene therapy in advanced hepatocellular carcinoma”, Cancer Gene Ther, vol. 17 / Issue 12, pp. 837-843, Dec. 2010.
[cited by applicant]
Tyynela et al., “Adenovirus-mediated herpes simplex Virus thymidine kinase gene therapy in BT4C rat glioma model”, Cancer Gene Therapy (Aug. 8, 2002) 9, 917-924.
[cited by applicant]
Tyynismaa, et al. (Aug. 14, 2009). A heterozygous truncating mutation in RRMZB causes autosomal-dominant progressive external ophthalmoplegia with multiple mtDNA deletions. Am. J. Hum. Genet. 85: 290-295.
[cited by applicant]
El-Hattab Ayman W et al: “Therapies for mitochondrial diseases and current clinical trials”, Molecular Genetics and Metabolism, Academic Press, Amsterdam, NL, vol. 122, No. 3, Sep. 18, 2017 (Sep. 18, 2017), pp. 1-9, XP0…
[cited by applicant]
Keeler et al., “Gene Therapy 2017: Progress and Future Directions,” Clin. Transl. Sci., vol. 10, published online May 23, 2017, pp. 242-248.
[cited by applicant]
Khan et al., “Molecular Genetics and Metabolism,” Mol. Genet. Metab., vol. 121, No. 3, Jul. 2017, pp. 227-240.
[cited by applicant]
https://grantome.com/grant/NIH/P01-HD080642-01-5121, May 31, 2015 publication date asserted by SIPO in counterpart China Divisional Patent Application No. 2023107576092.
[cited by applicant]
NCBI, GenBank Accession No. AAQ02499.1, “Thymidine Kinase 2, Mitochondrial, Partial (Synthetic Construct)”, Jun. 8, 2005.
[cited by applicant]