Gene therapy progress and prospects: targeted gene repair

Progress and problems with the use of viral vectors for gene therapy

Thomas, C. E., Ehrhardt, A., & Kay, M. A. (2003) · Nature Reviews Genetics · doi:10.1038/nrg1066 · Cited by 2,501 · see citing works

Genetic Engineering Using Homologous Recombination

Court, D. L., Sawitzke, J. A., & Thomason, L. C. (2002) · Annual Review of Genetics · doi:10.1146/annurev.genet.36.061102.093104 · Cited by 507 · see citing works

Mismatch repair and DNA damage signalling

Stojic, L., Brun, R., & Jiricny, J. (2004) · DNA Repair · doi:10.1016/j.dnarep.2004.06.006 · Cited by 396 · see citing works

Checking on the fork: the DNA-replication stress-response pathway

Osborn, A. J., Elledge, S. J., & Zou, L. (2002) · Trends in Cell Biology · doi:10.1016/s0962-8924(02)02380-2 · Cited by 345 · see citing works

Site-specific genomic integration produces therapeutic Factor IX levels in mice

Olivares, E. C., Hollis, R. P., Chalberg, T. W., Meuse, L. A., Kay, M. A., & Calos, M. P. (2002) · Nature Biotechnology · doi:10.1038/nbt753 · Cited by 286 · see citing works

Conservative homologous recombination preferentially repairs DNA double-strand breaks in the S phase of the cell cycle in human cells

Saleh-Gohari, N. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh703 · Cited by 270 · see citing works

Regulation of DNA replication by ATR: signaling in response to DNA intermediates

Shechter, D., Costanzo, V., & Gautier, J. (2004) · DNA repair · doi:10.1016/j.dnarep.2004.03.020 · Cited by 192 · see citing works

Chimeric recombinases with designed DNA sequence recognition

Akopian, A., He, J., Boocock, M. R., & Stark, W. M. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1533177100 · Cited by 100 · see citing works

Recombineering with overlapping single-stranded DNA oligonucleotides: Testing a recombination intermediate

Yu, D., Sawitzke, J. A., Ellis, H., & Court, D. L. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1232375100 · Cited by 97 · see citing works

Targeted gene modification in mismatch-repair-deficient embryonic stem cells by single-stranded DNA oligonucleotides

Dekker, M. (2003) · Nucleic Acids Research · doi:10.1093/nar/gng027 · Cited by 88 · see citing works

Implications of cell cycle progression on functional sequence correction by short single-stranded DNA oligonucleotides

Olsen, P. A., Randøl, M., & Krauss, S. J. K. (2005) · Gene Therapy · doi:10.1038/sj.gt.3302454 · Cited by 87 · see citing works

Camptothecin enhances the frequency of oligonucleotide-directed gene repair in mammalian cells by inducing DNA damage and activating homologous recombination

Ferrara, L. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh822 · Cited by 82 · see citing works

Sequence-specific modification of genomic DNA by small DNA fragments

Gruenert, D. C., Bruscia, E. M., Novelli, G., et al. (2003) · Journal of Clinical Investigation · doi:10.1172/jci19773 · Cited by 80 · see citing works

DNA mismatch repair and cancer

Li, G. (2003) · Frontiers in bioscience · doi:10.2741/1121 · Cited by 74 · see citing works

Gene repair in mammalian cells is stimulated by the elongation of S phase and transient stalling of replication forks

Brachman, E. E., & Kmiec, E. B. (2005) · DNA repair · doi:10.1016/j.dnarep.2004.11.007 · Cited by 67 · see citing works

Rad51p and Rad54p, but not Rad52p, elevate gene repair in Saccharomyces cerevisiae directed by modified single-stranded oligonucleotide vectors

Liu, L. (2002) · Nucleic Acids Research · doi:10.1093/nar/gkf397 · Cited by 64 · see citing works

Transcription affects formation and processing of intermediates in oligonucleotide-mediated gene alteration

Igoucheva, O. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg360 · Cited by 62 · see citing works

Strand bias in oligonucleotide-mediated dystrophin gene editing

Bertoni, C., Morris, G. E., & Rando, T. A. (2004) · Human Molecular Genetics · doi:10.1093/hmg/ddi020 · Cited by 62 · see citing works

Mechanisms underlying targeted gene correction using chimeric RNA/DNA and single-stranded DNA oligonucleotides

Andersen, M., Sørensen, C. B., Bolund, L., & Jensen, T. G. (2002) · Journal of Molecular Medicine · doi:10.1007/s00109-002-0393-8 · Cited by 62 · see citing works

Oligonucleotide-directed single-base DNA alterations in mouse embryonic stem cells

Pierce, E. A., Liu, Q., Igoucheva, O., Omarrudin, R., Ma, H., Diamond, S. L., & Yoon, K. (2003) · Gene Therapy · doi:10.1038/sj.gt.3301857 · Cited by 61 · see citing works

The development and regulation of gene repair

Liu, L., Parekh‐Olmedo, H., & Kmiec, E. B. (2003) · Nature Reviews Genetics · doi:10.1038/nrg1156 · Cited by 60 · see citing works

Oligonucleotide-Directed Mutagenesis and Targeted Gene Correction: A Mechanistic Point of View

Igoucheva, O., Alexeev, V. Y., & Yoon, K. (2004) · Current Molecular Medicine · doi:10.2174/1566524043360465 · Cited by 60 · see citing works

Cell Cycle Modulation of Gene Targeting by a Triple Helix-forming Oligonucleotide

Majumdar, A., Puri, N., Cuenoud, B. M., et al. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m211837200 · Cited by 59 · see citing works

Association of p53 and MSH2 with recombinative repair complexes during S phase

Zink, D., Mayr, C., Janz, C., & Wiesmüller, L. (2002) · Oncogene · doi:10.1038/sj.onc.1205614 · Cited by 56 · see citing works

Targeted conversion of the transthyretin gene in vitro and in vivo

Nakamura, M., Ando, Y., Nagahara, S., et al. (2004) · Gene Therapy · doi:10.1038/sj.gt.3302228 · Cited by 55 · see citing works

Genome Engineering Using Site-Specific Recombinases

Kolb, A. F. (2002) · Cloning and Stem Cells · doi:10.1089/153623002753632066 · Cited by 49 · see citing works

Restoration of dystrophin expression in mdx muscle cells by chimeraplast-mediated exon skipping

Bertoni, C. (2003) · Human Molecular Genetics · doi:10.1093/hmg/ddg133 · Cited by 49 · see citing works

Design of a nonviral vector for site‐selective, efficient integration into the human genome

Kaminski, J., Huber, M., Summers, J. B., & Ward, M. B. (2002) · The FASEB Journal · doi:10.1096/fj.02-0127hyp · Cited by 48 · see citing works

Enhanced oligonucleotide-directed gene targeting in mammalian cells following treatment with DNA damaging agents

Ferrara, L., Parekh‐Olmedo, H., & Kmiec, E. B. (2004) · Experimental Cell Research · doi:10.1016/j.yexcr.2004.06.021 · Cited by 47 · see citing works

DNA replication and transcription direct a DNA strand bias in the process of targeted gene repair in mammalian cells

Brachman, E. E., & Kmiec, E. B. (2004) · Journal of Cell Science · doi:10.1242/jcs.01250 · Cited by 46 · see citing works

Simultaneous targeted alteration of the tyrosinase and c-kit genes by single-stranded oligonucleotides

Alexeev, V. Y., Igoucheva, O., & Yoon, K. (2002) · Gene Therapy · doi:10.1038/sj.gt.3301862 · Cited by 45 · see citing works

Targeted Nucleotide Repair of cyc1 Mutations in Saccharomyces cerevisiae Directed by Modified Single-Stranded DNA Oligonucleotides

Brachman, E. E., & Kmiec, E. B. (2003) · Genetics · doi:10.1093/genetics/163.2.527 · Cited by 44 · see citing works

Correction/mutation of acid α-D-glucosidase gene by modified single-stranded oligonucleotides: in vitro and in vivo studies

Lu, I.-L., Lin, C.-Y., Lin, S.-B., Chen, S.-T., Yeh, L.-Y., Yang, F.-Y., & Lc, A. (2003) · Gene Therapy · doi:10.1038/sj.gt.3302096 · Cited by 44 · see citing works

Using Nucleases to Stimulate Homologous Recombination

Carroll, D. (2004) · Humana Press eBooks · doi:10.1385/1-59259-761-0:195 · Cited by 41 · see citing works

A comparison of gene repair strategies in cell culture using a lacZ reporter system

Nickerson, H. D., & Colledge, W. H. (2003) · Gene Therapy · doi:10.1038/sj.gt.3302049 · Cited by 41 · see citing works

Reaction Parameters of Targeted Gene Repair in Mammalian Cells

Hu, Y., Parekh‐Olmedo, H., Drury, M. D., et al. (2005) · Molecular Biotechnology · doi:10.1385/mb:29:3:197 · Cited by 38 · see citing works

Functional correction of episomal mutations withshort DNA fragments and RNA–DNA oligonucleotides

Thorpe, P. H., Stevenson, B. J., & Porteous, D. J. (2002) · The Journal of Gene Medicine · doi:10.1002/jgm.249 · Cited by 38 · see citing works

Optimising gene repair strategies in cell culture

Thorpe, P. H., Stevenson, B. J., & Porteous, D. J. (2002) · Gene Therapy · doi:10.1038/sj.gt.3301750 · Cited by 34 · see citing works

DNA pairing is an important step in the process of targeted nucleotide exchange

Drury, M. D. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg171 · Cited by 32 · see citing works

Unmodified oligodeoxynucleotides require single‐strandedness to induce targeted repair of a chromosomal EGFP gene

Radecke, F., Radecke, S. M., & Schwarz, K. (2004) · The Journal of Gene Medicine · doi:10.1002/jgm.613 · Cited by 31 · see citing works

The 'biased' evolution of targeted gene repair.

Brachman, E. E., & Kmiec, E. B. (2002) · PubMed · Cited by 30 · see citing works

Nuclear Extracts Promote Gene Correction and Strand Pairing of Oligonucleotides to the Homologous Plasmid

Igoucheva, O., Alexeev, V. Y., & Yoon, K. (2002) · Antisense and Nucleic Acid Drug Development · doi:10.1089/108729002320351557 · Cited by 25 · see citing works

Targeted beta-globin gene conversion in human hematopoietic CD34+ and Lin−CD38− cells

Liu, H., Agarwal, S., Kmiec, E. B., et al. (2002) · Gene Therapy · doi:10.1038/sj.gt.3301610 · Cited by 25 · see citing works

Branched oligonucleotides induce in vivo gene conversion of a mutated EGFP reporter

Olsen, P. A., McKeen, C. M., & Krauss, S. J. K. (2003) · Gene Therapy · doi:10.1038/sj.gt.3302079 · Cited by 22 · see citing works

The Effect of Hydroxyurea and Trichostatin A on Targeted Nucleotide Exchange in Yeast and Mammalian Cells

Parekh‐Olmedo, H., Engstrom, J. U., & Kmiec, E. B. (2003) · Annals of the New York Academy of Sciences · doi:10.1196/annals.1281.006 · Cited by 21 · see citing works

Targeted gene correction of hprt mutations by 45 base single-stranded oligonucleotides

Kenner, O., Kneisel, A., Klingler, J. A., et al. (2002) · Biochemical and Biophysical Research Communications · doi:10.1016/s0006-291x(02)02749-3 · Cited by 20 · see citing works

A LacZ-based transgenic mouse for detection of somatic gene repair events in vivo

Nickerson, H. D., & Colledge, W. H. (2004) · Gene Therapy · doi:10.1038/sj.gt.3302311 · Cited by 17 · see citing works

Low-dose bleomycin induces targeted gene repair frequency in cultured melan-c cells using chimeric RNA/DNA oligonucleotide transfection

Suzuki, T., Murai, A., & Muramatsu, T. (2003) · International Journal of Molecular Medicine · doi:10.3892/ijmm.12.1.109 · Cited by 11 · see citing works

Nuclease Activity of Saccharomyces cerevisiae Mre11 Functions in Targeted Nucleotide Alteration

Liu, L., Usher, M. J., Hu, Y., et al. (2003) · Applied and Environmental Microbiology · doi:10.1128/aem.69.10.6216-6224.2003 · Cited by 11 · see citing works

Concurrent targeted exchange of three bases in mammalian hprt by oligonucleotides

Kenner, O., Lutomska, A., Speit, G., et al. (2004) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2004.07.062 · Cited by 10 · see citing works

Therapeutic application of chimeric RNA/DNA oligonucleotide based gene therapy

Lai, L., & Lien, Y.-H. H. (2001) · Expert Opinion on Biological Therapy · doi:10.1517/14712598.1.1.41 · Cited by 8 · see citing works

713. Gene Correction Therapy Using Designed Zinc Finger-Based Endonucleases

(2004) · Molecular Therapy · doi:10.1016/j.ymthe.2004.06.619 · Cited by 4 · see citing works

Gene Targeting by Oligonucleotides in Keratinocytes

Igoucheva, O., & Yoon, K. (2004) · Humana Press eBooks · doi:10.1385/1-59259-830-7:287 · Cited by 4 · see citing works

1153. Strand Bias in Gene Repair Using Single-Stranded Oligonucleotides

(2003) · Molecular Therapy · doi:10.1016/s1525-0016(16)41595-9 · Cited by 2 · see citing works

714. Structure-Based Engineering of the FokI DNA Cleavage Domain in the Context of a Chimeric Endonuclease: Towards Maximally Efficient “Gene Editing” Therapy

(2004) · Molecular Therapy · doi:10.1016/j.ymthe.2004.06.620 · Cited by 1 · see citing works

Adeno‐associated virus gene repair corrects a mouse model of hereditary tyrosinemia in vivo†‡

Paulk, N. K., Wursthorn, K., Wang, Z., Finegold, M. J., Kay, M. A., & Grompe, M. (2010) · Hepatology · doi:10.1002/hep.23481 · Cited by 135 · see citing works

Advanced gene delivery : from concepts to pharmaceutical products

Rolland, A. P. (1999) · Cited by 25 · see citing works

Gene therapy for cardiovascular applications

Pacak, C. A., Mah, C. S., & Byrne, B. J. (2005) · Laboratory techniques in biochemistry and molecular biology · doi:10.1016/s0075-7535(05)31009-6

Targeting of drugs 5 : strategies for oligonucleotide and gene delivery in therapy

Gregoriadis, G. C., & McCormack, B. (1996) · Plenum Press eBooks · Cited by 13 · see citing works

Microbubble-enhanced ultrasound for vascular gene delivery

Lawrie, A., Brisken, A. F., Francis, S., et al. (2000) · Gene Therapy · doi:10.1038/sj.gt.3301339 · Cited by 343 · see citing works

Advance in treatment of rheumatoid arthritis.

Lu, Z. (2010) · Zhongguo redai yixue