Simple Monitoring of Gene Targeting Efficiency in Human Somatic Cell Lines Using the PIGA Gene

PLoS ONE

Volumn 7, Issue 10, 2012, Pages

  Karnan, Sivasundaram ^a   Konishi, Yuko ^a   Ota, Akinobu ^a   Takahashi, Miyuki ^a   Damdindorj, Lkhagvasuren ^a   Hosokawa, Yoshitaka ^a   Konishi, Hiroyuki ^a  

^a AICHI MEDICAL UNIVERSITY SCHOOL OF MEDICINE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

GLYCOSYLPHOSPHATIDYLINOSITOL; GLYCOSYLPHOSPHATIDYLINOSITOL ANCHORED PROTEIN; PHOSPHOGLYCERATE MUTASE;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ADENO ASSOCIATED VIRUS; ARTICLE; CELL LINE; CELL POPULATION; CELL PROLIFERATION; CELL SELECTION; CONTROLLED STUDY; EXON; FLOW CYTOMETRY; GENE; GENE LOCUS; GENE TARGETING; HUMAN; INTRON; LOXP SITE; PHOSPHATIDYLINOSITOL GLYCAN ANCHOR BIOSYNTHESIS CLASS A GENE; PIGA GENE; PLASMID; QUANTITATIVE ANALYSIS; REPORTER GENE; SOMATIC CELL; SOUTHERN BLOTTING;

BLOTTING, SOUTHERN; CELL PROLIFERATION; GENE FREQUENCY; GENE TARGETING; HCT116 CELLS; HUMANS; MEMBRANE PROTEINS; POLYMERASE CHAIN REACTION;

EID: 84867289692     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0047389     Document Type: Article

References (51)

1. Smithies O, Gregg RG, Boggs SS, Koralewski MA, Kucherlapati RS, (1985) Insertion of DNA sequences into the human chromosomal beta-globin locus by homologous recombination. Nature 317: 230-234.
2. Shirasawa S, Furuse M, Yokoyama N, Sasazuki T, (1993) Altered growth of human colon cancer cell lines disrupted at activated Ki-ras. Science 260: 85-88.
3. Sedivy JM, Vogelstein B, Liber HL, Hendrickson EA, Rosmarin A, (1999) Gene targeting in human cells without isogenic DNA. Science 283: 9a.
4. Di Nicolantonio F, Arena S, Gallicchio M, Zecchin D, Martini M, et al. (2008) Replacement of normal with mutant alleles in the genome of normal human cells unveils mutation-specific drug responses. Proc Natl Acad Sci U S A 105: 20864-20869.
5. Di Nicolantonio F, Arena S, Tabernero J, Grosso S, Molinari F, et al. (2010) Deregulation of the PI3K and KRAS signaling pathways in human cancer cells determines their response to everolimus. J Clin Invest 120: 2858-2866.
6. Russell DW, Hirata RK, (1998) Human gene targeting by viral vectors. Nat Genet 18: 325-330.
7. Khan IF, Hirata RK, Russell DW, (2011) AAV-mediated gene targeting methods for human cells. Nat Protoc 6: 482-501.
8. Hirata R, Chamberlain J, Dong R, Russell DW, (2002) Targeted transgene insertion into human chromosomes by adeno-associated virus vectors. Nat Biotechnol 20: 735-738.
9. Konishi H, Lauring J, Garay JP, Karakas B, Abukhdeir AM, et al. (2007) A PCR-based high-throughput screen with multiround sample pooling: application to somatic cell gene targeting. Nat Protoc 2: 2865-2874.
10. Arbones ML, Austin HA, Capon DJ, Greenburg G, (1994) Gene targeting in normal somatic cells: inactivation of the interferon-gamma receptor in myoblasts. Nat Genet 6: 90-97.
11. Miyata T, Takeda J, Iida Y, Yamada N, Inoue N, et al. (1993) The cloning of PIG-A, a component in the early step of GPI-anchor biosynthesis. Science 259: 1318-1320.
12. Takeda J, Miyata T, Kawagoe K, Iida Y, Endo Y, et al. (1993) Deficiency of the GPI anchor caused by a somatic mutation of the PIG-A gene in paroxysmal nocturnal hemoglobinuria. Cell 73: 703-711.
13. Parker C, Omine M, Richards S, Nishimura J, Bessler M, et al. (2005) Diagnosis and management of paroxysmal nocturnal hemoglobinuria. Blood 106: 3699-3709.
14. Brodsky RA, (2009) How I treat paroxysmal nocturnal hemoglobinuria. Blood 113: 6522-6527.
15. Chen R, Eshleman JR, Brodsky RA, Medof ME, (2001) Glycophosphatidylinositol-anchored protein deficiency as a marker of mutator phenotypes in cancer. Cancer Res 61: 654-658.
16. Araten DJ, Golde DW, Zhang RH, Thaler HT, Gargiulo L, et al. (2005) A quantitative measurement of the human somatic mutation rate. Cancer Res 65: 8111-8117.
17. Miura D, Dobrovolsky VN, Kasahara Y, Katsuura Y, Heflich RH, (2008) Development of an in vivo gene mutation assay using the endogenous Pig-A gene: I. Flow cytometric detection of CD59-negative peripheral red blood cells and CD48-negative spleen T-cells from the rat. Environ Mol Mutagen 49: 614-621.
18. Dobo KL, Fiedler RD, Gunther WC, Thiffeault CJ, Cammerer Z, et al. (2011) Defining EMS and ENU dose-response relationships using the Pig-a mutation assay in rats. Mutat Res 725: 13-21.
19. Zou J, Maeder ML, Mali P, Pruett-Miller SM, Thibodeau-Beganny S, et al. (2009) Gene targeting of a disease-related gene in human induced pluripotent stem and embryonic stem cells. Cell Stem Cell 5: 97-110.
20. Konishi H, Karakas B, Abukhdeir AM, Lauring J, Gustin JP, et al. (2007) Knock-in of mutant K-ras in nontumorigenic human epithelial cells as a new model for studying K-ras mediated transformation. Cancer Res 67: 8460-8467.
21. Hucl T, Rago C, Gallmeier E, Brody JR, Gorospe M, et al. (2008) A syngeneic variance library for functional annotation of human variation: application to BRCA2. Cancer Res 68: 5023-5030.
22. Gustin JP, Karakas B, Weiss MB, Abukhdeir AM, Lauring J, et al. (2009) Knockin of mutant PIK3CA activates multiple oncogenic pathways. Proc Natl Acad Sci U S A 106: 2835-2840.
23. Yun J, Rago C, Cheong I, Pagliarini R, Angenendt P, et al. (2009) Glucose deprivation contributes to the development of KRAS pathway mutations in tumor cells. Science 325: 1555-1559.
24. Vitolo MI, Weiss MB, Szmacinski M, Tahir K, Waldman T, et al. (2009) Deletion of PTEN promotes tumorigenic signaling, resistance to anoikis, and altered response to chemotherapeutic agents in human mammary epithelial cells. Cancer Res 69: 8275-8283.
25. Chung JH, Bunz F, (2010) Cdk2 is required for p53-independent G2/M checkpoint control. PLoS Genet 6: e1000863.
26. Fattah F, Lee EH, Weisensel N, Wang Y, Lichter N, et al. (2010) Ku regulates the non-homologous end joining pathway choice of DNA double-strand break repair in human somatic cells. PLoS Genet 6: e1000855.
27. Solomon DA, Kim T, Diaz-Martinez LA, Fair J, Elkahloun AG, et al. (2011) Mutational inactivation of STAG2 causes aneuploidy in human cancer. Science 333: 1039-1043.
28. Konishi H, Mohseni M, Tamaki A, Garay JP, Croessmann S, et al. (2011) Mutation of a single allele of the cancer susceptibility gene BRCA1 leads to genomic instability in human breast epithelial cells. Proc Natl Acad Sci U S A 108: 17773-17778.
29. Brodsky RA, Mukhina GL, Li S, Nelson KL, Chiurazzi PL, et al. (2000) Improved detection and characterization of paroxysmal nocturnal hemoglobinuria using fluorescent aerolysin. Am J Clin Pathol 114: 459-466.
30. Topaloglu O, Hurley PJ, Yildirim O, Civin CI, Bunz F, (2005) Improved methods for the generation of human gene knockout and knockin cell lines. Nucleic Acids Res 33: e158.
31. Hirata RK, Russell DW, (2000) Design and packaging of adeno-associated virus gene targeting vectors. J Virol 74: 4612-4620.
32. Porteus MH, Cathomen T, Weitzman MD, Baltimore D, (2003) Efficient gene targeting mediated by adeno-associated virus and DNA double-strand breaks. Mol Cell Biol 23: 3558-3565.
33. Mansour SL, Thomas KR, Capecchi MR, (1988) Disruption of the proto-oncogene int-2 in mouse embryo-derived stem cells: a general strategy for targeting mutations to non-selectable genes. Nature 336: 348-352.
34. Yagi T, Ikawa Y, Yoshida K, Shigetani Y, Takeda N, et al. (1990) Homologous recombination at c-fyn locus of mouse embryonic stem cells with use of diphtheria toxin A-fragment gene in negative selection. Proc Natl Acad Sci U S A 87: 9918-9922.
35. Porteus MH, Baltimore D, (2003) Chimeric nucleases stimulate gene targeting in human cells. Science 300: 763.
36. Suzuki K, Mitsui K, Aizawa E, Hasegawa K, Kawase E, et al. (2008) Highly efficient transient gene expression and gene targeting in primate embryonic stem cells with helper-dependent adenoviral vectors. Proc Natl Acad Sci U S A 105: 13781-13786.
37. Iiizumi S, Kurosawa A, So S, Ishii Y, Chikaraishi Y, et al. (2008) Impact of non-homologous end-joining deficiency on random and targeted DNA integration: implications for gene targeting. Nucleic Acids Res 36: 6333-6342.
38. Urnov FD, Miller JC, Lee YL, Beausejour CM, Rock JM, et al. (2005) Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435: 646-651.
39. Diep DB, Nelson KL, Raja SM, Pleshak EN, Buckley JT, (1998) Glycosylphosphatidylinositol anchors of membrane glycoproteins are binding determinants for the channel-forming toxin aerolysin. J Biol Chem 273: 2355-2360.
40. Sedivy JM, Dutriaux A, (1999) Gene targeting and somatic cell genetics-a rebirth or a coming of age? Trends Genet 15: 88-90.
41. Rutledge EA, Russell DW, (1997) Adeno-associated virus vector integration junctions. J Virol 71: 8429-8436.
42. Miller DG, Petek LM, Russell DW, (2004) Adeno-associated virus vectors integrate at chromosome breakage sites. Nat Genet 36: 767-773.
43. Miller DG, Trobridge GD, Petek LM, Jacobs MA, Kaul R, et al. (2005) Large-scale analysis of adeno-associated virus vector integration sites in normal human cells. J Virol 79: 11434-11442.
44. Voss AK, Thomas T, Gruss P, (1998) Efficiency assessment of the gene trap approach. Dev Dyn 212: 171-180.
45. McClive P, Pall G, Newton K, Lee M, Mullins J, et al. (1998) Gene trap integrations expressed in the developing heart: insertion site affects splicing of the PT1-ATG vector. Dev Dyn 212: 267-276.
46. Elmore CL, Wu X, Leclerc D, Watson ED, Bottiglieri T, et al. (2007) Metabolic derangement of methionine and folate metabolism in mice deficient in methionine synthase reductase. Mol Genet Metab 91: 85-97.
47. Debrand E, El Jai Y, Spence L, Bate N, Praekelt U, et al. (2009) Talin 2 is a large and complex gene encoding multiple transcripts and protein isoforms. FEBS J 276: 1610-1628.
48. Christian M, Cermak T, Doyle EL, Schmidt C, Zhang F, et al. (2010) Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186: 757-761.
49. Miller JC, Tan S, Qiao G, Barlow KA, Wang J, et al. (2011) A TALE nuclease architecture for efficient genome editing. Nat Biotechnol 29: 143-148.
50. Ishida Y, Leder P, (1999) RET: a poly A-trap retrovirus vector for reversible disruption and expression monitoring of genes in living cells. Nucleic Acids Res 27: e35.
51. Rago C, Vogelstein B, Bunz F, (2007) Genetic knockouts and knockins in human somatic cells. Nat Protoc 2: 2734-2746.