Advertisement

Engineering of Human-Induced Pluripotent Stem Cells for Precise Disease Modeling

  • P. Lisowski
Chapter

Abstract

Stem cell technologies and gene editing techniques are two of the most promising recent developments in biomedicine. The ability to reprogram common human cells into induced pluripotent stem cells (hiPSCs) and turn them into the cells of interest has already become a powerful research tool, thus providing a unique platform for disease studies. In combination with the use of designer nucleases approach to repair or to introduce disease-causing mutations, both are valuable in developing personalized disease models. This chapter provides an overview on designer nucleases-based gene editing in hiPSCs, describing the principles of CRISPR/Cas systems along with consecutive methodological steps such as nucleases selection, isolation, and genotyping of modified hiPSC clones with emphasis on the crucial role of isogenic cell lines in disease modeling. Moreover, the production of rare or complex genotypes in patient cell lines requires efficient and streamlined gene editing technologies. However, precise genome editing applications rely on infrequent homology-directed repair (HDR), with the abundant nonhomologous end joining (NHEJ) formed indels presenting a barrier to achieving high rates of precise sequence modification. The methods presented here are supported by theoretical framework to allow for the incorporation of inevitable improvements to achieve either higher rates of gene editing by promotion of HDR over NHEJ or application of different CRISPR/Cas platforms for robust and multiplex gene editing, toward decoding of neurodevelopmental as well as for modeling of late onset disorders by fast-forwarding the biological clock. Due to easy in theory but laborious and inefficient in practice, the precise and efficient genome editing in hiPSCs could be only achieved by the proper combination of the described methods in the process. This eventually would lead to generation of wide range of disease models for decoding of sporadic, polygenic, undiagnosed, and rare disorders using the adequate experimental design following appropriate gene editing toolbox selection.

Keywords

Human-induced pluripotent stem cells (hiPSCs) RNA-guided designer Cas9 nucleases CRISPR/Cas Gene editing Multiplex genome editing Genome engineering Personalized disease models hiPS cell-based disease modeling 

Notes

Acknowledgments

This work was supported by the National Science Centre, Poland Grant No. 2016/22/M/NZ2/00548. I would like to thank Dr. Ralf Kühn (Max-Delbrück-Centrum für Molekulare Medizin) for invaluable support and guidance in development and application of hiPSC gene editing technologies described in this work. I would like to thank Ms. Aleksandra Golonko (Bialystok University of Technology) for excellent support in manuscript preparation.

References

  1. 1.
    Rouet P, Smih F, Jasin M (1994) Expression of a site-specific endonuclease stimulates homologous recombination in mammalian cells. Proc Natl Acad Sci U S A 91:6064–6068PubMedPubMedCentralCrossRefGoogle Scholar
  2. 2.
    Rouet P, Smih F, Jasin M (1994) Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease. Mol Cell Biol 14:8096–8106PubMedPubMedCentralCrossRefGoogle Scholar
  3. 3.
    Morton J, Davis MW, Jorgensen EM, Carroll D (2006) Induction and repair of zinc-finger nuclease-targeted double-strand breaks in Caenorhabditis elegans somatic cells. Proc Natl Acad Sci 103:16370–16375PubMedPubMedCentralCrossRefGoogle Scholar
  4. 4.
    Wood AJ, Lo TW, Zeitler B, et al (2011) Targeted genome editing across species using ZFNs and TALENs. Science (80- ) 333:307PubMedPubMedCentralCrossRefGoogle Scholar
  5. 5.
    Beumer KJ, Trautman JK, Bozas A, Liu J-L, Rutter J, Gall JG, Carroll D (2008) Efficient gene targeting in Drosophila by direct embryo injection with zinc-finger nucleases. Proc Natl Acad Sci 105:19821–19826PubMedPubMedCentralCrossRefGoogle Scholar
  6. 6.
    Bibikova M, Golic M, Golic KG, Carroll D (2002) Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases. Genetics 161:1169–1175PubMedPubMedCentralGoogle Scholar
  7. 7.
    Bibikova M, Beumer K, Trautman JK, Carroll D (2003) Enhancing gene targeting with designed zinc finger nucleases. Science (80- ) 300:764PubMedCrossRefPubMedCentralGoogle Scholar
  8. 8.
    Urnov FD, Miller JC, Lee YL, Beausejour CM, Rock JM, Augustus S, Jamieson AC, Porteus MH, Gregory PD, Holmes MC (2005) Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435:646–651PubMedCrossRefPubMedCentralGoogle Scholar
  9. 9.
    Tebas P, Stein D, Tang WW et al (2014) Gene editing of CCR5 in autologous CD4 T cells of persons infected with HIV. N Engl J Med 370:901–910PubMedPubMedCentralCrossRefGoogle Scholar
  10. 10.
    DeKelver RC, Choi VM, Moehle EA et al (2010) Functional genomics, proteomics, and regulatory DNA analysis in isogenic settings using zinc finger nuclease-driven transgenesis into a safe harbor locus in the human genome. Genome Res 20:1133–1142PubMedPubMedCentralCrossRefGoogle Scholar
  11. 11.
    Hockemeyer D, Jaenisch R (2010) Gene targeting in human pluripotent cells. Cold Spring Harb Symp Quant Biol 75:201–209PubMedCrossRefPubMedCentralGoogle Scholar
  12. 12.
    Hockemeyer D, Soldner F, Beard C et al (2009) Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases. Nat Biotechnol 27:851–857PubMedPubMedCentralCrossRefGoogle Scholar
  13. 13.
    Lombardo A, Genovese P, Beausejour CM et al (2007) Gene editing in human stem cells using zinc finger nucleases and integrase-defective lentiviral vector delivery. Nat Biotechnol 25:1298–1306PubMedCrossRefPubMedCentralGoogle Scholar
  14. 14.
    Sexton AN, Regalado SG, Lai CS, Cost GJ, O’Neil CM, Urnov FD, Gregory PD, Jaenisch R, Collins K, Hockemeyer D (2014) Genetic and molecular identification of three human TPP1 functions in telomerase action: recruitment, activation, and homeostasis set point regulation. Genes Dev 28:1885–1899PubMedPubMedCentralCrossRefGoogle Scholar
  15. 15.
    Soldner F, Laganière J, Cheng AW et al (2011) Generation of isogenic pluripotent stem cells differing exclusively at two early onset parkinson point mutations. Cell 146:318–331PubMedPubMedCentralCrossRefGoogle Scholar
  16. 16.
    Zou J, Maeder ML, Mali P et al (2009) Gene targeting of a disease-related gene in human induced pluripotent stem and embryonic stem cells. Cell Stem Cell 5:97–110PubMedPubMedCentralCrossRefGoogle Scholar
  17. 17.
    Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM (2013) RNA-guided human genome engineering via Cas9. Science (80- ) 339:823–826PubMedPubMedCentralCrossRefGoogle Scholar
  18. 18.
    Xue X, Papusha A, Choi K et al (2016) Differential regulation of the anti-crossover and replication fork regression activities of mph1 by mte1. Genes Dev 30:687–699PubMedPubMedCentralCrossRefGoogle Scholar
  19. 19.
    Cong L, Ran FA, Cox D, et al (2013) Multiplex genome engineering using CRISPR/Cas systems. Science (80- ) 339:819–823PubMedPubMedCentralCrossRefGoogle Scholar
  20. 20.
    Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Yang L, Church GM (2013) CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol 31:833–838PubMedPubMedCentralCrossRefGoogle Scholar
  21. 21.
    Wang H, Yang H, Shivalila CS, Dawlaty MM, Cheng AW, Zhang F, Jaenisch R (2013) One-step generation of mice carrying mutations in multiple genes by CRISPR/cas-mediated genome engineering. Cell 153:910–918PubMedPubMedCentralCrossRefGoogle Scholar
  22. 22.
    Jinek M, East A, Cheng A, Lin S, Ma E, Doudna J (2013) RNA-programmed genome editing in human cells. elife 2013:e00471Google Scholar
  23. 23.
    Ding Q, Regan SN, Xia Y, Oostrom LA, Cowan CA, Musunuru K (2013) Enhanced efficiency of human pluripotent stem cell genome editing through replacing TALENs with CRISPRs. Cell Stem Cell 12:393–394PubMedPubMedCentralCrossRefGoogle Scholar
  24. 24.
    Fischer K, Kraner-Scheiber S, Petersen B et al (2016) Efficient production of multi-modified pigs for xenotransplantation by “combineering”, gene stacking and gene editing. Sci Rep 6:29081PubMedPubMedCentralCrossRefGoogle Scholar
  25. 25.
    Grzybek M, Golonko A, Walczak M, Lisowski P (2017) Epigenetics of cell fate reprogramming and its implications for neurological disorders modelling. Neurobiol Dis 99:84–120PubMedCrossRefPubMedCentralGoogle Scholar
  26. 26.
    Hockemeyer D, Jaenisch R (2016) Induced pluripotent stem cells meet genome editing. Cell Stem Cell 18:573–586PubMedPubMedCentralCrossRefGoogle Scholar
  27. 27.
    Yusa K, Rashid ST, Strick-Marchand H et al (2011) Targeted gene correction of α1-antitrypsin deficiency in induced pluripotent stem cells. Nature 478:391–394PubMedPubMedCentralCrossRefGoogle Scholar
  28. 28.
    Chung K, Wallace J, Kim SY et al (2013) Structural and molecular interrogation of intact biological systems. Nature 497:332–337PubMedPubMedCentralCrossRefGoogle Scholar
  29. 29.
    Ambasudhan R, Ryan SD, Dolatabadi N et al (2013) XIsogenic hman iPSC prkinson’s mdel shows ntrosative stress-induced dsfunction in MEF2-PGC1α tanscription. Cell 155:1351–1364PubMedPubMedCentralCrossRefGoogle Scholar
  30. 30.
    Wang Y, Li Y, Toth JI, Petroski MD, Zhang Z, Zhao JC (2014) N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells. Nat Cell Biol 16:191–198PubMedPubMedCentralCrossRefGoogle Scholar
  31. 31.
    Gurumurthy CB, Grati M, Ohtsuka M, Schilit SLP, Quadros RM, Liu XZ (2016) CRISPR: a versatile tool for both forward and reverse genetics research. Hum Genet 135:971–976PubMedPubMedCentralCrossRefGoogle Scholar
  32. 32.
    Mianné J, Chessum L, Kumar S et al (2016) Correction of the auditory phenotype in C57BL/6N mice via CRISPR/Cas9-mediated homology directed repair. Genome Med 8:16PubMedPubMedCentralCrossRefGoogle Scholar
  33. 33.
    Nelson CE, Hakim CH, Ousterout DG, et al (2016) In vivo genome editing improves muscle function in a mouse model of Duchenne muscular dystrophy. Science (80- ) 351:403–407Google Scholar
  34. 34.
    Yang Y, Wang L, Bell P et al (2016) A dual AAV system enables the Cas9-mediated correction of a metabolic liver disease in newborn mice. Nat Biotechnol 34:334–338PubMedPubMedCentralCrossRefGoogle Scholar
  35. 35.
    Platt RJ, Chen S, Zhou Y et al (2014) CRISPR-Cas9 knockin mice for genome editing and cancer modeling. Cell 159:440–455PubMedPubMedCentralCrossRefGoogle Scholar
  36. 36.
    Yoshimi K, Kunihiro Y, Kaneko T, Nagahora H, Voigt B, Mashimo T (2016) SsODN-mediated knock-in with CRISPR-Cas for large genomic regions in zygotes. Nat Commun 7:10431PubMedPubMedCentralCrossRefGoogle Scholar
  37. 37.
    Claussnitzer M, Dankel SN, Kim K-H et al (2015) FTO obesity variant circuitry and adipocyte Browning in humans. N Engl J Med 373:895–907PubMedPubMedCentralCrossRefGoogle Scholar
  38. 38.
    Orack JC, Deleidi M, Pitt D, Mahajan K, Nicholas JA, Boster AL, Racke MK, Comabella M, Watanabe F, Imitola J (2015) Concise review: modeling multiple sclerosis with stem cell biological platforms: toward functional validation of cellular and molecular phenotypes in inflammation-induced neurodegeneration. Stem Cells Transl Med 4:252–260PubMedPubMedCentralCrossRefGoogle Scholar
  39. 39.
    Shin JW, Kim K-H, Chao MJ, Atwal RS, Gillis T, MacDonald ME, Gusella JF, Lee J-M (2016) Permanent inactivation of Huntington’s disease mutation by personalized allele-specific CRISPR/Cas9. Hum Mol Genet 25(20):4566–4576. ddw286PubMedPubMedCentralGoogle Scholar
  40. 40.
    Yang H, Wang H, Shivalila CS, Cheng AW, Shi L, Jaenisch R (2013) XOne-step generation of mice carrying reporter and conditional alleles by CRISPR/cas-mediated genome engineering. Cell 154:1370–1379PubMedPubMedCentralCrossRefGoogle Scholar
  41. 41.
    Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA (2013) Repurposing CRISPR as an RNA-γuided platform for sequence-specific control of gene expression. Cell 152:1173–1183PubMedPubMedCentralCrossRefGoogle Scholar
  42. 42.
    Cheng AW, Wang H, Yang H, Shi L, Katz Y, Theunissen TW, Rangarajan S, Shivalila CS, Dadon DB, Jaenisch R (2013) Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system. Cell Res 23:1163–1171PubMedPubMedCentralCrossRefGoogle Scholar
  43. 43.
    Gilbert LA, Larson MH, Morsut L et al (2013) XCRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell.  https://doi.org/10.1016/j.cell.2013.06.044
  44. 44.
    Maeder ML, Linder SJ, Cascio VM, Fu Y, Ho QH, Joung JK (2013) CRISPR RNA-guided activation of endogenous human genes. Nat Methods 10:977–979PubMedPubMedCentralCrossRefGoogle Scholar
  45. 45.
    Perez-Pinera P, Kocak DD, Vockley CM et al (2013) RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat Methods 10:973–976PubMedPubMedCentralCrossRefGoogle Scholar
  46. 46.
    Tanenbaum ME, Gilbert LA, Qi LS, Weissman JS, Vale RD (2014) A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell 159:635–646PubMedPubMedCentralCrossRefGoogle Scholar
  47. 47.
    Zalatan JG, Lee ME, Almeida R et al (2015) Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160:339–350PubMedCrossRefPubMedCentralGoogle Scholar
  48. 48.
    Chakraborty S, Ji H, Kabadi AM, Gersbach CA, Christoforou N, Leong KW (2014) A CRISPR/Cas9-based system for reprogramming cell lineage specification. Stem Cell Rep 3:940–947CrossRefGoogle Scholar
  49. 49.
    Chen S, Sanjana NE, Zheng K et al (2015) Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis. Cell 160:1246–1260PubMedPubMedCentralCrossRefGoogle Scholar
  50. 50.
    Peng J, Zhou Y, Zhu S, Wei W (2015) High-throughput screens in mammalian cells using the CRISPR-Cas9 system. FEBS J 282:2089–2096PubMedCrossRefGoogle Scholar
  51. 51.
    Shen B, Zhang J, Wu H, Wang J, Ma K, Li Z, Zhang X, Zhang P, Huang X (2013) Generation of gene-modified mice via Cas9/RNA-mediated gene targeting. Cell Res 23:720–723PubMedPubMedCentralCrossRefGoogle Scholar
  52. 52.
    Wang T, Wei JJ, Sabatini DM, Lander ES (2014) Genetic screens in human cells using the CRISPR-Cas9 system. Science (80- ) 343:80–84PubMedPubMedCentralCrossRefGoogle Scholar
  53. 53.
    Zhou Y, Zhu S, Cai C, Yuan P, Li C, Huang Y, Wei W (2014) High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells. Nature 509:487–491PubMedCrossRefPubMedCentralGoogle Scholar
  54. 54.
    Wang X, Wang Y, Wu X, Wang J, Wang Y, Qiu Z, Chang T, Huang H, Lin RJ, Yee JK (2015) Unbiased detection of off-target cleavage by CRISPR-Cas9 and TALENs using integrase-defective lentiviral vectors. Nat Biotechnol 33:175–179PubMedCrossRefPubMedCentralGoogle Scholar
  55. 55.
    Tsai SQ, Zheng Z, Nguyen NT et al (2015) GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol 33:187–198PubMedCrossRefPubMedCentralGoogle Scholar
  56. 56.
    Haeussler M, Schönig K, Eckert H et al (2016) Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol 17:148PubMedPubMedCentralCrossRefGoogle Scholar
  57. 57.
    Hsu PD, Scott DA, Weinstein JA et al (2013) DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol 31:827–832PubMedPubMedCentralCrossRefGoogle Scholar
  58. 58.
    Bolukbasi MF, Gupta A, Wolfe SA (2015) Creating and evaluating accurate CRISPR-Cas9 scalpels for genomic surgery. Nat Methods 13:41–50CrossRefGoogle Scholar
  59. 59.
    Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F (2013) Genome engineering using the CRISPR-Cas9 system. Nat Protoc 8:2281–2308PubMedPubMedCentralCrossRefGoogle Scholar
  60. 60.
    Anders C, Niewoehner O, Duerst A, Jinek M (2014) Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature 513:569–573PubMedPubMedCentralCrossRefGoogle Scholar
  61. 61.
    Slaymaker IM, Gao L, Zetsche B, Scott DA, Yan WX, Zhang F (2016) Rationally engineered Cas9 nucleases with improved specificity. Science (80- ) 351:84–88PubMedPubMedCentralCrossRefGoogle Scholar
  62. 62.
    Kleinstiver BP, Pattanayak V, Prew MS, Tsai SQ, Nguyen NT, Zheng Z, Joung JK (2016) High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. Nature 529:490–495PubMedPubMedCentralCrossRefGoogle Scholar
  63. 63.
    Müller M, Lee CM, Gasiunas G, Davis TH, Cradick TJ, Siksnys V, Bao G, Cathomen T, Mussolino C (2016) Streptococcus thermophilus CRISPR-Cas9 systems enable specific editing of the human genome. Mol Ther 24:636–644PubMedPubMedCentralCrossRefGoogle Scholar
  64. 64.
    Fonfara I, Le Rhun A, Chylinski K, Makarova KS, Lécrivain AL, Bzdrenga J, Koonin EV, Charpentier E (2014) Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems. Nucleic Acids Res 42:2577–2590PubMedCrossRefPubMedCentralGoogle Scholar
  65. 65.
    Zetsche B, Gootenberg JS, Abudayyeh OO et al (2015) Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163:759–771PubMedPubMedCentralCrossRefGoogle Scholar
  66. 66.
    Fonfara I, Richter H, BratoviÄ M, Le Rhun A, Charpentier E (2016) The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA. Nature 532:517–521PubMedCrossRefGoogle Scholar
  67. 67.
    Kleinstiver BP, Prew MS, Tsai SQ et al (2015) Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature 523:481–485PubMedPubMedCentralCrossRefGoogle Scholar
  68. 68.
    Hirano S, Nishimasu H, Ishitani R, Nureki O (2016) Structural basis for the altered PAM specificities of engineered CRISPR-Cas9. Mol Cell 61:886–894PubMedCrossRefGoogle Scholar
  69. 69.
    González F, Zhu Z, Shi ZD, Lelli K, Verma N, Li QV, Huangfu D (2014) An iCRISPR platform for rapid, multiplexable, and inducible genome editing in human pluripotent stem cells. Cell Stem Cell 15:215–226PubMedPubMedCentralCrossRefGoogle Scholar
  70. 70.
    DeWitt MA, Corn JE, Carroll D (2017) Genome editing via delivery of Cas9 ribonucleoprotein. Methods 121–122:9–15PubMedCrossRefPubMedCentralGoogle Scholar
  71. 71.
    Lin S, Staahl BT, Alla RK, Doudna JA (2014) Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery. elife 3:e04766PubMedPubMedCentralCrossRefGoogle Scholar
  72. 72.
    Richardson CD, Ray GJ, DeWitt MA, Curie GL, Corn JE (2016) Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA. Nat Biotechnol 34:339–344PubMedCrossRefPubMedCentralGoogle Scholar
  73. 73.
    Yumlu S, Stumm J, Bashir S, Dreyer AK, Lisowski P, Danner E, Kühn R (2017) Gene editing and clonal isolation of human induced pluripotent stem cells using CRISPR/Cas9. Methods 121–122:29–44PubMedCrossRefPubMedCentralGoogle Scholar
  74. 74.
    Yang L, Guell M, Byrne S et al (2013) Optimization of scarless human stem cell genome editing. Nucleic Acids Res 41:9049–9061PubMedPubMedCentralCrossRefGoogle Scholar
  75. 75.
    Dahlem TJ, Hoshijima K, Jurynec MJ, Gunther D, Starker CG, Locke AS, Weis AM, Voytas DF, Grunwald DJ (2012) Simple methods for generating and detecting locus-specific mutations induced with TALENs in the zebrafish genome. PLoS Genet 8:e1002861PubMedPubMedCentralCrossRefGoogle Scholar
  76. 76.
    Brinkman EK, Chen T, Amendola M, Van Steensel B (2014) Easy quantitative assessment of genome editing by sequence trace decomposition. Nucleic Acids Res  https://doi.org/10.1093/nar/gku936 PubMedPubMedCentralCrossRefGoogle Scholar
  77. 77.
    Hill JT, Demarest BL, Bisgrove BW, Su YC, Smith M, Yost HJ (2014) Poly peak parser: method and software for identification of unknown indels using sanger sequencing of polymerase chain reaction products. Dev Dyn 243:1632–1636PubMedPubMedCentralCrossRefGoogle Scholar
  78. 78.
    Dehairs J, Talebi A, Cherifi Y, Swinnen JV (2016) CRISP-ID: decoding CRISPR mediated indels by Sanger sequencing. Sci Rep 6:28973PubMedPubMedCentralCrossRefGoogle Scholar
  79. 79.
    Pinello L, Canver MC, Hoban MD, Orkin SH, Kohn DB, Bauer DE, Yuan G-C (2016) Analyzing CRISPR genome-editing experiments with CRISPResso. Nat Biotechnol 34:695–697PubMedPubMedCentralCrossRefGoogle Scholar
  80. 80.
    Boel A, Steyaert W, De Rocker N, Menten B, Callewaert B, De Paepe A, Coucke P, Willaert A (2016) BATCH-GE: Batch analysis of next-generation sequencing data for genome editing assessment. Sci Rep 6:30330PubMedPubMedCentralCrossRefGoogle Scholar
  81. 81.
    Dodgson JB, Wells RD (1977) Action of single-strand specific nucleases on model DNA Heteroduplexes of defined size and sequence. Biochemistry 16:2374–2379PubMedCrossRefPubMedCentralGoogle Scholar
  82. 82.
    Bhattacharyya A, Lilley DMJ (1989) The contrasting structures of mismatched DNA sequences containing looped-out bases (bulges) and multiple mismatches (bubbles). Nucleic Acids Res 17:6821–6840PubMedPubMedCentralCrossRefGoogle Scholar
  83. 83.
    Wagner R, Debbie P, Radman M (1995) Mutation detection using immobilized mismatch binding protein (MutS). Nucleic Acids Res 23:3944–3948PubMedPubMedCentralCrossRefGoogle Scholar
  84. 84.
    Youil R, Kemper BW, Cotton RG (1995) Screening for mutations by enzyme mismatch cleavage with T4 endonuclease VII. Proc Natl Acad Sci U S A 92:87–91PubMedPubMedCentralCrossRefGoogle Scholar
  85. 85.
    Howard JT, Ward J, Watson JN, Roux KH (1999) Heteroduplex cleavage analysis using S1 nuclease. BioTechniques 27:18–19PubMedPubMedCentralCrossRefGoogle Scholar
  86. 86.
    Taylor GR, Deeble J (1999) Enzymatic methods for mutation scanning. Genet Anal Biomol Eng 14:181–186CrossRefGoogle Scholar
  87. 87.
    Yeung AT, Hattangadi D, Blakesley L, Nicolas E (2005) Enzymatic mutation detection technologies. BioTechniques 38:749–758PubMedCrossRefPubMedCentralGoogle Scholar
  88. 88.
    Babon JJ, Youil R, Cotton RGH (1995) Improved strategy for mutation detection – a modification to the enzyme mismatch cleavage method. Nucleic Acids Res 23:5082–5084PubMedPubMedCentralCrossRefGoogle Scholar
  89. 89.
    Hadden JM, Déclais AC, Carr SB, Lilley DMJ, Phillips SEV (2007) The structural basis of Holliday junction resolution by T7 endonuclease I. Nature 449:621–624PubMedCrossRefPubMedCentralGoogle Scholar
  90. 90.
    Freeman ADJ, Déclais AC, Lilley DMJ (2013) The importance of the N-terminus of T7 endonuclease i in the interaction with DNA junctions. J Mol Biol 425:395–410PubMedCrossRefPubMedCentralGoogle Scholar
  91. 91.
    Déclais AC, Lilley DM (2008) New insight into the recognition of branched DNA structure by junction-resolving enzymes. Curr Opin Struct Biol 18:86–95PubMedCrossRefPubMedCentralGoogle Scholar
  92. 92.
    Mashal RD, Koontz J, Sklar J (1995) Detection of mutations by cleavage of DNA heteroduplexes with bacteriophage resolvases. Nat Genet 9:177–183PubMedCrossRefPubMedCentralGoogle Scholar
  93. 93.
    Déclais AC, Liu J, Freeman ADJ, Lilley DMJ (2006) Structural recognition between a four-way DNA junction and a resolving enzyme. J Mol Biol 359:1261–1276PubMedCrossRefPubMedCentralGoogle Scholar
  94. 94.
    Gohlke C, Murchie AI, Lilley DM, Clegg RM (1994) Kinking of DNA and RNA helices by bulged nucleotides observed by fluorescence resonance energy transfer. Proc Natl Acad Sci U S A 91:11660–11664PubMedPubMedCentralCrossRefGoogle Scholar
  95. 95.
    Oleykowski CA, Bronson Mullins CR, Godwin AK, Yeung AT (1998) Mutation detection using a novel plant endonuclease. Nucleic Acids Res 26:4597–4602PubMedPubMedCentralCrossRefGoogle Scholar
  96. 96.
    Yang B, Wen X, Kodali NS, Oleykowski CA, Miller CG, Kulinski J, Besack D, Yeung JA, Kowalski D, Yeung AT (2000) Purification, cloning, and characterization of the CEL I nuclease. Biochemistry 39:3533–3541PubMedCrossRefPubMedCentralGoogle Scholar
  97. 97.
    Qiu P, Shandilya H, D’Alessio JM, O’Connor K, Durocher J, Gerard GF (2004) Mutation detection using Surveyor™ nuclease. BioTechniques 36:702–707PubMedCrossRefPubMedCentralGoogle Scholar
  98. 98.
    Voskarides K, Deltas C (2009) Screening for mutations in kidney-related genes using SURVEYOR nuclease for cleavage at heteroduplex mismatches. J Mol Diagn 11:311–318PubMedPubMedCentralCrossRefGoogle Scholar
  99. 99.
    Till BJ, Burtner C, Comai L, Henikoff S (2004) Mismatch cleavage by single-strand specific nucleases. Nucleic Acids Res 32:2632–2641PubMedPubMedCentralCrossRefGoogle Scholar
  100. 100.
    Bentley A, Maclennan B, Calvo J, Dearolf CR (2000) Targeted recovery of mutations in drosophila. Genetics 156:1169–1173PubMedPubMedCentralGoogle Scholar
  101. 101.
    Colbert T (2001) High-throughput screening for induced point mutations. Plant Physiol 126:480–484PubMedPubMedCentralCrossRefGoogle Scholar
  102. 102.
    Coghill EL, Hugill A, Parkinson N, Davison C, Glenister P, Clements S, Hunter J, Cox RD, Brown SDM (2002) A gene-driven approach to the identification of ENU mutants in the mouse. Nat Genet 30:255–256PubMedCrossRefPubMedCentralGoogle Scholar
  103. 103.
    Perry JA (2003) A TILLING reverse genetics tool and a web-accessible collection of mutants of the legume Lotus japonicus. Plant Physiol 131:866–871PubMedPubMedCentralCrossRefGoogle Scholar
  104. 104.
    Wienholds E, van Eeden F, Kosters M, Mudde J, Plasterk RHA, Cuppen E (2003) Efficient target-selected mutagenesis in zebrafish. Genome Res 13:2700–2707PubMedPubMedCentralCrossRefGoogle Scholar
  105. 105.
    Comai L, Young K, Till BJ et al (2004) Efficient discovery of DNA polymorphisms in natural populations by Ecotilling. Plant J 37:778–786PubMedCrossRefPubMedCentralGoogle Scholar
  106. 106.
    Slade AJ, Fuerstenberg SI, Loeffler D, Steine MN, Facciotti D (2005) A reverse genetic, nontransgenic approach to wheat crop improvement by TILLING. Nat Biotechnol 23:75–81PubMedCrossRefPubMedCentralGoogle Scholar
  107. 107.
    Geurts AM, Cost GJ, Freyvert Y, et al (2009) Knockout rats via embryo microinjection of zinc-finger nucleases. Science (80- ) 325:433Google Scholar
  108. 108.
    Guschin DY, Waite AJ, Katibah GE, Miller JC, Holmes MC, Rebar EJ (2010) A rapid and general assay for monitoring endogenous gene modification. Methods Mol Biol 649:247–256PubMedCrossRefPubMedCentralGoogle Scholar
  109. 109.
    Miller JC, Tan S, Qiao G et al (2011) A TALE nuclease architecture for efficient genome editing. Nat Biotechnol 29:143–150PubMedCrossRefPubMedCentralGoogle Scholar
  110. 110.
    Tesson L, Usal C, Meq́noret S et al (2011) Knockout rats generated by embryo microinjection of TALENs. Nat Biotechnol 29:695–696PubMedCrossRefPubMedCentralGoogle Scholar
  111. 111.
    Isalan M (2012) Zinc-finger nucleases: how to play two good hands. Nat Methods 9:32–34CrossRefGoogle Scholar
  112. 112.
    Sanjana NE, Cong L, Zhou Y, Cunniff MM, Feng G, Zhang F (2012) A transcription activator-like effector toolbox for genome engineering. Nat Protoc 7:171–192PubMedPubMedCentralCrossRefGoogle Scholar
  113. 113.
    Holkers M, Maggio I, Liu J, Janssen JM, Miselli F, Mussolino C, Recchia A, Cathomen T, Gonçalves MAFV (2013) Differential integrity of TALE nuclease genes following adenoviral and lentiviral vector gene transfer into human cells. Nucleic Acids Res 41:e63PubMedCrossRefPubMedCentralGoogle Scholar
  114. 114.
    Maier DA, Brennan AL, Jiang S et al (2013) Efficient clinical scale gene modification via zinc finger nuclease–targeted disruption of the HIV co-receptor CCR5. Hum Gene Ther 24:245–258PubMedPubMedCentralCrossRefGoogle Scholar
  115. 115.
    Van Rensburg R, Beyer I, Yao XY et al (2013) Chromatin structure of two genomic sites for targeted transgene integration in induced pluripotent stem cells and hematopoietic stem cells. Gene Ther 20:201–214PubMedCrossRefGoogle Scholar
  116. 116.
    Vouillot L, Thélie A, Pollet N (2015) Comparison of T7E1 and Surveyor mismatch cleavage assays to detect mutations triggered by engineered nucleases. G3: Genes|Genomes|Genetics 5:407–415PubMedPubMedCentralCrossRefGoogle Scholar
  117. 117.
    Gibson DG (2011) Enzymatic assembly of overlapping DNA fragments. Methods Enzymol 498:349–361PubMedCrossRefPubMedCentralGoogle Scholar
  118. 118.
    Merkle FT, Eggan K (2013) Modeling human disease with pluripotent stem cells: from genome association to function. Cell Stem Cell 12:656–668PubMedCrossRefPubMedCentralGoogle Scholar
  119. 119.
    Soldner F, Jaenisch R (2012) iPSC disease modeling. Science (80- ) 338:1155–1156PubMedCrossRefPubMedCentralGoogle Scholar
  120. 120.
    Soldner F, Stelzer Y, Shivalila CS, Abraham BJ, Latourelle JC, Barrasa MI, Goldmann J, Myers RH, Young RA, Jaenisch R (2016) Parkinson-associated risk variant in distal enhancer of α-synuclein modulates target gene expression. Nature 533:95–99PubMedPubMedCentralCrossRefGoogle Scholar
  121. 121.
    Collins FS, Lander ES, Rogers J, Waterson RH (2004) Finishing the euchromatic sequence of the human genome. Nature 431:931–945CrossRefGoogle Scholar
  122. 122.
    Auton A, Abecasis GR, Altshuler DM et al (2015) A global reference for human genetic variation. Nature 526:68–74PubMedCrossRefPubMedCentralGoogle Scholar
  123. 123.
    Dewey FE, Grove ME, Pan C et al (2014) Clinical interpretation and implications of whole-genome sequencing. JAMA J Am Med Assoc 311:1035–1044CrossRefGoogle Scholar
  124. 124.
    Mangino M, Cecelja M, Menni C, Tsai PC, Yuan W, Small K, Bell J, Mitchell GF, Chowienczyk P, Spector TD (2016) Integrated multiomics approach identifies calcium and integrin-binding protein-2 as a novel gene for pulse wave velocity. J Hypertens 34:79–87PubMedCrossRefPubMedCentralGoogle Scholar
  125. 125.
    Gerstung M, Pellagatti A, Malcovati L et al (2015) Combining gene mutation with gene expression data improves outcome prediction in myelodysplastic syndromes. Nat Commun 6:5901PubMedPubMedCentralCrossRefGoogle Scholar
  126. 126.
    Saykin AJ, Shen L, Yao X et al (2015) Genetic studies of quantitative MCI and AD phenotypes in ADNI: progress, opportunities, and plans. Alzheimers Dement 11:792–814PubMedPubMedCentralCrossRefGoogle Scholar
  127. 127.
    Shiraishi Y, Fujimoto A, Furuta M et al (2014) Integrated analysis of whole genome and transcriptome sequencing reveals diverse transcriptomic aberrations driven by somatic genomic changes in liver cancers. PLoS One 9:e114263PubMedPubMedCentralCrossRefGoogle Scholar
  128. 128.
    Piskol R, Ramaswami G, Li JB (2013) Reliable identification of genomic variants from RNA-seq data. Am J Hum Genet 93:641–651PubMedPubMedCentralCrossRefGoogle Scholar
  129. 129.
    Bell S, Peng H, Crapper L, Kolobova I, Maussion G, Vasuta C, Yerko V, Pan Wong T, Ernst C (2017) A rapid pipeline to model rare neurodevelopmental disorders with simultaneous CRISPR/Cas9 gene editing. Stem Cells Transl Med 6:886–896PubMedCrossRefPubMedCentralGoogle Scholar
  130. 130.
    Zhu Z, González F, Huangfu D (2014) The iCRISPR platform for rapid genome editing in human pluripotent stem cells. Methods Enzymol 546:215–250PubMedPubMedCentralCrossRefGoogle Scholar
  131. 131.
    Studer L, Vera E, Cornacchia D (2015) Programming and reprogramming cellular age in the era of induced pluripotency. Cell Stem Cell 16:591–600PubMedPubMedCentralCrossRefGoogle Scholar
  132. 132.
    Miller JD, Ganat YM, Kishinevsky S et al (2013) Human iPSC-based modeling of late-onset disease via progerin-induced aging. Cell Stem Cell 13:691–705PubMedPubMedCentralCrossRefGoogle Scholar
  133. 133.
    Byers B, Cord B, Nguyen HN, Schüle B, Fenno L, Lee PC, Deisseroth K, Langston JW, Pera RR, Palmer TD (2011) SNCA triplication parkinson’s patient’s iPSC-derived DA neurons accumulate α-Synuclein and are susceptible to oxidative stress. PLoS One 6:e26159PubMedPubMedCentralCrossRefGoogle Scholar
  134. 134.
    Cooper O, Seo H, Andrabi S et al (2012) Pharmacological rescue of mitochondrial deficits in iPSC-derived neural cells from patients with familial Parkinson’s disease. Sci Transl Med 4:141ra90PubMedPubMedCentralCrossRefGoogle Scholar
  135. 135.
    Liu GH, Ding Z, Izpisua Belmonte JC (2012) IPSC technology to study human aging and aging-related disorders. Curr Opin Cell Biol 24:765–774PubMedCrossRefPubMedCentralGoogle Scholar
  136. 136.
    Nguyen HN, Byers B, Cord B et al (2011) LRRK2 mutant iPSC-derived da neurons demonstrate increased susceptibility to oxidative stress. Cell Stem Cell 8:267–280PubMedPubMedCentralCrossRefGoogle Scholar
  137. 137.
    Reinhardt P, Schmid B, Burbulla LF et al (2013) Genetic correction of a lrrk2 mutation in human iPSCs links parkinsonian neurodegeneration to ERK-dependent changes in gene expression. Cell Stem Cell 12:354–367CrossRefPubMedGoogle Scholar
  138. 138.
    Seibler P, Graziotto J, Jeong H, Simunovic F, Klein C, Krainc D (2011) Mitochondrial Parkin recruitment is impaired in neurons derived from mutant PINK1 induced pluripotent stem cells. J Neurosci 31:5970–5976PubMedPubMedCentralCrossRefGoogle Scholar
  139. 139.
    Young SG, Jung H-J, Lee JM, Fong LG (2014) Nuclear Lamins and neurobiology. Mol Cell Biol 34:2776–2785PubMedPubMedCentralCrossRefGoogle Scholar
  140. 140.
    Baek JH, Schmidt E, Viceconte N et al (2015) Expression of progerin in aging mouse brains reveals structural nuclear abnormalities without detectible significant alterations in gene expression, hippocampal stem cells or behavior. Hum Mol Genet 24:1305–1321PubMedCrossRefPubMedCentralGoogle Scholar
  141. 141.
    Longo VD, Antebi A, Bartke A et al (2015) Interventions to slow aging in humans: are we ready? Aging Cell 14:497–510PubMedPubMedCentralCrossRefGoogle Scholar
  142. 142.
    Huang Y, Myers SJ, Dingledine R (1999) Transcriptional repression by REST: recruitment of Sin3A and histone deacetylase to neuronal genes. Nat Neurosci 2:867–872PubMedCrossRefGoogle Scholar
  143. 143.
    Lu T, Aron L, Zullo J et al (2014) REST and stress resistance in ageing and Alzheimer’s disease. Nature 507:448–454PubMedPubMedCentralCrossRefGoogle Scholar
  144. 144.
    Hitz C, Steuber-Buchberger P, Delic S, Wurst W, Kühn R (2009) Generation of shrna transgenic mice. Methods Mol Biol 530:101–129PubMedCrossRefPubMedCentralGoogle Scholar
  145. 145.
    Renaud JB, Boix C, Charpentier M et al (2016) Improved genome editing efficiency and flexibility using modified oligonucleotides with TALEN and CRISPR-Cas9 nucleases. Cell Rep 14:2263–2272PubMedCrossRefGoogle Scholar
  146. 146.
    Heyer W-D, Ehmsen KT, Liu J (2010) Regulation of homologous recombination in eukaryotes. Annu Rev Genet 44:113–139PubMedPubMedCentralCrossRefGoogle Scholar
  147. 147.
    Sfeir A, De Lange T (2012) Removal of shelterin reveals the telomere end-protection problem. Science (80- ) 336:593–597PubMedPubMedCentralCrossRefGoogle Scholar
  148. 148.
    Hustedt N, Durocher D (2017) The control of DNA repair by the cell cycle. Nat Cell Biol 19:1–9CrossRefGoogle Scholar
  149. 149.
    Corneo B, Wendland RL, Deriano L et al (2007) Rag mutations reveal robust alternative end joining. Nature 449:483–486PubMedCrossRefPubMedCentralGoogle Scholar
  150. 150.
    Deriano L, Roth DB (2013) Modernizing the nonhomologous end-joining repertoire: alternative and classical NHEJ share the stage. Annu Rev Genet 47:433–455PubMedCrossRefGoogle Scholar
  151. 151.
    Badie S, Carlos AR, Folio C, Okamoto K, Bouwman P, Jonkers J, Tarsounas M (2015) BRCA1 and CtIP promote alternative non-homologous end-joining at uncapped telomeres. EMBO J 34:828–828PubMedPubMedCentralCrossRefGoogle Scholar
  152. 152.
    San Filippo J, Sung P, Klein H (2008) Mechanism of eukaryotic homologous recombination. Annu Rev Biochem 77:229–257PubMedCrossRefGoogle Scholar
  153. 153.
    Sfeir A, Symington LS (2015) Microhomology-mediated end joining: a back-up survival mechanism or dedicated pathway? Trends Biochem Sci 40:701–714PubMedPubMedCentralCrossRefGoogle Scholar
  154. 154.
    Sakuma T, Nakade S, Sakane Y, Suzuki KIT, Yamamoto T (2016) MMEJ-assisted gene knock-in using TALENs and CRISPR-Cas9 with the PITCh systems. Nat Protoc 11:118–133PubMedCrossRefPubMedCentralGoogle Scholar
  155. 155.
    He X, Tan C, Wang F, Wang Y, Zhou R, Cui D, You W, Zhao H, Ren J, Feng B (2016) Knock-in of large reporter genes in human cells via CRISPR/Cas9-induced homology-dependent and independent DNA repair. Nucleic Acids Res 44:e85–e85PubMedPubMedCentralCrossRefGoogle Scholar
  156. 156.
    Suzuki K, Tsunekawa Y, Hernandez-Benitez R et al (2016) In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration. Nature 540:144–149PubMedPubMedCentralCrossRefGoogle Scholar
  157. 157.
    Danner E, Bashir S, Yumlu S, Wurst W, Wefers B, Kühn R (2017) Control of gene editing by manipulation of DNA repair mechanisms. Mamm Genome 28:262–274PubMedCrossRefPubMedCentralGoogle Scholar
  158. 158.
    Suzuki K, Izpisua Belmonte JC (2018) In vivo genome editing via the HITI method as a tool for gene therapy. J Hum Genet 63:157–164PubMedCrossRefPubMedCentralGoogle Scholar
  159. 159.
    Srivastava M, Nambiar M, Sharma S et al (2012) An inhibitor of nonhomologous end-joining abrogates double-strand break repair and impedes cancer progression. Cell 151:1474–1487PubMedCrossRefPubMedCentralGoogle Scholar
  160. 160.
    Maruyama T, Dougan SK, Truttmann MC, Bilate AM, Ingram JR, Ploegh HL (2015) Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining. Nat Biotechnol 33:538–542PubMedPubMedCentralCrossRefGoogle Scholar
  161. 161.
    Chu VT, Weber T, Wefers B, Wurst W, Sander S, Rajewsky K, Kühn R (2015) Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells. Nat Biotechnol 33:543–548PubMedCrossRefPubMedCentralGoogle Scholar
  162. 162.
    Greco GE, Matsumoto Y, Brooks RC, Lu Z, Lieber MR, Tomkinson AE (2016) SCR7 is neither a selective nor a potent inhibitor of human DNA ligase IV. DNA Repair (Amst) 43:18–23CrossRefGoogle Scholar
  163. 163.
    Menchon G, Bombarde O, Trivedi M et al (2016) Structure-based virtual ligand screening on the XRCC4/DNA ligase IV Interface. Sci Rep 6:22878PubMedPubMedCentralCrossRefGoogle Scholar
  164. 164.
    Robert F, Barbeau M, Éthier S, Dostie J, Pelletier J (2015) Pharmacological inhibition of DNA-PK stimulates Cas9-mediated genome editing. Genome Med 7:93PubMedPubMedCentralCrossRefGoogle Scholar
  165. 165.
    Byrum J, Jordan S, Safrany ST, Rodgers W (2004) Visualization of inositol phosphate-dependent mobility of Ku: depletion of the DNA-PK cofactor InsP6 inhibits Ku mobility. Nucleic Acids Res 32:2776–2784PubMedPubMedCentralCrossRefGoogle Scholar
  166. 166.
    Arras SDM, Fraser JA (2016) Chemical inhibitors of non-homologous end joining increase targeted construct integration in cryptococcus neoformans. PLoS One 11:e0163049PubMedPubMedCentralCrossRefGoogle Scholar
  167. 167.
    Tang J, Cho NW, Cui G, Manion EM, Shanbhag NM, Botuyan MV, Mer G, Greenberg RA (2013) Acetylation limits 53BP1 association with damaged chromatin to promote homologous recombination. Nat Struct Mol Biol 20:317–325PubMedPubMedCentralCrossRefGoogle Scholar
  168. 168.
    Xie A, Hartlerode A, Stucki M et al (2007) Distinct roles of chromatin-associated proteins MDC1 and 53BP1 in mammalian double-strand break repair. Mol Cell 28:1045–1057PubMedPubMedCentralCrossRefGoogle Scholar
  169. 169.
    Yoo E, Kim BU, Seung YL, Chae HC, Chung JH, Lee CH (2005) 53BP1 is associated with replication protein a and is required for RPA2 hyperphosphorylation following DNA damage. Oncogene 24:5423–5430PubMedCrossRefPubMedCentralGoogle Scholar
  170. 170.
    Orthwein A, Noordermeer SM, Wilson MD et al (2015) A mechanism for the suppression of homologous recombination in G1 cells. Nature 528:422–426PubMedPubMedCentralCrossRefGoogle Scholar
  171. 171.
    Shrivastav M, De Haro LP, Nickoloff JA (2008) Regulation of DNA double-strand break repair pathway choice. Cell Res 18:134–147PubMedCrossRefPubMedCentralGoogle Scholar
  172. 172.
    Bashir S, Kühn R (2017) Enhanced precision and efficiency. Nat Biomed Eng 1:856–857CrossRefGoogle Scholar
  173. 173.
    Paulsen BS, Mandal PK, Frock RL et al (2017) Ectopic expression of RAD52 and dn53BP1 improves homology-directed repair during CRISPR-Cas9 genome editing. Nat Biomed Eng 1:878–888CrossRefGoogle Scholar
  174. 174.
    Richardson CD, Kazane KR, Feng SJ, Bray NL, Schaefer AJ, Floor S, Corn J (2017) CRISPR-Cas9 genome editing in human cells works via The Fanconi Anemia Pathway. DoiOrg 136028Google Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Molecular BiologyInstitute of Genetics and Animal Breeding, Polish Academy of SciencesJastrzebiec, MagdalenkaPoland
  2. 2.Department of Medical GeneticsCentre for Preclinical Research and Technology (CePT), Warsaw Medical UniversityWarsawPoland
  3. 3.Mitochondria and Cell Fate Reprogramming Group, Department of Proteomics and Molecular Mechanisms of Neurodegenerative DiseasesMax Delbrück Center for Molecular Medicine (MDC) in the Helmholtz AssociationBerlinGermany

Personalised recommendations