Genes & CellsGenes & CellsГены и КлеткиGenes and Cells2313-18292500-2562Human Stem Cells Institute12055510.23868/gc120555ArticlesСтатьиReview ArticleApplication of CRISPR/Cas9 system for developing and studying cellular models of inherited diseaseПРИМЕНЕНИЕ СИСТЕМЫ CRISPR/Cas9 ДЛЯ СОЗДАНИЯ И ИССЛЕДОВАНИЯ КЛЕТОЧНЫХ МОДЕЛЕЙ НАСЛЕДСТВЕННЫХ ЗАБОЛЕВАНИЙ ЧЕЛОВЕКАValetdinovaK. RВалетдиноваК. Рvaletdinova@bionet.nsc.ruFederal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of SciencesФГБНУ «Федеральный исследовательский центр Институт цитологии и генетики СО РАН»Institute of Chemical Biology and Fundamental Medicine, the Siberian Branch of the Russian Academy of SciencesФГБНУ «Институт химической биологии и фундаментальной медицины СО РАН»State Research Institute of Circulation Pathology, Ministry of Healthcare of the Russian FederationФГБУ «Новосибирский научно-исследовательский институт патологии кровообращения имени академика Е.Н. Мешалкина» Министерства здравоохранения РФ15062016112VOL 11, NO2 (2016)ТОМ 11, №2 (2016)102005012023Copyright ©; 2016, Eco-VectorCopyright ©; 2016, Эко-Вектор2016Eco-VectorЭко-Векторhttps://genescells.ru/2313-1829/article/view/120555

Currently, more than 4500 diseases classified as an inherited diseases. Most forms of human inherited diseases are caused by gene mutations. Given to the development of new methods genome editing, particularly with the use of CRISPR/Cas9 system, it is possible to artificially introduce precise mutations in the genome, as well as to correct gene mutations. It is thus possible to create a cellular model of human inherited diseases, as well as to carry out experiments for testing hypotheses and principles of gene and cell therapy. In this review, we consider studies that provide insight into the possibilities of CRISPR/Cas9 system for developing and studying cellular models of human inherited diseases.

В настоящее время более 4500 заболеваний классифицируется как наследственные. Большинство форм наследственных заболеваний человека обусловлены генными мутациями. Благодаря развитию новых способов манипуляции с геномами, в частности с использованием системы CRISPR/Cas9, появилась возможность искусственно вводить ту или иную мутацию в геном исследуемого объекта, а также исправлять генные мутации. Тем самым можно создавать клеточные модели наследственных болезней человека, а также проводить эксперименты по проверке гипотез и принципов генной и клеточной терапии. В обзоре рассмотрены наиболее интересные примеры исследований, которые дают представление о возможностях и перспективах применения системы CRISPR/Cas9 для создания и исследования клеточных моделей наследственных заболеваний человека.

CRISPR/Cas9CRISPR/Cas9inherited diseasescellular modelpluripotent stem cellsнаследственные заболеванияклеточная модельплюрипотентные стволовые клеткиFreedman B.S., Brooks C.R., Lam A.Q. et al. Modelling kidney disease with CRISPR-mutant kidney organoids derived from human pluripotent epiblast spheroids. Nat. Commun. 2015; 6: 8715.Wang P., Lin M., Pedrosa E. et al. CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in neurodevelopment. Mol. Autism. 2015; 6: 55.Zhang J., Lian Q., Zhu G. et al. A human iPSC model of Hutchinson Gilford Progeria reveals vascular smooth muscle and mesenchymal stem cell defects. Cell Stem Cell 2011; 8(1): 31-45.Yung S.K., Tilgner K., Ledran M.H. et al. Brief report: human pluripotent stem cell models of fanconi anemia deficiency reveal an important role for fanconi anemia proteins in cellular reprogramming and survival of hematopoietic progenitors. Stem Cells 2013; 31(5): 1022-9.Tse H.F., Ho J.C., Choi S.W. et al. Patient-specific induced-pluripotent stem cells-derived cardiomyocytes recapitulate the pathogenic phenotypes of dilated cardiomyopathy due to a novel DES mutation identified by whole exome sequencing. Hum. Mol. Genet. 2013; 22(7): 1395-403.Barrangou R., Fremaux C., Deveau H., et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 2007; 315(5819): 1709-12.Makarova K.S., Haft D.H., Barrangou R. et al. Evolution and classification of the CRISPR-Cas systems. Nat. Rev. Microbiol. 2011; 9(6): 467-77.Jinek M., Chylinski K., Fonfara I. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 2012; 337(6096): 816-21.Cong L., Ran F.A., Cox D. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 2013; 339(6121): 819-23.Tse H.F., Ho J.C., Choi S.W. et al. Patient-specific induced-pluripotent stem cells-derived cardiomyocytes recapitulate the pathogenic phenotypes of dilated cardiomyopathy due to a novel DES mutation identified by whole exome sequencing. Hum. Mol. Genet. 2013; 22(7): 1395-403.Barrangou R., Fremaux C., Deveau H., et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 2007; 315(5819): 1709-12.Makarova K.S., Haft D.H., Barrangou R. et al. Evolution and classification of the CRISPR-Cas systems. Nat. Rev. Microbiol. 2011; 9(6): 467-77.Jinek M., Chylinski K., Fonfara I. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 2012; 337(6096): 816-21.Cong L., Ran F.A., Cox D. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 2013; 339(6121): 819-23.Doudna J.A., Charpentier E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 2014; 346(6213): 1258096.Nemudryi A.A., Valetdinova K.R., Medvedev S.P., et al. TALEN and CRISPR/Cas Genome Editing Systems: Tools of Discovery. Acta Naturae 2014; 6(3): 19-40.Jiang W., Bikard D., Cox D. et al. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat. Biotechnol. 2013; 31(3): 233-9.Nishimasu H., Ran F.A., Hsu P.D. et al. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 2014; 156(5): 935-49.Fu Y., Foden J.A., Khayter C. et al. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat. Biotechnol. 2013; 31(9): 822-6.Pellagatti A., Dolatshad H., Valletta S. et al. Application of CRISPR/Cas9 genome editing to the study and treatment of disease. Arch. Toxicol. 2015; 89(7): 1023-34.Smith C., Gore A., Yan W. et al. Whole-genome sequencing analysis reveals high specificity of CRISPR/Cas9 and TALEN-based genome editing in human iPSCs. Cell Stem Cell 2014; 15(1): 12-3.Chen J.R., Tang Z.H., Zheng J. et al. Effects of genetic correction on the differentiation of hair cell-like cells from iPSCs with MY015A mutation. Cell Death Differ. 2016; doi: 10.1038/ cdd.2016.16.Li H.L., Fujimoto N., Sasakawa N. et al. Precise correction of the dystrophin gene in duchenne muscular dystrophy patient induced pluripotent stem cells by TALEN and CRISPR-Cas9. Stem Cell Reports 2015; 4(1): 143-54.Ding Q., Regan S.N., Xia Y. et al. Enhanced efficiency of human pluripotent stem cell genome editing through replacing TALENs with CRISPRs. Cell Stem Cell 2013; 12(4): 393-4.Maggio I., Holkers M., Liu J. et al. Adenoviral vector delivery of RNA-guided CRISPR/Cas9 nuclease complexes induces targeted mutagenesis in a diverse array of human cells. Sci. Rep. 2014; 4: 5105.Li D., Qiu Z., Shao Y. et al. Heritable gene targeting in the mouse and rat using a CRISPR-Cas system. Nat. Biotechnol. 2013; 31(8): 681-3.Hsu P.D., Lander E.S., Zhang F. Development and applications of CRISPR-Cas9 for genome engineering. Cell 2014; 157(6): 1262Shen B., Zhang W., Zhang J., et al. Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects. Nat. Methods 2014; 11(4): 399-402.Guilinger J.P., Thompson D.B., Liu D.R. Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nat. Biotechnol. 2014; 32(6): 577-82.Fu Y., Sander J.D., Reyon D. et al. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat. Biotechnol. 2014; 32(3): 279-84.Pattanayak V., Lin S., Guilinger J.P. et al. High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat. Biotechnol. 2013; 31(9): 839-43.Hsu P.D., Scott D.A., Weinstein J.A. et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat. Biotechnol. 2013; 31(9): 827-32.Mali P., Esvelt K.M., Church G.M. Cas9 as a versatile tool for engineering biology. Nat. Methods 2013; 10(10): 957-63.Zhang Y., Rajan R., Seifert H.S., et al. DNase H Activity of Neisseria meningitidis Cas9. Mol Cell. 2015; 60(2): 242-55.Friedland A.E., Baral R., Singhal P. et al. Characterization of Staphylococcus aureus Cas9: a smaller Cas9 for all-in-one adeno-associated virus delivery and paired nickase applications. Genome Biol. 2015; 16: 257.Zetsche B., Gootenberg J.S., Abudayyeh 0.0. et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 2015; 163(3): 759-71.Chang C.W., Lai Y.S., Westin E. et al. Modeling Human Severe Combined Immunodeficiency and Correction by CRISPR/Cas9-Enhanced Gene Targeting. Cell Rep. 2015; 12(10): 1668-77.Mianne J., Chessum L., Kumar S. et al. Correction of the auditory phenotype in C57BL/6N mice via CRISPR/Cas9-mediated homology directed repair. Genome Med. 2016; 8(1): 16.Wang X., Cao C., Huang J. et al. One-step generation of triple gene-targeted pigs using CRISPR/Cas9 system. Sci. Rep. 2016; 6: 20620.De Rubeis S., Buxbaum J.D. Genetics and genomics of autism spectrum disorder: embracing complexity. Hum. Mol. Genet. 2015; 24(R1): R24-31.Neale B.M., Kou Y., Liu L. et al. Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature 2012; 485(7397): 242-5.O'Roak B.J., Vives L., Girirajan S. et al. Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature 2012; 485(7397): 246-50.Chang C.J., Bouhassira E.E. Zinc-finger nuclease-mediated correction of alpha-thalassemia in iPS cells. Blood 2012; 120(19): 3906-14.Rio P., Banos R., Lombardo A. et al. Targeted gene therapy and cell reprogramming in Fanconi anemia. EMBO Mol. Med. 2014; 6(6): 835-48.Ousterout D.G., Kabadi A.M., Thakore P.I. et al. Multiplex CRISPR/Cas9-based genome editing for correction of dystrophin mutations that cause Duchenne muscular dystrophy. Nat. Commun. 2015; 6: 6244.Park C.Y., Kim D.H., Son J.S. et al. Functional Correction of Large Factor VIII Gene Chromosomal Inversions in Hemophilia A Patient-Derived iPSCs Using CRISPR-Cas9. Cell Stem Cell 2015; 17(2): 213-20.Firth A.L., Menon T., Parker G.S. et al. Functional Gene Correction for Cystic Fibrosis in Lung Epithelial Cells Generated from Patient iPSCs. Cell Rep. 2015; 12(9): 1385-90.Penagarikano 0., Mulle J.G., Warren S.T. The pathophysiology of fragile x syndrome. Annu. Rev. Genomics Hum. Genet. 2007; 8: 109-29.Crawford D.C., Acuna J.M., Sherman S.L. FMR1 and the fragile X syndrome: human genome epidemiology review. Genet. Med. 2001; 3(5): 359-71.Urbach A., Bar-Nur 0., Daley G.Q. et al. Differential modeling of fragile X syndrome by human embryonic stem cells and induced pluripotent stem cells. Cell Stem Cell 2010; 6(5): 407-11.Avitzour M., Mor-Shaked H., Yanovsky-Dagan S. et al. FMR1 epigenetic silencing commonly occurs in undifferentiated fragile X-affected embryonic stem cells. Stem Cell Reports 2014; 3(5): 699706.Pearson C.E., Nichol Edamura K., Cleary J.D. Repeat instability: mechanisms of dynamic mutations. Nat. Rev. Genet. 2005; 6(10): 729-42.Eiges R., Urbach A., Malcov M. et al. Developmental study of fragile X syndrome using human embryonic stem cells derived from preimplantation genetically diagnosed embryos. Cell Stem Cell 2007; 1(5): 568-77.Bar-Nur 0., Caspi I., Benvenisty N. Molecular analysis of FMR1 reactivation in fragile-X induced pluripotent stem cells and their neuronal derivatives. J. Mol. Cell Biol. 2012; 4(3): 180-3.Park C.Y., Halevy T., Lee D.R. et al. Reversion of FMR1 Methylation and Silencing by Editing the Triplet Repeats in Fragile X iPSC-Derived Neurons. Cell Rep. 2015; 13(2): 234-41.Rommens J.M., Iannuzzi M.C., Kerem B. et al. Identification of the cystic fibrosis gene: chromosome walking and jumping. Science 1989; 245(4922): 1059-65.Riordan J.R., Rommens J.M., Kerem B. et al. Identification of the cystic fibrosis gene: cloning and characterization of complementary DNA. Science 1989; 245(4922): 1066-73.Kerem B., Rommens J.M., Buchanan J.A. et al. Identification of the cystic fibrosis gene: genetic analysis. Science 1989; 245(4922): 1073-80.Schwank G., Koo B.K., Sasselli V. et al. Functional repair of CFTR by CRISPR/Cas9 in intestinal stem cell organoids of cystic fibrosis patients. Cell Stem Cell 2013; 13(6): 653-8.Huch M., Bonfanti P., Boj S.F. et al. Unlimited in vitro expansion of adult bi-potent pancreas progenitors through the Lgr5/R-spondin axis. EMB0 J. 2013; 32(20): 2708-21.Huch M., Dorrell C., Boj S.F. et al. In vitro expansion of single Lgr5+ liver stem cells induced by Wnt-driven regeneration. Nature 2013; 494(7436): 247-50.Barker N., Huch M., Kujala P. et al. Lgr5(+ve) stem cells drive self-renewal in the stomach and build long-lived gastric units in vitro. Cell Stem Cell 2010; 6(1): 25-36.Zou J., Mali P., Huang X. et al. Site-specific gene correction of a point mutation in human iPS cells derived from an adult patient with sickle cell disease. Blood 2011; 118(17): 4599-608.Sun N., Zhao H. Seamless correction of the sickle cell disease mutation of the HBB gene in human induced pluripotent stem cells using TALENs. Biotechnol. Bioeng. 2014; 111(5): 1048-53.Huang X., Wang Y., Yan W. et al. Production of Gene-Corrected Adult Beta Globin Protein in Human Erythrocytes Differentiated from Patient iPSCs After Genome Editing of the Sickle Point Mutation. Stem Cells 2015; 33(5): 1470-9.Cavazzana-Calvo M., Payen E., Negre 0. et al. Transfusion independence and HMGA2 activation after gene therapy of human beta-thalassaemia. Nature 2010; 467(7313): 318-22.Hacein-Bey-Abina S., Von Kalle C., Schmidt M. et al. LM02-associated clonal T cell proliferation in two patients after gene therapy for SCID-X1. Science 2003; 302(5644): 415-9.Woods N.B., Bottero V., Schmidt M. et al. Gene therapy: therapeutic gene causing lymphoma. Nature 2006; 440(7088): 1123.Xu P., Tong Y., Liu X.Z. et al. Both TALENs and CRISPR/ Cas9 directly target the HBB IVS2-654 (C > T) mutation in beta-thalassemia-derived iPSCs. Sci. Rep. 2015; 5: 12065.Song B., Fan Y., He W. et al. Improved hematopoietic differentiation efficiency of gene-corrected beta-thalassemia induced pluripotent stem cells by CRISPR/Cas9 system. Stem Cells Dev. 2015; 24(9): 1053-65.Yang Y., Zhang X., Yi L. et al. Naive Induced Pluripotent Stem Cells Generated From beta-Thalassemia Fibroblasts Allow Efficient Gene Correction With CRISPR/Cas9. Stem Cells Transl. Med. 2016; 5(1): 8-19.Xie F., Ye L., Chang J.C. et al. Seamless gene correction of beta-thalassemia mutations in patient-specific iPSCs using CRISPR/ Cas9 and piggyBac. Genome Res. 2014; 24(9): 1526-33.Hotta A., Yamanaka S. From Genomics to Gene Therapy: Induced Pluripotent Stem Cells Meet Genome Editing. Annu. Rev. Genet. 2015; 49: 47-70.Konermann S., Brigham M.D., Trevino A.E. et al. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 2015; 517(7536): 583-8.Wang T., Wei J.J., Sabatini D.M. et al. Genetic screens in human cells using the CRISPR-Cas9 system. Science 2014; 343(6166): 80-4.Li C., Guan X., Du T. et al. Inhibition of HIV-1 infection of primary CD4+ T-cells by gene editing of CCR5 using adenovirus-delivered CRISPR/Cas9. J. Gen. Virol. 2015; 96(8): 2381-93.Kennedy E.M., Bassit L.C., Mueller H. et al. Suppression of hepatitis B virus DNA accumulation in chronically infected cells using a bacterial CRISPR/Cas RNA-guided DNA endonuclease. Virology 2015; 476: 196-205.Price A.A., Sampson T.R., Ratner H.K. et al. Cas9-mediated targeting of viral RNA in eukaryotic cells. PNAS USA 2015; 112(19): 6164-9.Turan S., Farruggio A.P., Srifa W. et al. Precise correction of disease mutations in induced pluripotent stem cells derived from patients with limb girdle muscular dystrophy. Mol. Ther. 2016; doi: 10.1038/mt.2016.40.Osborn M.J., Gabriel R., Webber B.R. et al. Fanconi anemia gene editing by the CRISPR/Cas9 system. Hum. Gene Ther. 2015; 26(2): 114-26.Flynn R., Grundmann A., Renz P. et al. CRISPR-mediated genotypic and phenotypic correction of a chronic granulomatous disease mutation in human iPS cells. Exp. Hematol. 2015; 43(10): 838-48 e3.Bassuk A.G., Zheng A., Li Y. et al. Precision Medicine: Genetic Repair of Retinitis Pigmentosa in Patient-Derived Stem Cells. Sci. Rep. 2016; 6: 19969.