Generation of a Hutchinson–Gilford progeria syndrome monkey model by base editing

doi:10.1007/s13238-020-00740-8

Protein Cell

2020, Vol. 11

Issue (11) : 809-824 https://doi.org/10.1007/s13238-020-00740-8

RESEARCH ARTICLE

Generation of a Hutchinson–Gilford progeria syndrome monkey model by base editing

Fang Wang^1,², Weiqi Zhang^3,^4,^5,⁶, Qiaoyan Yang⁷, Yu Kang¹, Yanling Fan^4,⁵, Jingkuan Wei¹, Zunpeng Liu^6,⁸, Shaoxing Dai¹, Hao Li^4,^5,⁶, Zifan Li¹, Lizhu Xu¹, Chu Chu^1,², Jing Qu^3,^6,⁸, Chenyang Si^1,², Weizhi Ji¹(

), Guang-Hui Liu^3,^6,^9,¹⁰(

), Chengzu Long^7,^11,¹²(

), Yuyu Niu^1,²(

)

¹. Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
². Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
³. Institute for Stem Cell and Regeneration, Chinese Academy of Science, Beijing 100101, China
⁴. CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
⁵. China National Center for Bioinformation, Beijing 100101, China
⁶. University of Chinese Academy of Sciences, Beijing 100049, China
⁷. The Leon H Charney Division of Cardiology, New York University School of Medicine, New York, NY 10016, USA
⁸. State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
⁹. State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
¹⁰. Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
¹¹. Department of Neuroscience and Physiology, New York University School of Medicine, New York, NY 10016, USA
¹². Department of Neurology, New York University School of Medicine, New York, NY 10016, USA

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Abstract

Many human genetic diseases, including Hutchinson-Gilford progeria syndrome (HGPS), are caused by single point mutations. HGPS is a rare disorder that causes premature aging and is usually caused by a de novo point mutation in the LMNA gene. Base editors (BEs) composed of a cytidine deaminase fused to CRISPR/Cas9 nickase are highly efficient at inducing C to T base conversions in a programmable manner and can be used to generate animal disease models with single amino-acid substitutions. Here, we generated the first HGPS monkey model by delivering a BE mRNA and guide RNA (gRNA) targeting the LMNA gene via microinjection into monkey zygotes. Five out of six newborn monkeys carried the mutation specifically at the target site. HGPS monkeys expressed the toxic form of lamin A, progerin, and recapitulated the typical HGPS phenotypes including growth retardation, bone alterations, and vascular abnormalities. Thus, this monkey model genetically and clinically mimics HGPS in humans, demonstrating that the BE system can efficiently and accurately generate patient-specific disease models in non-human primates.

Keywords base editing non-human primate HGPS

Corresponding Author(s): Weizhi Ji,Guang-Hui Liu,Chengzu Long,Yuyu Niu

Online First Date: 22 September 2020 Issue Date: 07 December 2020

Cite this article:

Fang Wang,Weiqi Zhang,Qiaoyan Yang, et al. Generation of a Hutchinson–Gilford progeria syndrome monkey model by base editing[J]. Protein Cell, 2020, 11(11): 809-824.

URL:

https://academic.hep.com.cn/pac/EN/10.1007/s13238-020-00740-8
https://academic.hep.com.cn/pac/EN/Y2020/V11/I11/809

1	S Aktas, M Kiyak, K Ozdil, I Kurtca, S Kibar, S Ahbab, Y Karadeniz, T Saler (2013) Gastrointestinal tract hemorrhage due to angiodysplasia in hutchinson gilfort Progeria syndrome. J Med Cases 4(8):576–578 https://doi.org/10.4021/jmc1379w
2	S Anders, PT Pyl, W Huber (2015) HTSeq–a Python framework to work with high-throughput sequencing data. Bioinformatics 31:166–169 https://doi.org/10.1093/bioinformatics/btu638
3	S Bae, J Park, JS Kim (2014) Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNAguided endonucleases. Bioinformatics 30:1473–1475 https://doi.org/10.1093/bioinformatics/btu048
4	BC Capell, FS Collins (2006) Human laminopathies: nuclei gone genetically awry. Nat Rev Genet 7:940–952 https://doi.org/10.1038/nrg1906
5	AWS Chan (2013) Progress and prospects for genetic modiﬁcation of nonhuman primate models in biomedical research. ILAR J 54:211–223 https://doi.org/10.1093/ilar/ilt035
6	S Chen, Y Zhou, Y Chen, J Gu (2018) fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884–i890 https://doi.org/10.1093/bioinformatics/bty560
7	Y Chu, Z-G Xu, Z Xu, L Ma (2015) Hutchinson-Gilford progeria syndrome caused by an LMNA mutation: a case report. Pediatr Dermatol 32:271–275 https://doi.org/10.1111/pde.12406
8	F Debacq-Chainiaux, JD Erusalimsky, J Campisi, O Toussaint (2009) Protocols to detect senescence-associated beta-galactosidase (SA-betagal) activity, a biomarker of senescent cells in culture and in vivo. Nat Protoc 4:1798–1806 https://doi.org/10.1038/nprot.2009.191
9	Z Ding, L Sui, R Ren, Y Liu, X Xu, L Fu, R Bai, T Yuan, Y Hao, W Zhanget al. (2015) A widely adaptable approach to generate integration-free iPSCs from non-invasively acquired human somatic cells. Protein Cell 6:386–389 https://doi.org/10.1007/s13238-014-0117-1
10	B Dorado, GG Ploen, A Barettino, A Macias, P Gonzalo, MJ AndresManzano, C Gonzalez-Gomez, C Galan-Arriola, JM Alfonso, M Loboet al. (2019) Generation and characterization of a novel knockin minipig model of Hutchinson–Gilford progeria syndrome. Cell Discov 5:16 https://doi.org/10.1038/s41421-019-0084-z
11	Y Doubaj, A Lamzouri, SC Elalaoui, FZ Laarabi, A Seﬁani (2011) Syndrome d’Hutchinson-Gilford (progéria). À propos de 3 cas. Archives de Pédiatrie 18:156–159 https://doi.org/10.1016/j.arcped.2010.11.014
12	N Erdem, AT Güneş, O Avcı, E Osma (1994) A case of Hutchinson– Gilford progeria syndrome mimicking scleredema in early infancy. Dermatology 188:318–321 https://doi.org/10.1159/000247175
13	JG Fleischer, R Schulte, HH Tsai, S Tyagi, A Ibarra, MN Shokhirev, L Huang, MW Hetzer, S Navlakha (2018) Predicting age from the transcriptome of human dermal ﬁbroblasts. Genome Biol 19:221 https://doi.org/10.1186/s13059-018-1599-6
14	A Giangreco, M Qin, JE Pintar, FM Watt (2008) Epidermal stem cells are retained in vivo throughout skin aging. Aging Cell 7:250–259 https://doi.org/10.1111/j.1474-9726.2008.00372.x
15	CM Gordon, LB Gordon, BD Snyder, A Nazarian, N Quinn, S Huh, A Giobbie-Hurder, D Neuberg, R Cleveland, M Kleinmanet al. (2011) Hutchinson–gilford progeria is a skeletal dysplasia. J Bone Miner Res 26:1670–1679 https://doi.org/10.1002/jbmr.392
16	LB Gordon, IA Harten, ME Patti, AH Lichtenstein (2005) Reduced adiponectin and HDL cholesterol without elevated C-reactive protein: clues to the biology of premature atherosclerosis in Hutchinson–Gilford progeria syndrome. J Pediatr 146:336–341 https://doi.org/10.1016/j.jpeds.2004.10.064
17	B Gordon Leslie, E Kleinman Monica, J Massaro, B D’Agostino Ralph, H Shappell, M Gerhard-Herman, B Smoot Leslie, M Gordon Catherine, H Cleveland Robert, A Nazarianet al. (2016) Clinical trial of the protein farnesylation inhibitors lonafarnib, pravastatin, and zoledronic acid in children with Hutchinson–Gilford progeria syndrome. Circulation 134:114–125 https://doi.org/10.1161/CIRCULATIONAHA.116.022188
18	RCM Hennekam (2006) Hutchinson-Gilford progeria syndrome: review of the phenotype. Am J Med Genet A 140A:2603–2624 https://doi.org/10.1002/ajmg.a.31346
19	H-J Jung, C Cofﬁnier, Y Choe, AP Beigneux, BSJ Davies, SH Yang, RH Barnes, J Hong, T Sun, SJ Pleasureet al. (2012) Regulation of prelamin A but not lamin C by miR-9, a brain-speciﬁc microRNA. Proc Natl Acad Sci USA 109:E423–E431 https://doi.org/10.1073/pnas.1111780109
20	Y Kang, C Chu, F Wang, Y Niu (2019) CRISPR/Cas9-mediated genome editing in nonhuman primates. Dis Models Mech 12:39982 https://doi.org/10.1242/dmm.039982
21	MM Khalifa (1989) Hutchinson-Gilford progeria syndrome: report of a Libyan family and evidence of autosomal recessive inheritance. Clin Genet 35:125–132 https://doi.org/10.1111/j.1399-0004.1989.tb02917.x
22	D Kim, B Langmead, SL Salzberg (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12:357–360 https://doi.org/10.1038/nmeth.3317
23	K Kim, S-M Ryu, S-T Kim, G Baek, D Kim, K Lim, E Chung, S Kim, J-S Kim (2017) Highly efﬁcient RNA-guided base editing in mouse embryos. Nat Biotechnol 35:435 https://doi.org/10.1038/nbt.3816
24	S Kim, K Schefﬂer, AL Halpern, MA Bekritsky, E Noh, M Kallberg, X Chen, Y Kim, D Beyter, P Kruscheet al. (2018) Strelka2: fast and accurate calling of germline and somatic variants. Nat Methods 15:591–594 https://doi.org/10.1038/s41592-018-0051-x
25	LW Koblan, JL Doman, C Wilson, JM Levy, T Tay, GA Newby, JP Maianti, A Raguram, DR Liu (2018a) Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction. Nat Biotechnol 36:843–846 https://doi.org/10.1038/nbt.4172
26	LW Koblan, JL Doman, C Wilson, JM Levy, T Tay, GA Newby, JP Maianti, A Raguram, DR Liu (2018b) Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction. Nat Biotechnol 36:843–846 https://doi.org/10.1038/nbt.4172
27	AC Komor, YB Kim, MS Packer, JA Zuris, DR Liu (2016) Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533:420 https://doi.org/10.1038/nature17946
28	B Korf (2008) Hutchinson–Gilford progeria syndrome, aging, and the nuclear lamina. N Engl J Med 358:552–555 https://doi.org/10.1056/NEJMp0800071
29	N Kubben, W Zhang, L Wang, TC Voss, J Yang, J Qu, GH Liu, T Misteli (2016) Repression of the antioxidant NRF2 pathway in premature aging. Cell 165:1361–1374 https://doi.org/10.1016/j.cell.2016.05.017
30	MJ Landrum, JM Lee, M Benson, G Brown, C Chao, S Chitipiralla, B Gu, J Hart, D Hoffman, J Hooveret al. (2016) ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res 44:D862–D868 https://doi.org/10.1093/nar/gkv1222
31	H Li, R Durbin (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754–1760 https://doi.org/10.1093/bioinformatics/btp324
32	H Li, B Handsaker, A Wysoker, T Fennell, J Ruan, N Homer, G Marth, G Abecasis, R Durbin, Genome Project Data Processing, S (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079 https://doi.org/10.1093/bioinformatics/btp352
33	P Liang, C Ding, H Sun, X Xie, Y Xu, X Zhang, Y Sun, Y Xiong, W Ma, Y Liuet al. (2017) Correction of β-thalassemia mutant by base editor in human embryos. Protein Cell 8:811–822 https://doi.org/10.1007/s13238-017-0475-6
34	GH Liu, BZ Barkho, S Ruiz, D Diep, J Qu, SL Yang, AD Panopoulos, K Suzuki, L Kurian, C Walshet al. (2011a) Recapitulation of premature ageing with iPSCs from Hutchinson–Gilford progeria syndrome. Nature 472:221–225 https://doi.org/10.1038/nature09879
35	GH Liu, K Suzuki, J Qu, I Sancho-Martinez, F Yi, M Li, S Kumar, E Nivet, J Kim, RD Soligallaet al. (2011b) Targeted gene correction of laminopathy-associated LMNA mutations in patientspeciﬁc iPSCs. Cell Stem Cell 8:688–694 https://doi.org/10.1016/j.stem.2011.04.019
36	Z Liu, M Chen, S Chen, J Deng, Y Song, L Lai, Z Li (2018a) Highly efﬁcient RNA-guided base editing in rabbit. Nat Commun 9:2717 https://doi.org/10.1038/s41467-018-05232-2
37	Z Liu, M Chen, S Chen, J Deng, Y Song, L Lai, Z Li (2018b) Highly efﬁcient RNA-guided base editing in rabbit. Nat Commun 9:2717 https://doi.org/10.1038/s41467-018-05232-2
38	MI Love, W Huber, S Anders (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550 https://doi.org/10.1186/s13059-014-0550-8
39	MA Merideth, LB Gordon, S Clauss, V Sachdev, ACM Smith, MB Perry, CC Brewer, C Zalewski, HJ Kim, B Solomonet al. (2008) Phenotype and course of Hutchinson–Gilford progeria syndrome. N Engl J Med 358:592–604 https://doi.org/10.1056/NEJMoa0706898
40	JUV Monu, LBO Benka-Coker, Y Fatunde (1990) Hutchinson– Gilford progeria syndrome in siblings. Skeletal Radiol 19:585–590 https://doi.org/10.1007/BF00241281
41	National Genomics Data Center, M., and Partners (2020) Database Resources of the National Genomics Data Center in 2020. Nucleic Acids Res 48:D24–D33
42	Y Niu, Y Yu, A Bernat, S Yang, X He, X Guo, D Chen, Y Chen, S Ji, W Siet al. (2010) Transgenic rhesus monkeys produced by gene transfer into early-cleavage-stage embryos using a simian immunodeﬁciency virus-based vector. Proc Natl Acad Sci USA 107:17663–17667 https://doi.org/10.1073/pnas.1006563107
43	FG Osorio, CL Navarro, J Cadinanos, IC Lopez-Mejia, PM Quiros, C Bartoli, J Rivera, J Tazi, G Guzman, I Varelaet al. (2011) Splicing-directed therapy in a new mouse model of human accelerated aging. Sci Transl Med 3:106ra107 https://doi.org/10.1126/scitranslmed.3002847
44	MB Ozonoff, AR Clemett (1967) Progressive osteolysis in progeria. Am J Roentgenol 100:75–79 https://doi.org/10.2214/ajr.100.1.75
45	A Pickar-Oliver, CA Gersbach (2019) The next generation of CRISPR–Cas technologies and applications. Nat Rev Mol Cell Biol 20:490–507 https://doi.org/10.1038/s41580-019-0131-5
46	A Prakash, LB Gordon, ME Kleinman, EB Gurary, J Massaro, R Sr D’Agostino, MW Kieran, M Gerhard-Herman, L Smoot (2018) Cardiac abnormalities in patients with Hutchinson–Gilford progeria syndrome. JAMA Cardiol 3:326–334 https://doi.org/10.1001/jamacardio.2017.5235
47	R Rastogi, S Chander Mohan (2008) Progeria syndrome: a case report. Indian J Orthopaedics 42:97–99 https://doi.org/10.4103/0019-5413.38591
48	J Rivera-Torres, CJ Calvo, A Llach, G Guzmán-Martínez, R Caballero, C González-Gómez, LJ Jiménez-Borreguero, JA Guadix, FG Osorio, C López-Otínet al. (2016) Cardiac electrical defects in progeroid mice and Hutchinson–Gilford progeria syndrome patients with nuclear lamina alterations. Proc Natl Acad Sci USA 113:E7250–E7259 https://doi.org/10.1073/pnas.1603754113
49	JF Rork, JT Huang, LB Gordon, M Kleinman, MW Kieran, MG Liang (2014) Initial cutaneous manifestations of Hutchinson–Gilford progeria syndrome. Pediatr Dermatol 31:196–202 https://doi.org/10.1111/pde.12284
50	E Selvin, SS Najjar, TC Cornish, MK Halushka (2010) A comprehensive histopathological evaluation of vascular medial ﬁbrosis: insights into the pathophysiology of arterial stiffening. Atherosclerosis 208:69–74 https://doi.org/10.1016/j.atherosclerosis.2009.06.025
51	VM Silvera, LB Gordon, DB Orbach, SE Campbell, JT Machan, NJ Ullrich (2013) Imaging characteristics of cerebrovascular arteriopathy and stroke in Hutchinson-Gilford progeria syndrome. Am J Neuroradiol 34:1091–1097 https://doi.org/10.3174/ajnr.A3341
52	WE Stehbens, SJ Wakeﬁeld, E Gilbert-Barness, RE Olson, J Ackerman (1999) Histological and ultrastructural features of atherosclerosis in progeria. Cardiovasc Pathol 8:29–39 https://doi.org/10.1016/S1054-8807(98)00023-4
53	A Tarasov, AJ Vilella, E Cuppen, IJ Nijman, P Prins (2015) Sambamba: fast processing of NGS alignment formats. Bioinformatics 31:2032–2034 https://doi.org/10.1093/bioinformatics/btv098
54	NJ Ullrich, LB Gordon (2015) Chapter 18 – Hutchinson–Gilford progeria syndrome. In: Islam MP, Roach ES (eds) Handbook of clinical neurology. Elsevier, Amsterdam, pp 249–264 https://doi.org/10.1016/B978-0-444-62702-5.00018-4
55	NJ Ullrich, VM Silvera, SE Campbell, LB Gordon (2012) Craniofacial abnormalities in Hutchinson–Gilford progeria syndrome. Am J Neuroradiol 33:1512–1518 https://doi.org/10.3174/ajnr.A3088
56	Y Wang, F Song, J Zhu, S Zhang, Y Yang, T Chen, B Tang, L Dong, N Ding, Q Zhanget al. (2017) GSA: genome sequence archive. Genomics Proteomics Bioinform 15:14–18 https://doi.org/10.1016/j.gpb.2017.01.001
57	Q Wei, X Zhan, X Zhong, Y Liu, Y Han, W Chen, B Li (2015) A Bayesian framework for de novo mutation calling in parentsoffspring trios. Bioinformatics 31:1375–1381 https://doi.org/10.1093/bioinformatics/btu839
58	Z Wu, W Zhang, M Song, W Wang, G Wei, W Li, J Lei, Y Huang, Y Sang, P Chanet al. (2018) Differential stem cell aging kinetics in Hutchinson–Gilford progeria syndrome and Werner syndrome. Protein Cell 9:333–350 https://doi.org/10.1007/s13238-018-0517-8
59	S Xu, Z-G Jin (2019) Hutchinson–Gilford progeria syndrome: cardiovascular pathologies and potential therapies. Trends Biochem Sci 44:561–564 https://doi.org/10.1016/j.tibs.2019.03.010
60	M Zhang, C Zhou, Y Wei, C Xu, H Pan, W Ying, Y Sun, Y Sun, Q Xiao, N Yaoet al. (2019a) Human cleaving embryos enable robust homozygotic nucleotide substitutions by base editors. Genome Biol 20:101 https://doi.org/10.1186/s13059-019-1703-6
61	W Zhang, H Wan, G Feng, J Qu, J Wang, Y Jing, R Ren, Z Liu, L Zhang, Z Chenet al. (2018) SIRT6 deﬁciency results in developmental retardation in cynomolgus monkeys. Nature 560:661–665 https://doi.org/10.1038/s41586-018-0437-z
62	X Zhang, Z Liu, X Liu, S Wang, Y Zhang, X He, S Sun, S Ma, N ShyhChang, F Liuet al. (2019b) Telomere-dependent and telomereindependent roles of RAP1 in regulating human stem cell homeostasis. Protein Cell 10:649–667 https://doi.org/10.1007/s13238-019-0610-7
63	C Zhou, M Zhang, Y Wei, Y Sun, Y Sun, H Pan, N Yao, W Zhong, Y Li, W Liet al. (2017) Highly efﬁcient base editing in human tripronuclear zygotes. Protein Cell 8:772–775 https://doi.org/10.1007/s13238-017-0459-6
64	Y Zhou, B Zhou, L Pache, M Chang, AH Khodabakhshi, O Tanaseichuk, C Benner, SK Chanda (2019) Metascape provides a biologistoriented resource for the analysis of systems-level datasets. Nat Commun 10:1523 https://doi.org/10.1038/s41467-019-09234-6
65	E Zuo, Y Sun, W Wei, T Yuan, W Ying, H Sun, L Yuan, LM Steinmetz, Y Li, H Yang (2019) Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos. Science. 364(6437):289 https://doi.org/10.1126/science.aav9973

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