CRISPR/Cas9-mediated targeted gene correction in amyotrophic lateral sclerosis patient iPSCs
Lixia Wang1,2,3, Fei Yi4, Lina Fu1,3, Jiping Yang1,3, Si Wang1,3, Zhaoxia Wang5, Keiichiro Suzuki6,7, Liang Sun9, Xiuling Xu1, Yang Yu8, Jie Qiao8, Juan Carlos Izpisua Belmonte6, Ze Yang9, Yun Yuan5(), Jing Qu2,3(), Guang-Hui Liu1,3,10,11()
1. National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China 2. State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China 3. University of Chinese Academy of Sciences, Beijing 100049, China 4. Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA 5. Department of Neurology, Peking University First Hospital, Beijing 100034, China 6. Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA 7. Universidad Católica San Antonio de Murcia (UCAM), Campus de los Jerónimos, N 135 Guadalupe, 30107 Murcia, Spain 8. Department of Gynecology and Obstetrics, Peking University Third Hospital, Beijing 100191, China 9. Beijing Hospital of the Ministry of Health, Beijing 100730, China 10. Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou 510632, China 11. Beijing Institute for Brain Disorders, Capital Medical University, Beijing 100069, China
Amyotrophic lateral sclerosis (ALS) is a complex neurodegenerative disease with cellular and molecular mechanisms yet to be fully described. Mutations in a number of genes including SOD1 and FUS are associated with familial ALS. Here we report the generation of induced pluripotent stem cells (iPSCs) from fibroblasts of familial ALS patients bearing SOD1+/A272C and FUS+/G1566A mutations, respectively. We further generated gene corrected ALS iPSCs using CRISPR/Cas9 system. Genome-wide RNA sequencing (RNA-seq) analysis ofmotor neurons derived from SOD1+/A272C and corrected iPSCs revealed 899 aberrant transcripts. Our work may shed light on discovery of early biomarkers and pathways dysregulated in ALS, as well as provide a basis for novel therapeutic strategies to treat ALS.
Al-ChalabiA, HardimanO (2013) The epidemiology of ALS: a conspiracy of genes, environment and time. Nat Rev Neurol9:617–623 https://doi.org/10.1038/nrneurol.2013.203
2
AlexianuME, HoBK, MohamedAH, La BellaV, SmithRG, AppelSH (1994) The role of calcium-binding proteins in selective motoneuron vulnerability in amyotrophic lateral sclerosis. Ann Neurol36:846–858 https://doi.org/10.1002/ana.410360608
AronicaE, CataniaMV, GeurtsJ, YankayaB, TroostD (2001) Immunohistochemical localization of group I and II metabotropic glutamate receptors in control and amyotrophic lateral sclerosis human spinal cord: upregulation in reactive astrocytes. Neuroscience105:509–520 https://doi.org/10.1016/S0306-4522(01)00181-6
5
BaechtoldH, KurodaM, SokJ, RonD, , LopezBS, AkhmedovAT (1999) Human 75-kDa DNA-pairing protein is identical to the prooncoprotein TLS/FUS and is able to promote D-loop formation. J Biol Chem274:34337–34342 https://doi.org/10.1074/jbc.274.48.34337
6
BoscoDA, MorfiniG, KarabacakNM, SongY, Gros-LouisF, PasinelliP,GoolsbyH, FontaineBA, LemayN, McKenna-YasekDet al. (2010) Wild-type and mutant SOD1 share an aberrant conformation and a common pathogenic pathway in ALS. Nat Neurosci13:1396–1403 https://doi.org/10.1038/nn.2660
7
BoultingGL, KiskinisE, CroftGF, AmorosoMW, OakleyDH, WaingerBJ, WilliamsDJ, KahlerDJ, YamakiM, DavidowL, RodolfaCTet al. (2011) A functionally characterized test set of human induced pluripotent stem cells. Nat Biotechnol29:279–286. https://doi.org/10.1038/nbt.1783
8
BruijnLI, HouseweartMK, KatoS, AndersonKL, AndersonSD, OhamaE, ReaumeAG, ScottRW, ClevelandDW (1998) Aggregation and motor neuron toxicity of an ALS-linked SOD1 mutant independent from wild-type SOD1. Science281:1851–1854 https://doi.org/10.1126/science.281.5384.1851
ChenH, QianK, DuZ, CaoJ, PetersenA, LiuH, BlackbournLW, HuangCL, ErrigoA, YinYet al. (2014) Modeling ALS with iPSCs reveals that mutant SOD1 misregulates neurofilament balance in motor neurons. Cell Stem Cell14:796–809. https://doi.org/10.1016/j.stem.2014.02.004
12
ChiL, GanL, LuoC, LuoC, LienL, LiuR (2007) Temporal response of neural progenitor cells to disease onset and progression in amyotrophic lateral sclerosis-like transgenic mice. Stem Cells Dev16:5579–5588 https://doi.org/10.1089/scd.2006.0120
13
CirilloG, ColangeloAM, De LucaC, SavareseL, BarillariMR, AlberghinaL, PapaM (2016) Modulation of matrix metalloproteinases activity in the ventral horn of the spinal cord restores neuroglial synaptic homeostasis and neurotrophic support following peripheral nerve injury. PLoS ONE11:152750–152762 https://doi.org/10.1371/journal.pone.0152750
CortiS, NizzardoM, SimoneC, FalconeM, NardiniM, RonchiD, DonadoniC, SalaniS, RiboldiG, MagriFet al. (2012) Genetic correction of human induced pluripotent stem cells from patients with spinal muscular atrophy. Sci Transl Med4:165–197 https://doi.org/10.1126/scitranslmed.3004108
16
CrozatA, AmanP, MandahlN, MandahlN, RonD (1993) Fusion of CHOP to a novel RNA-binding protein in human myxoid liposarcoma. Nature363:640–644 https://doi.org/10.1038/363640a0
17
De LucaC, PapaMA (2016) Looking inside the matrix: perineuronal nets in plasticity, maladaptive plasticity and neurological disorders. Neurochem Res41:1507–1515 https://doi.org/10.1007/s11064-016-1876-2
18
DingQ, ReganSN, XiaY, OostromLA, CowanCA, MusunuruK (2013) Enhanced efficiency of human pluripotent stem cell genome editing through replacing TALENs with CRISPRs. Cell Stem Cell12:393–394 https://doi.org/10.1016/j.stem.2013.03.006
19
DingZ, SuiL, RenR, LiuY, XuX, FuL, BaiR, YuanT, HaoY, ZhangWet al. (2015) A widely adaptable approach to generate integration-free iPSCs from non-invasively acquired human somatic cells. Protein Cell6:386–389 https://doi.org/10.1007/s13238-014-0117-1
DuZW, ChenH, LiuH, LuJ, QianK, HuangCL, ZhongX, FanF, ZhangSC (2015) Generation and expansion of highly pure motor neuron progenitors from human pluripotent stem cells. Nat Commun6:6626–6638 https://doi.org/10.1038/ncomms7626
22
DuanS, YuanG, LiuX, RenR, LiJ, ZhangW, WuJ, XuX, FuL, LiYet al. (2015) PTEN deficiency reprogrammes human neural stem cells towards a glioblastoma stem cell-like phenotype. Nat Commun6:10068–10082 https://doi.org/10.1038/ncomms10068
23
EgawaN, KitaokaS, TsukitaK, NaitohM, TakahashiK, YamamotoT, AdachiF, KondoT, OkitaK, AsakaI, AoiTet al. (2012) Drug screening for ALS using patient-specific induced pluripotent stem cells. Sci Transl Med4:145104–145112 https://doi.org/10.1126/scitranslmed.3004052
24
FischerLR, CulverDG, TennantP, DavisAA, WangM, Castellano-SanchezA, KhanJ, PolakMA, GlassJD (2004) Amyotrophic lateral sclerosis is a distal axonopathy: evidence in mice and man. Exp Neurol185:232–240 https://doi.org/10.1016/j.expneurol.2003.10.004
HigelinJ, DemestreM, PutzS, DellingJP, JacobC, LutzAK, BausingerJ, HuberAK, KlingensteinM, BarbiGet al. (2016) FUS mislocalization and vulnerability to DNA damage in ALS patients derived hiPSCs and aging motoneurons. Front Cell Neurosci10:290–311 https://doi.org/10.3389/fncel.2016.00290
27
HuangC, ZhouH, TongJ, ChenH, LiuYJ, WangD, WeiX, XiaXG (2011) FUS transgenic rats develop the phenotypes of amyotrophic lateral sclerosis and frontotemporal lobar degeneration. PLoS Genet7:1–10 https://doi.org/10.1371/journal.pgen.1002011
28
IchiyanagiN, FujimoriK, YanoM, Ishihara-FujisakiC, SoneT, AkiyamaT, OkadaY, AkamatsuW, MatsumotoT, IshikawaMet al. (2016) Establishment of in vitro FUS-associated familial amyotrophic lateral sclerosis model using human induced pluripotent stem cells. Stem Cell Rep6:496–510 https://doi.org/10.1016/j.stemcr.2016.02.011
KiskinisE, SandoeJ, WilliamsLA, BoultingGL, MocciaR, WaingerBJ, HanS, PengT, ThamsS, MikkilineniSet al. (2014) Pathways disrupted in human ALS motor neurons identified through genetic correction of mutant SOD1. Cell Stem Cell14:781–795 https://doi.org/10.1016/j.stem.2014.03.004
32
KubbenN, ZhangW, WangL, VossTC, YangJ, QuJ, LiuGH, MisteliT (2016) Repression of the antioxidant NRF2 pathway in premature aging. Cell165:1361–1374 https://doi.org/10.1016/j.cell.2016.05.017
33
KudoLC, ParfenovaL, ViN, LauK, PomakianJ, ValdmanisP, RouleauGA, VintersHV, Wiedau-PazosM, KarstenSL (2010) Integrative gene–tissue microarray-based approach for identification of human disease biomarkers: application to amyotrophic lateral sclerosis. Hum Mol Genet19:3233–3253 https://doi.org/10.1093/hmg/ddq232
LeeJH, KwonDH (2013) Calumenin has a role in the alleviation of ER stress in neonatal rat cardiomyocytes. Biochem Biophys Res Commun439:327–332 https://doi.org/10.1016/j.bbrc.2013.08.087
38
LeeS, ShangY, RedmondSA, UrismanA, TangAA, LiKH, BurlingameAL, PakRA, JovicicA, GitlerADet al. (2016) Activation of HIPK2 promotes ER stress-mediated neurodegeneration in amyotrophic lateral sclerosis. Neuron91:41–55 https://doi.org/10.1016/j.neuron.2016.05.021
39
LenziJ, De SantisR, de TurrisV, MorlandoM, LaneveP, CalvoA, CaliendoV, ChioA, RosaA, BozzoniI (2015) ALS mutant FUS proteins are recruited into stress granules in induced pluripotent stem cell-derived motoneurons. Dis Model Mech8:755–766 https://doi.org/10.1242/dmm.020099
40
LiY, BalasubramanianU, CohenD, ZhangP-W, MosmillerE, SattlerR, MaragakisNJ, RothsteinJD (2015) A comprehensive library of familial human amyotrophic lateral sclerosis induced pluripotent stem cells. PLOS ONE10:118266–118279 https://doi.org/10.1371/journal.pone.0118266
41
LiY, ZhangW, ChangL, HanY, SunL, GongX, TangH, LiuZ, DengH, YeYet al. (2016) Vitamin C alleviates aging defects in a stem cell model for Werner syndrome. Protein Cell7:478–488 https://doi.org/10.1007/s13238-016-0278-1
42
LiangP, XuY, ZhangX, DingC, HuangR, ZhangZ, LvJ, XieX, ChenY, LiYet al. (2015) CRISPR/Cas9-mediated gene editing in human tripronuclear zygotes. Protein Cell6:363–372 https://doi.org/10.1007/s13238-015-0153-5
43
LiuG-H, DingZ, Izpisua BelmonteJC (2012a) iPSC technology to study human aging and aging-related disorders. Curr Opin Cell Biol24:765–774 https://doi.org/10.1016/j.ceb.2012.08.014
44
LiuGH, BarkhoBZ, RuizS, DiepD, QuJ, YangS-L, PanopoulosAD, SuzukiK, KurianL, WalshC, ThompsonJet al. (2011a) Recapitulation of premature ageing with iPSCs from Hutchinson-Gilford progeria syndrome. Nature472: 221–225 https://doi.org/10.1038/nature09879
45
LiuGH, QuJ, SuzukiK, NivetE, LiM, MontserratN, YiF, XuX, RuizS, ZhangWet al. (2012b) Progressive degeneration of human neural stem cells caused by pathogenic LRRK2. Nature491:603–607 https://doi.org/10.1038/nature11557
LiuX, ChenJ, LiuW, LiX, ChenQ, LiuT, GaoS, DengM (2015) The fused in sarcoma protein forms cytoplasmic aggregates in motor neurons derived from integration-free induced pluripotent stem cells generated from a patient with familial amyotrophic lateral sclerosis carrying the FUS-P525L mutation. Neurogenetics16:223–231 https://doi.org/10.1007/s10048-015-0448-y
49
MaliP, YangL, EsveltKM, AachJ, GuellM, DiCarloJE, NorvilleJE, ChurchGM (2013). RNA-guided human genome engineering via Cas9. Science339:823–826 https://doi.org/10.1126/science.1232033
50
MauryY, ComeJ, PiskorowskiRA, Salah-MohellibiN, ChevaleyreV, PeschanskiM, MartinatC, NedelecS (2015) Combinatorial analysis of developmental cues efficiently converts human pluripotent stem cells into multiple neuronal subtypes. Nat Biotechnol33:89–96 https://doi.org/10.1038/nbt.3049
OkitaK, MatsumuraY, SatoY, OkadaA, MorizaneA, OkamotoS, HongH, NakagawaM, TanabeK, TezukaKet al. (2011) A more efficient method to generate integration-free human iPS cells. Nat Methods8:409–412 https://doi.org/10.1038/nmeth.1591
53
PanH, GuanD, LiuX, LiJ, WangL, WuJ, ZhouJ, ZhangW, RenR, ZhangWet al. (2016) SIRT6 safeguards human mesenchymal stem cells from oxidative stress by coactivating NRF2. Cell Research26:190–205 https://doi.org/10.1038/cr.2016.4
54
PasinelliP, BrownRH (2006) Molecular biology of amyotrophic lateral sclerosis: insights from genetics. Nat Rev Neurosci7:710–723 https://doi.org/10.1038/nrn1971
55
PetersDT, CowanCA, MusunuruK (2013) Genome editing in human pluripotent stem cells. StemBook.
56
QuQ, LiD, LouisKR, LiX, YangH, SunQ, CrandallSR, TsangS, ZhouJ, CoxCLet al. (2014) High-efficiency motor neuron differentiation from human pluripotent stem cells and the function of Islet-1. Nat Commun5:3449–3462 https://doi.org/10.1038/ncomms4449
57
RenR, DengL, XueY, SuzukiK, ZhangW, YuY, WuJ, SunL, GongX, LuanHet al. (2017) Visualization of aging-associated chromatin alterations with an engineered TALE system https://doi.org/10.1038/cr.2017.18
58
RobberechtW, PhilipsT (2013) The changing scene of amyotrophic lateral sclerosis. Nat Rev Neurosci14:248–264 https://doi.org/10.1038/nrn3430
59
RosenDR, SiddiqueT, PattersonD, FiglewiczDA, SappP, HentatiA, DonaldsonD, GotoJ, O’ReganJP, DengH-Xet al. (1993) Mutations in Cu/Zn superoxide dismutase gene are associated with familial amyotrophic lateral sclerosis. Nature362:59–62 https://doi.org/10.1038/362059a0
60
SharmaA, LyashchenkoAK, LuL, NasrabadySE, ElmalehM, MendelsohnM, NemesA, TapiaJC, MentisGZ, ShneiderNA (2016) ALS-associated mutant FUS induces selective motor neuron degeneration through toxic gain of function. Nat Commun7:10465–10479 https://doi.org/10.1038/ncomms10465
TakahashiK, TanabeK, OhnukiM, NaritaM, IchisakaT, TomodaK, YamanakaS (2007) Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell131:861–872 https://doi.org/10.1016/j.cell.2007.11.019
TurnerBJ, TalbotK (2008) Transgenics, toxicity and therapeutics in rodent models of mutant SOD1-mediated familial ALS. Prog Neurobiol85:94–134 https://doi.org/10.1016/j.pneurobio.2008.01.001
67
VanceC, RogeljB, HortobágyiT, De VosKJ, NishimuraAL, SreedharanJ, HuX, SmithB, RuddyD, WrightPet al. (2009) Mutations in FUS, an RNA processing protein, cause familial amyotrophic lateral sclerosis type 6. Science323:1208–1211 https://doi.org/10.1126/science.1165942
68
VeresA, GosisBS, DingQ, CollinsR, RagavendranA, BrandH, ErdinS, TalkowskiME, MusunuruK (2014) Low incidence of offtarget mutations in individual CRISPR-Cas9 and TALEN targeted human stem cell clones detected by whole-genome sequencing. Cell Stem Cell15:27–30 https://doi.org/10.1016/j.stem.2014.04.020
69
Wainger BrianJ, KiskinisE, MellinC, WiskowO, Han SteveSW, SandoeJ, Perez NumaP, Williams LuisA, LeeS, BoultingGet al. (2014) Intrinsic membrane hyperexcitability of amyotrophic lateral sclerosis patient-derived motor neurons. Cell Reports7:1–11 https://doi.org/10.1016/j.celrep.2014.03.019
70
WoehlbierU, ColomboA, SaaranenMJ, PerezV, OjedaJ, BustosFJ, AndreuCI, TorresM, ValenzuelaV, MedinasDBet al. (2016) ALS-linked protein disulfide isomerase variants cause motor dysfunction. EMBO J35:845–865 https://doi.org/10.15252/embj.201592224
71
Yang YinM, Gupta ShaileshK, Kim KevinJ, Powers BeritE, CerqueiraA, Wainger BrianJ, Ngo HienD, Rosowski KathrynA, Schein PamelaA, Ackeifi CourtneyAet al. (2013) A small molecule screen in stem-cell-derived motor neurons identifies a kinase inhibitor as a candidate therapeutic for ALS. Cell Stem Cell12:713–726 https://doi.org/10.1016/j.stem.2013.04.003
72
ZhangW, LiJ, SuzukiK, QuJ, WangP, ZhouJ, LiuX, RenR, XuX, OcampoAet al. (2015) A Werner syndrome stem cell model unveils heterochromatin alterations as a driver of human aging. Science348:1160–1163 https://doi.org/10.1126/science.aaa1356
73
ZhuY, FotinosA, MaoLL, AtassiN, ZhouEW, AhmadS, GuanY, BerryJD, CudkowiczME, WangX (2014) Neuroprotective agents target molecular mechanisms of disease in ALS. Drug Discov Today20:65–75 https://doi.org/10.1016/j.drudis.2014.08.016
74
ZhuY, FotinosA, MaoLL, AtassiN, ZhouEW, AhmadS, GuanY, BerryJD, CudkowiczME, WangX (2015) Neuroprotective agents target molecular mechanisms of disease in ALS. Drug Discov Today20:65–75 https://doi.org/10.1016/j.drudis.2014.08.016