Induced pluripotent stem cells (iPSCs) can serve as a biological resource for functional and conservation research for various species. This realization has led to the generation of iPSCs from many species, including those identified as endangered. However, the understanding of species variation in mammalian iPSCs remains largely unknown. To gain insight into species variation in iPSCs, we generated iPSCs from a new species Grevy's zebra (Equus grevyi; gz-iPSCs), which has been listed as endangered in the IUCN (International Union for Conservation of Nature) Red List. We isolated primary fibroblast cells from an individual and successfully reprogrammed them into iPSCs. The generated gz-iPSCs continued to grow under primed-type culture condition and showed pluripotency and differentiation potential. To describe the molecular characteristics of gz-iPSCs, we performed RNA sequencing analysis. The gz-iPSC transcriptome showed robust expression of pluripotency-associated genes reported in human and mouse, suggesting evolutionary conservation among the species. This study provides insight into the iPSCs from a rare species and helps the understanding of the gene expression basis underlying mammalian pluripotent stem cells.
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References
1.
RyderOA and OnumaM. (2018). Viable cell culture banking for biodiversity characterization and conservation. Annu Rev Anim Biosci, 6:83–98.
2.
TakahashiK, TanabeK, OhnukiM, NaritaM, IchisakaT, TomodaK and YamanakaS. (2007). Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell, 131:861–872.
3.
TakahashiK and YamanakaS. (2006). Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell, 126:663–676.
4.
BogliottiYS, WuJ, VilarinoM, OkamuraD, SotoDA, ZhongC, SakuraiM, SampaioRV, SuzukiK, Izpisua BelmonteJC and RossPJ. (2018). Efficient derivation of stable primed pluripotent embryonic stem cells from bovine blastocysts. Proc Natl Acad Sci U S A, 115:2090–2095.
5.
FukudaT, DoiK, DonaiK, TakahashiK, KobayashiH, HiranoT, NishimoriK and YasueH. (2019). Global transcriptome analysis of pig induced pluripotent stem cells derived from six and four reprogramming factors. Sci Data, 6:190034.
BretonA, SharmaR, DiazAC, ParhamAG, GrahamA, NeilC, WhitelawCB, MilneE and DonadeuFX. (2013). Derivation and characterization of induced pluripotent stem cells from equine fibroblasts. Stem Cells Dev, 22:611–621.
10.
KhodadadiK, SumerH, PashaiaslM, LimS, WilliamsonM and VermaPJ. (2012). Induction of pluripotency in adult equine fibroblasts without c-MYC. Stem Cells Int, 2012:429160.
11.
MiyawakiS, KawamuraY, OiwaY, ShimizuA, HachiyaT, BonoH, KoyaI, OkadaY, KimuraT, et al. (2016). Tumour resistance in induced pluripotent stem cells derived from naked mole-rats. Nat Commun, 7:11471.
12.
DevikaAS, WruckW, AdjayeJ and SudheerS. (2019). The quest for pluripotency: a comparative analysis across mammalian species. Reproduction, 158:R97–R111.
EzashiT, YuanY and RobertsRM. (2016). Pluripotent stem cells from domesticated mammals. Annu Rev Anim Biosci, 4:223–253.
15.
KorodyML, FordSM, NguyenTD, PivaroffCG, Valiente-AlandiI, PetersonSE, RyderOA and LoringJF. (2021). Rrewinding extinction in the northern white rhinoceros: genetically diverse induced pluripotent stem cell bank for genetic rescue. Stem Cells Dev, 30:177–189.
16.
WeeratungaP, ShahsavariA, OvchinnikovDA, WolvetangEJ and WhitworthDJ. (2018). Induced pluripotent stem cells from a marsupial, the tasmanian devil (Sarcophilus harrisii): insight into the evolution of mammalian pluripotency. Stem Cells Dev, 27:112–122.
17.
WhitworthDJ, LimniosIJ, GauthierM-E, WeeratungaP, OvchinnikovDA, BaillieG, GrimmondSM, GravesJAM and WolvetangEJ. (2019). Platypus induced pluripotent stem cells: the unique pluripotency signature of a monotreme. Stem Cells Dev, 28:151–164.
18.
WunderlichS, KircherM, ViethB, HaaseA, MerkertS, BeierJ, GöhringG, GlageS, SchambachA, et al. (2014). Primate iPS cells as tools for evolutionary analyses. Stem Cell Res, 12:622–629.
19.
SemiK and TakashimaY. (2021). Pluripotent stem cells for the study of early human embryology. Dev Growth Differ, 63:104–115.
20.
LiX, PeiD and ZhengH. (2014). Transitions between epithelial and mesenchymal states during cell fate conversions. Protein Cell, 5:580–591.
21.
LiM and BelmonteJCI. (2017). Ground rules of the pluripotency gene regulatory network. Nat Rev Genet, 18:180–191.
22.
BrawandD, SoumillonM, NecsuleaA, JulienP, CsárdiG, HarriganP, WeierM, LiechtiA, Aximu-PetriA, et al. (2011). The evolution of gene expression levels in mammalian organs. Nature, 478:343–348.
23.
EndoY, KameiK and Inoue-MurayamaM. (2020). Genetic signatures of evolution of the pluripotency gene regulating network across mammals. Genome Biol Evol, 12:1806–1818.
24.
LiuY, MaY, YangJY, ChengD, LiuX, MaX, WestFD and WangH. (2014). Comparative gene expression signature of pig, human and mouse induced pluripotent stem cell lines reveals insight into pig pluripotency gene networks. Stem Cell Rev Reports, 10:162–176.
25.
RubensteinD, Low MackeyB, DavidsonZ, KebedeF and KingSRB. (2016). Equus grevyi. IUCN Red List Threat Species 8235. DOI: 10.2305/IUCN.UK.2016-3.RLTS.T7950A89624491.en.
26.
ItoH, LangenhorstT, OgdenR and Inoue-MurayamaM. (2015). Population genetic diversity and hybrid detection in captive zebras. Sci Rep, 5:13171.
27.
GlennVL, SchellJP, FakunleES, SimonR and PetersonSE. (2012). Isolation of human dermal fibroblasts from biopsies. In: Human Stem Cell Manual. LoringJF and PetersonSE, eds. Elsevier, Boston, MA, pp 129–141.
28.
LudwigTE, BergendahlV, LevensteinME, YuJ, ProbascoMD and ThomsonJA. (2006). Feeder-independent culture of human embryonic stem cells. Nat Methods, 3:637–646.
De CosterW, D'HertS, SchultzDT, CrutsM and Van BroeckhovenC. (2018). NanoPack: visualizing and processing long-read sequencing data. Bioinformatics, 34:2666–2669.
31.
LiH. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34:3094–3100.
32.
PatroR, DuggalG, LoveMI, IrizarryRA and KingsfordC. (2017). Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods, 14:417–419.
33.
SonesonC, LoveMI and RobinsonMD. (2016). Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000Research, 4:1521.
34.
KinsellaRJ, KahariA, HaiderS, ZamoraJ, ProctorG, SpudichG, Almeida-KingJ, StainesD, DerwentP, et al. (2011). Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database (Oxford), 2011:bar030.
35.
LoveMI, HuberW and AndersS. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol, 15:550.
36.
BenjaminiY and HochbergY. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B, 57:289–300.
37.
ZhuA, IbrahimJG and LoveMI. (2019). Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences. Bioinformatics, 35:2084–2092.
38.
MiH, EbertD, MuruganujanA, MillsC, AlbouL-P, MushayamahaT and ThomasPD. (2021). PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API. Nucleic Acids Res, 49:D394–D403.
39.
CarbonS, DouglassE, GoodBM, UnniDR, HarrisNL, MungallCJ, BasuS, ChisholmRL, DodsonRJ, et al. (2021). The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Res, 49:D325–D334.
40.
AshburnerM, BallCA, BlakeJA, BotsteinD, ButlerH, CherryJM, DavisAP, DolinskiK, DwightSS, et al. (2000). Gene Ontology: tool for the unification of biology. Nat Genet, 25:25–29.
41.
WatanabeK, UenoM, KamiyaD, NishiyamaA, MatsumuraM, WatayaT, TakahashiJB, NishikawaS, NishikawaS, MugurumaK and SasaiY. (2007). A ROCK inhibitor permits survival of dissociated human embryonic stem cells. Nat Biotechnol, 25:681–686.
42.
HannaJH, ChengAW, SahaK, KimJ, LengnerCJ, SoldnerF, CassadyJP, MuffatJ, CareyBW and JaenischR. (2010). Human embryonic stem cells with biological and epigenetic characteristics similar to those of mouse ESCs. Proc Natl Acad Sci U S A, 107:9222–9227.
43.
MusilovaP, KubickovaS, ZrnovaE, HorinP, VahalaJ and RubesJ. (2007). Karyotypic relationships among Equus grevyi, Equus burchelli and domestic horse defined using horse chromosome arm-specific probes. Chromosom Res, 15:807–813.
44.
Schell JP. (2012). Spontaneous differentiation of human pluripotent stem cells via embryoid body formation. In: Human Stem Cell Manual. LoringJF and PetersonSE, eds. Elsevier, Boston, MA, pp 363–373.
45.
LowryWE, RichterL, YachechkoR, PyleAD, TchieuJ, SridharanR, ClarkAT and PlathK. (2008). Generation of human induced pluripotent stem cells from dermal fibroblasts. Proc Natl Acad Sci U S A, 105:2883–2888.
46.
TanakaY, HysolliE, SuJ, XiangY, KimKY, ZhongM, LiY, HeydariK, EuskirchenG, et al. (2015). Transcriptome signature and regulation in human somatic cell reprogramming. Stem Cell Reports, 4:1125–1139.
47.
WuX, Dao ThiVL, HuangY, BillerbeckE, SahaD, HoffmannH-H, WangY, SilvaLAV, SarbanesS, et al. (2018). Intrinsic immunity shapes viral resistance of stem cells. Cell, 172:423.e25–438.e25.
48.
ChaY, HanM-J, ChaH-J, ZoldanJ, BurkartA, JungJH, JangY, KimC-H, JeongH-C, et al. (2017). Metabolic control of primed human pluripotent stem cell fate and function by the miR-200c–SIRT2 axis. Nat Cell Biol, 19:445–456.
49.
ThomsonJA, Itskovitz-EldorJ, ShapiroSS, WaknitzMA, SwiergielJJ, MarshallVS and JonesJM. (1998). Embryonic stem cell lines derived from human blastocysts. Science, 282:1145–1147.
50.
NiwaH, MiyazakiJ and SmithAG. (2000). Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells. Nat Genet, 24:372–376.
51.
NicholsJ, ZevnikB, AnastassiadisK, NiwaH, Klewe-NebeniusD, ChambersI, SchölerH and SmithA. (1998). Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4. Cell, 95:379–391.
52.
OkanoM, BellDW, HaberDA and LiE. (1999). DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell, 99:247–257.
53.
FagooneeS, BearziC, Di CuntoF, ClohessyJG, RizziR, ReschkeM, TolosanoE, ProveroP, PandolfiPP, SilengoL and AltrudaF (2013). The RNA binding protein ESRP1 fine-tunes the expression of pluripotency-related factors in mouse embryonic stem cells. PLoS One, 8:e72300.
54.
GonzálezB, DenzelS, MackB, ConradM and GiresO. (2009). EpCAM is involved in maintenance of the murine embryonic stem cell phenotype. Stem Cells, 27:1782–1791.
55.
PokuttaS and WeisWI. (2007). Structure and mechanism of cadherins and catenins in cell-cell contacts. Annu Rev Cell Dev Biol, 23:237–261.
56.
SoncinF, MohametL, EckardtD, RitsonS, EasthamAM, BobolaN, RussellA, DaviesS, KemlerR, MerryCLR and WardCM. (2009). Abrogation of E-cadherin-mediated cell-cell contact in mouse embryonic stem cells results in reversible LIF-independent self-renewal. Stem Cells, 27:2069–2080.
57.
MuoriaPK, MuruthiP, KariukiWK, HassanBA, MijeleD and OgugeNO. (2007). Anthrax outbreak among Grevy's zebra (Equus grevyi) in Samburu, Kenya. Afr J Ecol, 45:483–489.
58.
LermenD, BlömekeB, BrowneR, ClarkeA, DycePW, FixemerT, FuhrGR, HoltWV, JewgenowK, et al. (2009). Cryobanking of viable biomaterials: implementation of new strategies for conservation purposes. Mol Ecol, 18:1030–1033.
59.
YoshimatsuS, NakajimaM, IguchiA, SanosakaT, SatoT, NakamuraM, NakajimaR, AraiE, IshikawaM, et al. (2021). Non-viral induction of transgene-free iPSCs from somatic fibroblasts of multiple mammalian species. Stem Cell Reports, 16:754–770.
60.
GuentherMG, FramptonGM, SoldnerF, HockemeyerD, MitalipovaM, JaenischR and YoungRA. (2010). Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells. Cell Stem Cell, 7:249–257.
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