CoChat
Sign Up
Cited by 310Pluripotent Stem Cells ResearchCRISPR and Genetic EngineeringDevelopmental Biology and Gene Regulation

A reference human induced pluripotent stem cell line for large-scale collaborative studies

Open access
Pantazis, Caroline B., Yang, Andrian, Lara, Erika, McDonough, Justin A., Blauwendraat, Cornelis, Peng, Lirong, Oguro, Hideyuki, Kanaujiya, Jitendra +87 more·2022·Cell Stem Cell
DOI 10.1016/j.stem.2022.11.004PMC PMC9782786

Published version of a preprint

Open this paper in CoChat — free accountOpen PDF

Abstract

Abstract Human induced pluripotent stem cell (iPSC) lines are a powerful tool for studying development and disease, but the considerable phenotypic variation between lines makes it challenging to replicate key findings and integrate data across research groups. To address this issue, we sub-cloned candidate iPSC lines and deeply characterised their genetic properties using whole genome sequencing, their genomic stability upon CRISPR/Cas9-based gene editing, and their phenotypic properties including differentiation to commonly-used cell types. These studies identified KOLF2.1J as an all-around well-performing iPSC line. We then shared KOLF2.1J with groups around the world who tested its performance in head-to-head comparisons with their own preferred iPSC lines across a diverse range of differentiation protocols and functional assays. On the strength of these findings, we have made KOLF2.1J and hundreds of its gene-edited derivative clones readily accessible to promote the standardization required for large-scale collaborative science in the stem cell field. Summary The authors of this collaborative study deeply characterized human induced pluripotent stem cell (iPSC) lines to rationally select a clonally-derived cell line that performs well across multiple modalities. KOLF2.1J was identified as a candidate reference cell line based on single-cell analysis of its gene expression in the pluripotent state, whole genome sequencing, genomic stability after highly efficient CRISPR-mediated gene editing, integrity of the p53 pathway, and the efficiency with which it differentiated into multiple target cell populations. Since it is deeply characterized and can be readily acquired, KOLF2.1J is an attractive reference cell line for groups working with iPSCs. Graphical abstract

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1016/j.stem.2022.11.004

Cites

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • The study used two isogenic iPSC sets (KOLF2.1J and BIONi037) to ensure rigor and reproducibility.

    “To ensure rigor and reproducibility, we chose to isolate lipid droplets from human iPSC-derived astrocytes derived from two iPSC sets (KOLF2.1 J and BIONi037)38,39(Fig. 1A).”

    From APOE genotypes differentially remodel the astrocytic lipid droplet proteome to shape lipid droplet dynamics (2026) · cites this paper as [39]

    The Results section, “Distribution and community-based characterization of KOLF2.1J” (page unavailable), reports that KOLF2.1J was differentiated into astrocytes; the Discussion presents it as a reference line intended to improve reproducibility. Our copy does not identify BIONi037 or describe the two named lines as isogenic iPSC sets. The lipid-droplet isolation is the citing authors’ own method, not a finding attributed to this source. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

  • The iPSCs were generated as previously described from the KOLF2.1 J parental cell line.

    “These iPSCs were generated as previously described from the KOLF2.1 J parental cell line 54 .”

    From APOE4-drives brain bioenergetic shifts independent of Alzheimer’s disease pathology (2026) · cites this paper as [54]

  • Three ApoE3 and ApoE4 isogenic iPSC pairs were used to determine the effect of APOE4 genotype without inter-donor variability.

    “Three ApoE3 and ApoE4 isogenic iPSCs pairs were used to determine the effect of APOE4 genotype without inter-donor variability.5”

    From ApoE4-dependent lysosomal cholesterol accumulation impairs mitochondrial homeostasis and oxidative phosphorylation in human astrocytes (2023) · cites this paper as [12]

    The Introduction says that genetic background can influence iPSC phenotypes and describes the value of isogenic comparisons. The Results identify APOE E4 in two cell lines, but neither passage reports using three APOE3/APOE4 isogenic pairs to assess genotype effects. Searches for the pairs and inter-donor variability found no passage establishing that study design. (LLM, conf=0.76)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

No citation lists for this paper

No citation lists for this paper yet — checked again daily.

References 115 · Cited by 310

Research works printed but not linked: 92

  1. [1]Kwart D, Gregg A, Scheckel C, Murphy EA, Paquet D, Duffield M, Fak J, Olsen O, Darnell RB, and Tessier-Lavigne M (2019). A Large Panel of Isogenic APP and PSEN1 Mutant Human iPSC Neurons Reveals Shared Endosomal Abnormalities Mediated by APP beta-CTFs, Not Abeta. Neuron 104, 256– 270 e255. 10.1016/j.neuron.2019.07.010. 31416668 · DOI
  2. [2]Konttinen H, Cabral-da-Silva MEC, Ohtonen S, Wojciechowski S, Shakirzyanova A, Caligola S, Giugno R, Ishchenko Y, Hernandez D, Fazaludeen MF, (2019). PSEN1DeltaE9, APPswe, and APOE4 Confer Disparate Phenotypes in Human iPSC-Derived Microglia. Stem Cell Reports 13, 669– 683. 10.1016/j.stemcr.2019.08.004. 31522977 PMC6829767 · DOI · Paper page
  3. [3]Guttikonda SR, Sikkema L, Tchieu J, Saurat N, Walsh RM, Harschnitz O, Ciceri G, Sneeboer M, Mazutis L, Setty M, (2021). Fully defined human pluripotent stem cell-derived microglia and tri-culture system model C3 production in Alzheimer’s disease. Nat Neurosci 24, 343– 354. 10.1038/s41593-020-00796-z. 33558694 PMC8382543 · DOI
  4. [4]Doetschman T (2009). Influence of genetic background on genetically engineered mouse phenotypes. Methods Mol Biol 530, 423– 433. 10.1007/978-1-59745-471-1_23. 19266333 PMC2805848 · DOI
  5. [6]Threadgill DW, Dlugosz AA, Hansen LA, Tennenbaum T, Lichti U, Yee D, LaMantia C, Mourton T, Herrup K, Harris RC, and (1995). Targeted disruption of mouse EGF receptor: effect of genetic background on mutant phenotype. Science 269, 230– 234. 10.1126/science.7618084. 7618084 · DOI
  6. [7]Sterken MG, Snoek LB, Kammenga JE, and Andersen EC (2015). The laboratory domestication of Caenorhabditis elegans. Trends Genet 31, 224– 231. 10.1016/j.tig.2015.02.009. 25804345 PMC4417040 · DOI
  7. [8]Mackay TFC, and Huang W (2018). Charting the genotype-phenotype map: lessons from the Drosophila melanogaster Genetic Reference Panel. Wiley Interdiscip Rev Dev Biol 7. 10.1002/wdev.289. PMC5746472 28834395 · DOI
  8. [9]Sittig LJ, Carbonetto P, Engel KA, Krauss KS, Barrios-Camacho CM, and Palmer AA (2016). Genetic Background Limits Generalizability of Genotype-Phenotype Relationships. Neuron 91, 1253– 1259. 10.1016/j.neuron.2016.08.013. 27618673 PMC5033712 · DOI
  9. [10]Roberts B, Haupt A, Tucker A, Grancharova T, Arakaki J, Fuqua MA, Nelson A, Hookway C, Ludmann SA, Mueller IA, (2017). Systematic gene tagging using CRISPR/Cas9 in human stem cells to illuminate cell organization. Mol Biol Cell 28, 2854– 2874. 10.1091/mbc.E17-03-0209. 28814507 PMC5638588 · DOI · Paper page
  10. [11]Roberts B, Hendershott MC, Arakaki J, Gerbin KA, Malik H, Nelson A, Gehring J, Hookway C, Ludmann SA, Yang R, (2019). Fluorescent Gene Tagging of Transcriptionally Silent Genes in hiPSCs. Stem Cell Reports 12, 1145– 1158. 10.1016/j.stemcr.2019.03.001. 30956114 PMC6522946 · DOI
  11. [12]Ramos DM, Skarnes WC, Singleton AB, Cookson MR, and Ward ME (2021). Tackling neurodegenerative diseases with genomic engineering: A new stem cell initiative from the NIH. Neuron 109, 1080– 1083. 10.1016/j.neuron.2021.03.022. 33831364 PMC8985232 · DOI
  12. [13]Reilly L, Peng L, Lara E, Ramos D, Fernandopulle M, Pantazis CB, Stadler J, Santiana M, Dadu A, Iben J, (2021). A fully automated FAIMS-DIA proteomic pipeline for high-throughput characterization of iPSC-derived neurons. bioRxiv, 2021.2011.2024.469921. 10.1101/2021.11.24.469921. · DOI
  13. [14]Mekhoubad S, Bock C, de Boer AS, Kiskinis E, Meissner A, and Eggan K (2012). Erosion of dosage compensation impacts human iPSC disease modeling. Cell Stem Cell 10, 595– 609. 10.1016/j.stem.2012.02.014. 22560080 PMC3603710 · DOI
  14. [15]Bar S, Seaton LR, Weissbein U, Eldar-Geva T, and Benvenisty N (2019). Global Characterization of X Chromosome Inactivation in Human Pluripotent Stem Cells. Cell Rep 27, 20– 29 e23. 10.1016/j.celrep.2019.03.019. 30943402 · DOI
  15. [16]Hildebrandt MR, Reuter MS, Wei W, Tayebi N, Liu J, Sharmin S, Mulder J, Lesperance LS, Brauer PM, Mok RSF, (2019). Precision Health Resource of Control iPSC Lines for Versatile Multilineage Differentiation. Stem Cell Reports 13, 1126– 1141. 10.1016/j.stemcr.2019.11.003. 31813827 PMC6915802 · DOI
  16. [17]Robinson E, McKenna MJ, Bedford JS, Goodwin EH, Cornforth MN, Bailey SM, and Ray FA (2019). Directional Genomic Hybridization (dGH) for Detection of Intrachromosomal Rearrangements. Methods Mol Biol 1984, 107– 116. 10.1007/978-1-4939-9432-8_13. 31267426 · DOI
  17. [19]Halliwell J, Barbaric I, and Andrews PW (2020). Acquired genetic changes in human pluripotent stem cells: origins and consequences. Nat Rev Mol Cell Biol 21, 715– 728. 10.1038/s41580-020-00292-z. 32968234 · DOI
  18. [21]Avior Y, Lezmi E, Eggan K, and Benvenisty N (2021). Cancer-Related Mutations Identified in Primed Human Pluripotent Stem Cells. Cell Stem Cell 28, 10– 11. 10.1016/j.stem.2020.11.013. 33321073 · DOI
  19. [22]Ihry RJ, Worringer KA, Salick MR, Frias E, Ho D, Theriault K, Kommineni S, Chen J, Sondey M, Ye C, (2018). p53 inhibits CRISPR-Cas9 engineering in human pluripotent stem cells. Nat Med 24, 939– 946. 10.1038/s41591-018-0050-6. 29892062 · DOI · Paper page
  20. [23]Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alfoldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP, (2020). The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581, 434– 443. 10.1038/s41586-020-2308-7. 32461654 PMC7334197 · DOI · Paper page
  21. [24]Nothen MM, Cichon S, Hemmer S, Hebebrand J, Remschmidt H, Lehmkuhl G, Poustka F, Schmidt M, Catalano M, Fimmers R, and (1994). Human dopamine D4 receptor gene: frequent occurrence of a null allele and observation of homozygosity. Hum Mol Genet 3, 2207– 2212. 10.1093/hmg/3.12.2207. 7881421 · DOI
  22. [25]Shaheen R, Sebai MA, Patel N, Ewida N, Kurdi W, Altweijri I, Sogaty S, Almardawi E, Seidahmed MZ, Alnemri A, (2017). The genetic landscape of familial congenital hydrocephalus. Ann Neurol 81, 890– 897. 10.1002/ana.24964. 28556411 · DOI
  23. [27]Nalls MA, Blauwendraat C, Vallerga CL, Heilbron K, Bandres-Ciga S, Chang D, Tan M, Kia DA, Noyce AJ, Xue A, (2019). Identification of novel risk loci, causal insights, and heritable risk for Parkinson’s disease: a meta-analysis of genome-wide association studies. Lancet Neurol 18, 1091– 1102. 10.1016/S1474-4422(19)30320-5. 31701892 PMC8422160 · DOI · Paper page
  24. [28]Skarnes WC, Ning G, Giansiracusa S, Cruz AS, Blauwendraat C, Saavedra B, Holden K, Cookson MR, Ward ME, and McDonough JA (2021). Controlling homology-directed repair outcomes in human stem cells with dCas9. bioRxiv, 2021.2012.2016.472942. 10.1101/2021.12.16.472942. · DOI
  25. [29]Skarnes WC, Pellegrino E, and McDonough JA (2019). Improving homology-directed repair efficiency in human stem cells. Methods 164–165, 18– 28. 10.1016/j.ymeth.2019.06.016. 31216442 · DOI
  26. [30]Apte SS, Mattei MG, and Olsen BR (1994). Cloning of the cDNA encoding human tissue inhibitor of metalloproteinases-3 (TIMP-3) and mapping of the TIMP3 gene to chromosome 22. Genomics 19, 86– 90. 10.1006/geno.1994.1016. 8188246 · DOI
  27. [32]Merkle FT, Neuhausser WM, Santos D, Valen E, Gagnon JA, Maas K, Sandoe J, Schier AF, and Eggan K (2015). Efficient CRISPR-Cas9-mediated generation of knockin human pluripotent stem cells lacking undesired mutations at the targeted locus. Cell Rep 11, 875– 883. 10.1016/j.celrep.2015.04.007. 25937281 PMC5533178 · DOI · Paper page
  28. [33]Blauwendraat C, Faghri F, Pihlstrom L, Geiger JT, Elbaz A, Lesage S, Corvol JC, May P, Nicolas A, Abramzon Y, (2017). NeuroChip, an updated version of the NeuroX genotyping platform to rapidly screen for variants associated with neurological diseases. Neurobiol Aging 57, 247 e249– 247 e213. 10.1016/j.neurobiolaging.2017.05.009. PMC5534378 28602509 · DOI
  29. [35]International Stem Cell I, Amps K, Andrews PW, Anyfantis G, Armstrong L, Avery S, Baharvand H, Baker J, Baker D, Munoz MB, (2011). Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage. Nat Biotechnol 29, 1132– 1144. 10.1038/nbt.2051. 22119741 PMC3454460 · DOI
  30. [37]Lefort N, Feyeux M, Bas C, Feraud O, Bennaceur-Griscelli A, Tachdjian G, Peschanski M, and Perrier AL (2008). Human embryonic stem cells reveal recurrent genomic instability at 20q11.21. Nat Biotechnol 26, 1364– 1366. 10.1038/nbt.1509. 19029913 · DOI
  31. [38]Narva E, Autio R, Rahkonen N, Kong L, Harrison N, Kitsberg D, Borghese L, Itskovitz-Eldor J, Rasool O, Dvorak P, (2010). High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity. Nat Biotechnol 28, 371– 377. 10.1038/nbt.1615. 20351689 · DOI
  32. [39]Spits C, Mateizel I, Geens M, Mertzanidou A, Staessen C, Vandeskelde Y, Van der Elst J, Liebaers I, and Sermon K (2008). Recurrent chromosomal abnormalities in human embryonic stem cells. Nat Biotechnol 26, 1361– 1363. 10.1038/nbt.1510. 19029912 · DOI
  33. [40]Wu H, Kim KJ, Mehta K, Paxia S, Sundstrom A, Anantharaman T, Kuraishy AI, Doan T, Ghosh J, Pyle AD, (2008). Copy number variant analysis of human embryonic stem cells. Stem Cells 26, 1484– 1489. 10.1634/stemcells.2007-0993. 18369100 PMC3901366 · DOI
  34. [41]Markouli C, Couvreu De Deckersberg E, Regin M, Nguyen HT, Zambelli F, Keller A, Dziedzicka D, De Kock J, Tilleman L, Van Nieuwerburgh F, (2019). Gain of 20q11.21 in Human Pluripotent Stem Cells Impairs TGF-beta-Dependent Neuroectodermal Commitment. Stem Cell Reports 13, 163– 176. 10.1016/j.stemcr.2019.05.005. 31178415 PMC6627003 · DOI · Paper page
  35. [42]Lee JH, Park IH, Gao Y, Li JB, Li Z, Daley GQ, Zhang K, and Church GM (2009). A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells. PLoS Genet 5, e1000718. 10.1371/journal.pgen.1000718. 19911041 PMC2766639 · DOI
  36. [44]Fadista J, Oskolkov N, Hansson O, and Groop L (2017). LoFtool: a gene intolerance score based on loss-of-function variants in 60 706 individuals. Bioinformatics 33, 471– 474. 10.1093/bioinformatics/btv602. 27563026 · DOI
  37. [45]Rehm HL, Berg JS, Brooks LD, Bustamante CD, Evans JP, Landrum MJ, Ledbetter DH, Maglott DR, Martin CL, Nussbaum RL, (2015). ClinGen--the Clinical Genome Resource. N Engl J Med 372, 2235– 2242. 10.1056/NEJMsr1406261. 26014595 PMC4474187 · DOI · Paper page
  38. [46]Fenske P, Grauel MK, Brockmann MM, Dorrn AL, Trimbuch T, and Rosenmund C (2019). Autaptic cultures of human induced neurons as a versatile platform for studying synaptic function and neuronal morphology. Sci Rep 9, 4890. 10.1038/s41598-019-41259-1. 30894602 PMC6427022 · DOI
  39. [47]Rhee HJ, Shaib AH, Rehbach K, Lee C, Seif P, Thomas C, Gideons E, Guenther A, Krutenko T, Hebisch M, (2019). An Autaptic Culture System for Standardized Analyses of iPSC-Derived Human Neurons. Cell Rep 27, 2212– 2228 e2217. 10.1016/j.celrep.2019.04.059. 31091457 · DOI
  40. [48]Meijer M, Rehbach K, Brunner JW, Classen JA, Lammertse HCA, van Linge LA, Schut D, Krutenko T, Hebisch M, Cornelisse LN, (2019). A Single-Cell Model for Synaptic Transmission and Plasticity in Human iPSC-Derived Neurons. Cell Rep 27, 2199– 2211 e2196. 10.1016/j.celrep.2019.04.058. 31091456 · DOI
  41. [49]Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, Tomoda K, and Yamanaka S (2007). Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131, 861– 872. 10.1016/j.cell.2007.11.019. 18035408 · DOI · Paper page
  42. [50]Bennett DA, Buchman AS, Boyle PA, Barnes LL, Wilson RS, and Schneider JA (2018). Religious Orders Study and Rush Memory and Aging Project. J Alzheimers Dis 64, S161– S189. 10.3233/JAD-179939. 29865057 PMC6380522 · DOI · Paper page
  43. [52]Jerber J, Seaton DD, Cuomo ASE, Kumasaka N, Haldane J, Steer J, Patel M, Pearce D, Andersson M, Bonder MJ, (2021). Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation. Nat Genet 53, 304– 312. 10.1038/s41588-021-00801-6. 33664506 PMC7610897 · DOI
  44. [53]Mitchell JM, Nemesh J, Ghosh S, Handsaker RE, Mello CJ, Meyer D, Raghunathan K, de Rivera H, Tegtmeyer M, Hawes D, (2020). Mapping genetic effects on cellular phenotypes with “cell villages”. bioRxiv, 2020.2006.2029.174383. 10.1101/2020.06.29.174383. · DOI
  45. [54]Merkle FT, Ghosh S, Genovese G, Handsaker RE, Kashin S, Meyer D, Karczewski KJ, O’Dushlaine C, Pato C, Pato M, (2022). Whole-genome analysis of human embryonic stem cells enables rational line selection based on genetic variation. Cell Stem Cell 29, 472– 486 e477. 10.1016/j.stem.2022.01.011. 35176222 PMC8900618 · DOI
  46. [55]Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ, (2017). Common genetic variation drives molecular heterogeneity in human iPSCs. Nature 546, 370– 375. 10.1038/nature22403. 28489815 PMC5524171 · DOI · Paper page
  47. [56]Bruntraeger M, Byrne M, Long K, and Bassett AR (2019). Editing the Genome of Human Induced Pluripotent Stem Cells Using CRISPR/Cas9 Ribonucleoprotein Complexes. Methods Mol Biol 1961, 153– 183. 10.1007/978-1-4939-9170-9_11. 30912046 · DOI
  48. [57]Tian R, Abarientos A, Hong J, Hashemi SH, Yan R, Drager N, Leng K, Nalls MA, Singleton AB, Xu K, (2021). Genome-wide CRISPRi/a screens in human neurons link lysosomal failure to ferroptosis. Nat Neurosci 24, 1020– 1034. 10.1038/s41593-021-00862-0. 34031600 PMC8254803 · DOI · Paper page
  49. [59]Li Z, Farias FHG, Dube U, Del-Aguila JL, Mihindukulasuriya KA, Fernandez MV, Ibanez L, Budde JP, Wang F, Lake AM, (2020). The TMEM106B FTLD-protective variant, rs1990621, is also associated with increased neuronal proportion. Acta Neuropathol 139, 45– 61. 10.1007/s00401-019-02066-0. 31456032 PMC6942643 · DOI · Paper page
  50. [60]Assou S, Girault N, Plinet M, Bouckenheimer J, Sansac C, Combe M, Mianne J, Bourguignon C, Fieldes M, Ahmed E, (2020). Recurrent Genetic Abnormalities in Human Pluripotent Stem Cells: Definition and Routine Detection in Culture Supernatant by Targeted Droplet Digital PCR. Stem Cell Reports 14, 1– 8. 10.1016/j.stemcr.2019.12.004. 31902703 PMC6962701 · DOI
  51. [61]el-Deiry WS, Tokino T, Velculescu VE, Levy DB, Parsons R, Trent JM, Lin D, Mercer WE, Kinzler KW, and Vogelstein B (1993). WAF1, a potential mediator of p53 tumor suppression. Cell 75, 817– 825. 10.1016/0092-8674(93)90500-p. 8242752 · DOI · Paper page
  52. [62]Yusa K, Zhou L, Li MA, Bradley A, and Craig NL (2011). A hyperactive piggyBac transposase for mammalian applications. Proc Natl Acad Sci U S A 108, 1531– 1536. 10.1073/pnas.1008322108. 21205896 PMC3029773 · DOI
  53. [63]Ray FA, Zimmerman E, Robinson B, Cornforth MN, Bedford JS, Goodwin EH, and Bailey SM (2013). Directional genomic hybridization for chromosomal inversion discovery and detection. Chromosome Res 21, 165– 174. 10.1007/s10577-013-9345-0. 23572395 PMC3627024 · DOI
  54. [64]Howe B, Umrigar A, and Tsien F (2014). Chromosome preparation from cultured cells. J Vis Exp, e50203. 10.3791/50203. 24513647 PMC4091199 · DOI
  55. [65]Wang K, Li M, and Hakonarson H (2010). ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38, e164. 10.1093/nar/gkq603. 20601685 PMC2938201 · DOI
  56. [66]Bycroft C, Freeman C, Petkova D, Band G, Elliott LT, Sharp K, Motyer A, Vukcevic D, Delaneau O, O’Connell J, (2018). The UK Biobank resource with deep phenotyping and genomic data. Nature 562, 203– 209. 10.1038/s41586-018-0579-z. 30305743 PMC6786975 · DOI · Paper page
  57. [67]Gogarten SM, Bhangale T, Conomos MP, Laurie CA, McHugh CP, Painter I, Zheng X, Crosslin DR, Levine D, Lumley T, (2012). GWASTools: an R/Bioconductor package for quality control and analysis of genome-wide association studies. Bioinformatics 28, 3329– 3331. 10.1093/bioinformatics/bts610. 23052040 PMC3519456 · DOI
  58. [68]Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, and Li H (2021). Twelve years of SAMtools and BCFtools. Gigascience 10. 10.1093/gigascience/giab008. PMC7931819 33590861 · DOI
  59. [69]Robinson JT, Thorvaldsdottir H, Wenger AM, Zehir A, and Mesirov JP (2017). Variant Review with the Integrative Genomics Viewer. Cancer Res 77, e31– e34. 10.1158/0008-5472.CAN-17-0337. 29092934 PMC5678989 · DOI
  60. [70]Fernandopulle MS, Prestil R, Grunseich C, Wang C, Gan L, and Ward ME (2018). Transcription Factor-Mediated Differentiation of Human iPSCs into Neurons. Curr Protoc Cell Biol 79, e51. 10.1002/cpcb.51. 29924488 PMC6993937 · DOI · Paper page
  61. [71]Kirwan P, Jura M, and Merkle FT (2017). Generation and Characterization of Functional Human Hypothalamic Neurons. Curr Protoc Neurosci 81, 3 33 31– 33 33 24. 10.1002/cpns.40. 29064566 · DOI
  62. [72]Merkle FT, Maroof A, Wataya T, Sasai Y, Studer L, Eggan K, and Schier AF (2015). Generation of neuropeptidergic hypothalamic neurons from human pluripotent stem cells. Development 142, 633– 643. 10.1242/dev.117978. 25670790 PMC4325380 · DOI
  63. [73]McGinnis CS, Patterson DM, Winkler J, Conrad DN, Hein MY, Srivastava V, Hu JL, Murrow LM, Weissman JS, Werb Z, (2019). MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices. Nat Methods 16, 619– 626. 10.1038/s41592-019-0433-8. 31209384 PMC6837808 · DOI · Paper page
  64. [74]Lun ATL, Riesenfeld S, Andrews T, Dao TP, Gomes T, participants in the 1st Human Cell Atlas J, and Marioni JC (2019). EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data. Genome Biol 20, 63. 10.1186/s13059-019-1662-y. 30902100 PMC6431044 · DOI
  65. [75]Lun AT, McCarthy DJ, and Marioni JC (2016). A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor. F1000Res 5, 2122. 10.12688/f1000research.9501.2. 27909575 PMC5112579 · DOI
  66. [76]Tirosh I, Izar B, Prakadan SM, Wadsworth MH 2nd, Treacy D, Trombetta JJ, Rotem A, Rodman C, Lian C, Murphy G, (2016). Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science 352, 189– 196. 10.1126/science.aad0501. 27124452 PMC4944528 · DOI · Paper page
  67. [78]Bais AS, and Kostka D (2020). scds: computational annotation of doublets in single-cell RNA sequencing data. Bioinformatics 36, 1150– 1158. 10.1093/bioinformatics/btz698. 31501871 PMC7703774 · DOI · Paper page
  68. [82]Boulting GL, Kiskinis E, Croft GF, Amoroso MW, Oakley DH, Wainger BJ, Williams DJ, Kahler DJ, Yamaki M, Davidow L, (2011). A functionally characterized test set of human induced pluripotent stem cells. Nat Biotechnol 29, 279– 286. 10.1038/nbt.1783. 21293464 PMC3229307 · DOI
  69. [83]Chen Y, Tristan CA, Chen L, Jovanovic VM, Malley C, Chu PH, Ryu S, Deng T, Ormanoglu P, Tao D, (2021). A versatile polypharmacology platform promotes cytoprotection and viability of human pluripotent and differentiated cells. Nat Methods 18, 528– 541. 10.1038/s41592-021-01126-2. 33941937 PMC8314867 · DOI
  70. [85]Kriks S, Shim JW, Piao J, Ganat YM, Wakeman DR, Xie Z, Carrillo-Reid L, Auyeung G, Antonacci C, Buch A, (2011). Dopamine neurons derived from human ES cells efficiently engraft in animal models of Parkinson’s disease. Nature 480, 547– 551. 10.1038/nature10648. 22056989 PMC3245796 · DOI
  71. [86]Shi Y, Kirwan P, and Livesey FJ (2012). Directed differentiation of human pluripotent stem cells to cerebral cortex neurons and neural networks. Nat Protoc 7, 1836– 1846. 10.1038/nprot.2012.116. 22976355 · DOI · Paper page
  72. [87]Arber C, Precious SV, Cambray S, Risner-Janiczek JR, Kelly C, Noakes Z, Fjodorova M, Heuer A, Ungless MA, Rodriguez TA, (2015). Activin A directs striatal projection neuron differentiation of human pluripotent stem cells. Development 142, 1375– 1386. 10.1242/dev.117093. 25804741 PMC4378247 · DOI
  73. [88]Surmacz B, Fox H, Gutteridge A, Fish P, Lubitz S, and Whiting P (2012). Directing differentiation of human embryonic stem cells toward anterior neural ectoderm using small molecules. Stem Cells 30, 1875– 1884. 10.1002/stem.1166. 22761025 · DOI
  74. [89]Moya N, Cutts J, Gaasterland T, Willert K, and Brafman DA (2014). Endogenous WNT signaling regulates hPSC-derived neural progenitor cell heterogeneity and specifies their regional identity. Stem Cell Reports 3, 1015– 1028. 10.1016/j.stemcr.2014.10.004. 25458891 PMC4264562 · DOI
  75. [90]Heinrich L, Zafar F, Morato Torres CA, Singh J, Khan A, Chen MY, Hempel C, Nikulina N, Mulholland J, Braubach O, and Schule B (2022). Multiplex imaging of human induced pluripotent stem cell-derived neurons with CO-Detection by indEXing (CODEX) technology. J Neurosci Methods 378, 109653. 10.1016/j.jneumeth.2022.109653. 35724898 · DOI
  76. [92]Srinivasaraghavan V, Zafar F, and Schuele B (2022). Gene Expression Analysis in Stem Cell-derived Cortical Neuronal Cultures Using Multi-well SYBR Green Quantitative PCR Arrays. Bio-Protocol 12, e4283. 10.21769/BioProtoc.4283. PMC9350924 35978575 · DOI
  77. [94]Schmid B, Holst B, Poulsen U, Jorring I, Clausen C, Rasmussen M, Mau-Holzmann UA, Steeg R, Nuthall H, Ebneth A, and Cabrera-Socorro A (2021). Generation of two gene edited iPSC-lines carrying a DOX-inducible NGN2 expression cassette with and without GFP in the AAVS1 locus. Stem Cell Res 52, 102240. 10.1016/j.scr.2021.102240. 33610017 · DOI
  78. [97]Reifschneider A, Robinson S, van Lengerich B, Gnorich J, Logan T, Heindl S, Vogt MA, Weidinger E, Riedl L, Wind K, (2022). Loss of TREM2 rescues hyperactivation of microglia, but not lysosomal deficits and neurotoxicity in models of progranulin deficiency. EMBO J 41, e109108. 10.15252/embj.2021109108. 35019161 PMC8844989 · DOI · Paper page
  79. [98]Dalby B, Cates S, Harris A, Ohki EC, Tilkins ML, Price PJ, and Ciccarone VC (2004). Advanced transfection with Lipofectamine 2000 reagent: primary neurons, siRNA, and high-throughput applications. Methods 33, 95– 103. 10.1016/j.ymeth.2003.11.023. 15121163 · DOI · Paper page
  80. [100]Sposito T, Preza E, Mahoney CJ, Seto-Salvia N, Ryan NS, Morris HR, Arber C, Devine MJ, Houlden H, Warner TT, (2015). Developmental regulation of tau splicing is disrupted in stem cell-derived neurons from frontotemporal dementia patients with the 10 + 16 splice-site mutation in MAPT. Hum Mol Genet 24, 5260– 5269. 10.1093/hmg/ddv246. 26136155 PMC4550814 · DOI · Paper page
  81. [101]Chal J, Al Tanoury Z, Hestin M, Gobert B, Aivio S, Hick A, Cherrier T, Nesmith AP, Parker KK, and Pourquie O (2016). Generation of human muscle fibers and satellite-like cells from human pluripotent stem cells in vitro. Nat Protoc 11, 1833– 1850. 10.1038/nprot.2016.110. 27583644 · DOI
  82. [102]Gantner CW, Hunt CPJ, Niclis JC, Penna V, McDougall SJ, Thompson LH, and Parish CL (2021). FGF-MAPK signaling regulates human deep-layer corticogenesis. Stem Cell Reports 16, 1262– 1275. 10.1016/j.stemcr.2021.03.014. 33836146 PMC8185433 · DOI
  83. [103]Coyne AN, Zaepfel BL, Hayes L, Fitchman B, Salzberg Y, Luo EC, Bowen K, Trost H, Aigner S, Rigo F, (2020). G4C2 Repeat RNA Initiates a POM121-Mediated Reduction in Specific Nucleoporins in C9orf72 ALS/FTD. Neuron 107, 1124– 1140 e1111. 10.1016/j.neuron.2020.06.027. 32673563 PMC8077944 · DOI · Paper page
  84. [104]Martinez FJ, Pratt GA, Van Nostrand EL, Batra R, Huelga SC, Kapeli K, Freese P, Chun SJ, Ling K, Gelboin-Burkhart C, (2016). Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System. Neuron 92, 780– 795. 10.1016/j.neuron.2016.09.050. 27773581 PMC5123850 · DOI
  85. [105]Gutbier S, Wanke F, Dahm N, Rummelin A, Zimmermann S, Christensen K, Kochl F, Rautanen A, Hatje K, Geering B, (2020). Large-Scale Production of Human iPSC-Derived Macrophages for Drug Screening. Int J Mol Sci 21. 10.3390/ijms21134808. PMC7370446 32645954 · DOI
  86. [106]Schmidt EJ, Funes S, McKeon JE, Morgan BR, Boopathy S, O’Connor LC, Bilsel O, Massi F, Jegou A, and Bosco DA (2021). ALS-linked PFN1 variants exhibit loss and gain of functions in the context of formin-induced actin polymerization. Proc Natl Acad Sci U S A 118. 10.1073/pnas.2024605118. PMC8201830 34074767 · DOI
  87. [108]Novotny R, Langer F, Mahler J, Skodras A, Vlachos A, Wegenast-Braun BM, Kaeser SA, Neher JJ, Eisele YS, Pietrowski MJ, (2016). Conversion of Synthetic Abeta to In Vivo Active Seeds and Amyloid Plaque Formation in a Hippocampal Slice Culture Model. J Neurosci 36, 5084– 5093. 10.1523/JNEUROSCI.0258-16.2016. 27147660 PMC6601857 · DOI
  88. [109]Mayer D, Fischer H, Schneider U, Heimrich B, and Schwemmle M (2005). Borna disease virus replication in organotypic hippocampal slice cultures from rats results in selective damage of dentate granule cells. J Virol 79, 11716– 11723. 10.1128/JVI.79.18.11716-11723.2005. 16140749 PMC1212617 · DOI
  89. [110]Takata K, Kozaki T, Lee CZW, Thion MS, Otsuka M, Lim S, Utami KH, Fidan K, Park DS, Malleret B, (2017). Induced-Pluripotent-Stem-Cell-Derived Primitive Macrophages Provide a Platform for Modeling Tissue-Resident Macrophage Differentiation and Function. Immunity 47, 183– 198 e186. 10.1016/j.immuni.2017.06.017. 28723550 · DOI
  90. [111]Bankhead P, Loughrey MB, Fernandez JA, Dombrowski Y, McArt DG, Dunne PD, McQuaid S, Gray RT, Murray LJ, Coleman HG, (2017). QuPath: Open source software for digital pathology image analysis. Sci Rep 7, 16878. 10.1038/s41598-017-17204-5. 29203879 PMC5715110 · DOI · Paper page
  91. [112]Kim TW, Piao J, Koo SY, Kriks S, Chung SY, Betel D, Socci ND, Choi SJ, Zabierowski S, Dubose BN, (2021). Biphasic Activation of WNT Signaling Facilitates the Derivation of Midbrain Dopamine Neurons from hESCs for Translational Use. Cell Stem Cell 28, 343– 355 e345. 10.1016/j.stem.2021.01.005. 33545081 PMC8006469 · DOI
  92. [113]Sarrafha L, Parfitt GM, Reyes R, Goldman C, Coccia E, Kareva T, and Ahfeldt T (2021). High-throughput generation of midbrain dopaminergic neuron organoids from reporter human pluripotent stem cells. STAR Protoc 2, 100463. 10.1016/j.xpro.2021.100463. 33997803 PMC8086141 · DOI

Authors
Pantazis, C. B., Yang, A., Lara, E., McDonough, J. A., Blauwendraat, C., Peng, L., Oguro, H., Kanaujiya, J., Zou, J., Sebesta, D., Pratt, G., Cross, E., Blockwick, J., Buxton, P., Kinner-Bibeau, L., Medura, C., Tompkins, C., Hughes, S., Santiana, M., Faghri, F., Nalls, M. A., Vitale, D., Ballard, S., Qi, Y. A., Ramos, D. M., Anderson, K. M., Stadler, J., Narayan, P., Papademetriou, J., Reilly, L., Nelson, M. P., Aggarwal, S., Rosen, L. U., Kirwan, P., Pisupati, V., Coon, S. L., Scholz, S. W., Priebe, T., Öttl, M., Dong, J., Meijer, M., Janssen, L. J. M., Lourenco, V. S., van der Kant, R., Crusius, D., Paquet, D., Raulin, A.-C., Bu, G., Held, A., Wainger, B. J., Gabriele, R. M. C., Casey, J. M., Wray, S., Abu-Bonsrah, D., Parish, C. L., Beccari, M. S., Cleveland, D. W., Li, E., Rose, I. V. L., Kampmann, M., Calatayud Aristoy, C., Verstreken, P., Heinrich, L., Chen, M. Y., Schüle, B., Dou, D., Holzbaur, E. L. F., Zanellati, M. C., Basundra, R., Deshmukh, M., Cohen, S., Khanna, R., Raman, M., Nevin, Z. S., Matia, M., Van Lent, J., Timmerman, V., Conklin, B. R., Johnson Chase, K., Zhang, K., Funes, S., Bosco, D. A., Erlebach, L., Welzer, M., Kronenberg-Versteeg, D., Lyu, G., Arenas, E., Coccia, E., Sarrafha, L., Ahfeldt, T., Marioni, J. C., Skarnes, W. C., Cookson, M. R., Ward, M. E., & Merkle, F. T.
Affiliations
  • National Institutes of Health (US)
  • European Bioinformatics Institute (GB)
  • The Jackson Laboratory for Genomic Medicine (US)
  • KromaTiD (United States) (US)
  • Wellcome/MRC Cambridge Stem Cell Institute (GB)
  • Johns Hopkins University (US)
  • Amsterdam Neuroscience (NL)
  • Institut für Schlaganfall- und Demenzforschung (DE)
  • Munich Cluster for Systems Neurology (DE)
  • Mayo Clinic in Florida (US)
  • Harvard University (US)
  • Broad Institute (US)
  • UCL Queen Square Institute of Neurology (GB)
  • The University of Melbourne (AU)
  • University of California San Diego (US)
  • University of California, San Francisco (US)
  • VIB-KU Leuven Center for Brain & Disease Research (BE)
  • Stanford Medicine (US)
  • University of Pennsylvania (US)
  • University of North Carolina at Chapel Hill (US)
  • Tufts University (US)
  • Gladstone Institutes (US)
  • University of Antwerp (BE)
  • University of Massachusetts Chan Medical School (US)
  • German Center for Neurodegenerative Diseases (DE)
  • Karolinska Institutet (SE)
  • Icahn School of Medicine at Mount Sinai (US)
Corresponding author
  • Skarnes, William C.
  • Cookson, Mark R.
  • Ward, Michael E.
  • Merkle, Florian T.
ORCID
Venue
Cell Stem Cell
Publisher
Elsevier BV
Published
2022-12
Volume
29
Issue
12
Pages
1685-1702.e22
ISSN
  • 1875-9777 (ISSN-L)
  • 1934-5909
DOI
10.1016/j.stem.2022.11.004
PMC
PMC9782786
OpenAlex
W4310773007
Cited by
310
References
115
Citations by year
2026: 121 · 2025: 93 · 2024: 66 · 2023: 23 · 2022: 6
FWCI
15.97
Type
journal article
Language
en
Open access
Licence
Locations
  • Cell stem cell (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed (publishedVersion)
  • Amsterdam UMC (VU Amsterdam) - Institutional Repository (publishedVersion, other-oa)
  • PubMed Central (acceptedVersion)
  • Lirias (submittedVersion, cc-by)
  • Pure Amsterdam UMC (submittedVersion, cc-by)
  • UCL Discovery (University College London) (submittedVersion)
  • Open access LMU (Ludwid Maxmilian's Universitat Munchen) (submittedVersion, cc-by)
  • eScholarship (California Digital Library) (submittedVersion, cc-by)
  • mediaTUM – the media and publications repository of the Technical University Munich (Technical University Munich) (submittedVersion, other-oa)
  • The Mouseion at the JAXlibrary (Jackson Laboratory) (submittedVersion, cc-by)
  • DZNE Pub (submittedVersion, other-oa)
  • Rare & Special e-Zone (The Hong Kong University of Science and Technology) (submittedVersion)
  • VU Research Portal (submittedVersion, other-oa)
  • Apollo (University of Cambridge) (submittedVersion, cc-by-nc-nd)
  • Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
  • Apollo
Funders
  • U.S. Department of Health and Human Services (ZO1 AG000535)
  • California Institute for Regenerative Medicine (EDUC4-12812)
  • New York Stem Cell Foundation (NYSCF-R-156, C32561GG, NYSCF-I-R44)
  • New York State Department of Health (NYSTEM-C32561GG)
  • Alzheimer Forschung Initiative
  • Wellcome Trust (211221/Z/18/Z)
  • European Bioinformatics Institute (C9545/A29580)
  • New York State Stem Cell Science (NYSTEM‐C32561GG, C32561GG)
  • Target ALS
  • European Molecular Biology Laboratory
  • Chan Zuckerberg Initiative (191942)
  • International Max Planck Research School for Environmental, Cellular and Molecular Microbiology
  • Cancer Research UK (A:29580, EU H2020, C9545, C9545/A29580)
  • National Institute for Health and Care Research (MR/R015724/1)
  • University College London
  • European Commission (235147)
  • Deutsche Forschungsgemeinschaft (EXC 2145, 471227244, EXC 2145SyNergy, 390857198)
  • ZonMw (09150161810052)
  • Cancerfonden (CAN 2016/572)
  • Fonds Wetenschappelijk Onderzoek (H2020-MSCA-ITN-2018, H2020-MSCA-ITN)
  • Nederlandse Organisatie voor Wetenschappelijk Onderzoek
  • Karolinska Institutet (2020-01426)
  • Studienstiftung des Deutschen Volkes
  • Universiteit Antwerpen
  • Vlaamse regering
  • International Max Planck Research School for Advanced Methods in Process and Systems Engineering
  • UK Regenerative Medicine Platform (MR/R015724/1)
  • National Institutes of Health (W81XWH, H2020, NS060698, NS27036)
  • Horizon 2020 Framework Programme (899687, MSCA‐ITN‐2018, H2020-MSCA, 813851, EU‐H2020, H2020-MSCA-ITN-2018, H2020-MSCA-ITN)
  • National Defense Science and Engineering Graduate
  • Medical Research Council (MR/R015724/1, MR/P501967/1)
  • Cancer Research UK Cambridge Institute, University of Cambridge (A29580, C9545/A29580)
  • National Institute on Aging (T32AG066596, ZO1 AG000535, AG000535, RF1AG072052, R01AG072052, T32AG000255, ZIAAG000535)
  • National Institute of General Medical Sciences (R01GM127557)
  • National Institute of Diabetes and Digestive and Kidney Diseases (R01DK125747)
  • National Institute of Neurological Disorders and Stroke (F32NS114319, NS 27036, 33601, NS060698, ZO1 AG000535, R01NS117461, R01NS060698, R01NS027036, T32NS115706)
  • H2020 European Research Council (884608)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Pluripotent Stem Cells Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
Keywords
human induced pluripotent stem cells, genome stability, CRISPR/Cas9 genome editing, iPSC differentiation, reproducibility, whole genome sequencing
MeSH terms
Gene Editing, Biological Assay, Cell Differentiation, Humans, Induced Pluripotent Stem Cells

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review