Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature

PLoS Genetics

Volumn 11, Issue 5, 2015, Pages

  Thomas, Samantha M ^a   Kagan, Courtney ^a   Pavlovic, Bryan J ^a   Burnett, Jonathan ^a   Patterson, Kristen ^a   Pritchard, Jonathan K ^b   Gilad, Yoav ^a  

^a THE UNIVERSITY OF CHICAGO   (United States)

^b STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL MATURATION; CONTROLLED STUDY; GENE CONTROL; GENE EXPRESSION; GENE FREQUENCY; GENE NUMBER; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE; HUMAN; HUMAN CELL; LYMPHOBLASTOID CELL LINE; NUCLEAR REPROGRAMMING; PHENOTYPIC VARIATION; PLURIPOTENT STEM CELL; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM; B LYMPHOCYTE; CELL DIFFERENTIATION; CELL LINE; CYTOLOGY; EPSTEIN BARR VIRUS; GENE EXPRESSION REGULATION; GENETIC ASSOCIATION STUDY; INDUCED PLURIPOTENT STEM CELL; METABOLISM; PHENOTYPE; REPRODUCIBILITY;

TRANSCRIPTOME;

B-LYMPHOCYTES; CELL DIFFERENTIATION; CELL LINE; CELLULAR REPROGRAMMING; GENE EXPRESSION REGULATION; GENETIC ASSOCIATION STUDIES; HERPESVIRUS 4, HUMAN; HUMANS; INDUCED PLURIPOTENT STEM CELLS; PHENOTYPE; REPRODUCIBILITY OF RESULTS; TRANSCRIPTOME;

EID: 84930810293     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1005216     Document Type: Article

References (33)

1. Hu VW, Frank BC, Heine S, Lee NH, Quackenbush J, Gene expression profiling of lymphoblastoid cell lines from monozygotic twins discordant in severity of autism reveals differential regulation of neurologically relevant genes. BMC Genomics. 2006;7:118. doi: 10.1186/1471-2164-7-118 16709250; PubMed Central PMCID: PMCPMC1525191.
2. Huang RS, Duan S, Kistner EO, Hartford CM, Dolan ME, Genetic variants associated with carboplatin-induced cytotoxicity in cell lines derived from Africans. Molecular cancer therapeutics. 2008;7(9):3038–46. doi: 10.1158/1535-7163.MCT-08-0248 18765826
3. Wen Y, Gamazon ER, Bleibel WK, Wing C, Mi S, McIlwee BE, et al. An eQTL-based method identifies CTTN and ZMAT3 as pemetrexed susceptibility markers. Hum Mol Genet. 2012;21(7):1470–80. doi: 10.1093/hmg/ddr583 22171072; PubMed Central PMCID: PMCPMC3298275.
4. Ziliak D, O'Donnell PH, Im HK, Gamazon ER, Chen P, Delaney S, et al. Germline polymorphisms discovered via a cell-based, genome-wide approach predict platinum response in head and neck cancers. Transl Res. 2011;157(5):265–72. doi: 10.1016/j.trsl.2011.01.005 21497773; PubMed Central PMCID: PMCPMC3079878.
5. Moyer AM, Fridley BL, Jenkins GD, Batzler AJ, Pelleymounter LL, Kalari KR, et al. Acetaminophen-NAPQI hepatotoxicity: a cell line model system genome-wide association study. Toxicological sciences: an official journal of the Society of Toxicology. 2011;120(1):33–41. doi: 10.1093/toxsci/kfq375
6. Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, et al. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature. 2010;464(7289):768–72. Epub 2010/03/12. doi: 10.1038/nature08872 20220758; PubMed Central PMCID: PMC3089435.
7. Banovich NE, Lan X, McVicker G, van de Geijn B, Degner JF, Blischak JD, et al. Methylation QTLs Are Associated with Coordinated Changes in Transcription Factor Binding, Histone Modifications, and Gene Expression Levels. PLoS Genet. 2014;10(9):e1004663. doi: 10.1371/journal.pgen.1004663 25233095; PubMed Central PMCID: PMCPMC4169251.
8. Choy E, Yelensky R, Bonakdar S, Plenge RM, Saxena R, De Jager PL, et al. Genetic analysis of human traits in vitro: drug response and gene expression in lymphoblastoid cell lines. PLoS Genet. 2008;4(11):e1000287. doi: 10.1371/journal.pgen.1000287 19043577; PubMed Central PMCID: PMCPMC2583954.
9. Plagnol V, Uz E, Wallace C, Stevens H, Clayton D, Ozcelik T, et al. Extreme clonality in lymphoblastoid cell lines with implications for allele specific expression analyses. PLoS One. 2008;3(8):e2966. doi: 10.1371/journal.pone.0002966 18698422; PubMed Central PMCID: PMCPMC2494943.
10. Stark AL, Zhang W, Mi S, Duan S, O'Donnell PH, Huang RS, et al. Heritable and non-genetic factors as variables of pharmacologic phenotypes in lymphoblastoid cell lines. Pharmacogenomics J. 2010;10(6):505–12. doi: 10.1038/tpj.2010.3 20142840; PubMed Central PMCID: PMCPMC2975793.
11. Hannula K, Lipsanen-Nyman M, Scherer SW, Holmberg C, Höglund P, Kere J, Maternal and paternal chromosomes 7 show differential methylation of many genes in lymphoblast DNA. Genomics. 2001;73(1):1–9. doi: 10.1006/geno.2001.6502 11352560.
12. Carter KL, Cahir-McFarland E, Kieff E, Epstein-barr virus-induced changes in B-lymphocyte gene expression. J Virol. 2002;76(20):10427–36. 12239319; PubMed Central PMCID: PMCPMC136539.
13. Min JL, Barrett A, Watts T, Pettersson FH, Lockstone HE, Lindgren CM, et al. Variability of gene expression profiles in human blood and lymphoblastoid cell lines. BMC Genomics. 2010;11:96. doi: 10.1186/1471-2164-11-96 20141636; PubMed Central PMCID: PMCPMC2841682.
14. Caliskan M, Cusanovich DA, Ober C, Gilad Y, The effects of EBV transformation on gene expression levels and methylation profiles. Hum Mol Genet. 2011;20(8):1643–52. doi: 10.1093/hmg/ddr041 21289059; PubMed Central PMCID: PMCPMC3063990.
15. Powell JE, Henders AK, McRae AF, Wright MJ, Martin NG, Dermitzakis ET, et al. Genetic control of gene expression in whole blood and lymphoblastoid cell lines is largely independent. Genome Res. 2012;22(3):456–66. doi: 10.1101/gr.126540.111 22183966; PubMed Central PMCID: PMCPMC3290781.
16. Calışkan M, Pritchard JK, Ober C, Gilad Y, The effect of freeze-thaw cycles on gene expression levels in lymphoblastoid cell lines. PLoS One. 2014;9(9):e107166. doi: 10.1371/journal.pone.0107166 25192014; PubMed Central PMCID: PMCPMC4156430.
17. Mills JA, Wang K, Paluru P, Ying L, Lu L, Galvão AM, et al. Clonal genetic and hematopoietic heterogeneity among human-induced pluripotent stem cell lines. Blood. 2013;122(12):2047–51. doi: 10.1182/blood-2013-02-484444 23940280; PubMed Central PMCID: PMCPMC3778548.
18. Boulting GL, Kiskinis E, Croft GF, Amoroso MW, Oakley DH, Wainger BJ, et al. A functionally characterized test set of human induced pluripotent stem cells. Nat Biotechnol. 2011;29(3):279–86. doi: 10.1038/nbt.1783 21293464; PubMed Central PMCID: PMCPMC3229307.
19. Kajiwara M, Aoi T, Okita K, Takahashi R, Inoue H, Takayama N, Donor-dependent variations in hepatic differentiation from human-induced pluripotent stem cells. Proceedings of the National Academy of Sciences. 2012;109(36):14716-. doi: 10.1073/pnas.1212710109
20. Rouhani F, Kumasaka N, de Brito MC, Bradley A, Vallier L, Gaffney D, Genetic background drives transcriptional variation in human induced pluripotent stem cells. PLoS Genet. 2014;10(6):e1004432. doi: 10.1371/journal.pgen.1004432 24901476; PubMed Central PMCID: PMCPMC4046971.
21. Okita K, Matsumura Y, Sato Y, Okada A, Morizane A, Okamoto S, et al. A more efficient method to generate integration-free human iPS cells. Nat Methods. 2011;8(5):409–12. doi: 10.1038/nmeth.1591 21460823.
22. Choi SM, Liu H, Chaudhari P, Kim Y, Cheng L, Feng J, et al. Reprogramming of EBV-immortalized B-lymphocyte cell lines into induced pluripotent stem cells. Blood. 2011;118(7):1801–5. doi: 10.1182/blood-2011-03-340620 21628406; PubMed Central PMCID: PMCPMC3158714.
23. Rajesh D, Dickerson SJ, Yu J, Brown ME, Thomson JA, Seay NJ, Human lymphoblastoid B-cell lines reprogrammed to EBV-free induced pluripotent stem cells. Blood. 2011;118(7):1797–800. doi: 10.1182/blood-2011-01-332064 21708888.
24. Müller FJ, Schuldt BM, Williams R, Mason D, Altun G, Papapetrou EP, et al. A bioinformatic assay for pluripotency in human cells. Nat Methods. 2011;8(4):315–7. doi: 10.1038/nmeth.1580 21378979; PubMed Central PMCID: PMCPMC3265323.
25. Johnson WE, Li C, Rabinovic A, Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics. 2007;8(1):118–27. doi: 10.1093/biostatistics/kxj037 16632515.
26. Smyth GK, Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 2004;3:Article3. doi: 10.2202/1544-6115.1027 16646809.
27. Sulakhe D, Balasubramanian S, Xie B, Feng B, Taylor A, Wang S, et al. Lynx: a database and knowledge extraction engine for integrative medicine. Nucleic Acids Res. 2014;42(Database issue):D1007–12. doi: 10.1093/nar/gkt1166 24270788; PubMed Central PMCID: PMCPMC3965040.
28. Kagan CL, Banovich NE, Pavlovic BJ, Patterson K, Gallego Romero I, Pritchard JK, et al. Genetic Variation, Not Cell Type of Origin, Underlies Regulatory Differences in iPSCs. bioRxiv. 2015. doi: 10.1101/013888
29. Garfield DA, Runcie DE, Babbitt CC, Haygood R, Nielsen WJ, Wray GA, The impact of gene expression variation on the robustness and evolvability of a developmental gene regulatory network. PLoS Biol. 2013;11(10):e1001696. doi: 10.1371/journal.pbio.1001696 24204211; PubMed Central PMCID: PMCPMC3812118.
30. Roux J, Robinson-Rechavi M, Developmental constraints on vertebrate genome evolution. PLoS Genet. 2008;4(12):e1000311. doi: 10.1371/journal.pgen.1000311 19096706; PubMed Central PMCID: PMCPMC2600815.
31. Gallego Romero I, Pavlovic BJ, Hernando-Herraez I, Banovich NE, Kagan CL, Burnett JE, et al. Generation of a Panel of Induced Pluripotent Stem Cells From Chimpanzees: a Resource for Comparative Functional Genomics. bioRxiv. 2014. doi: 10.1101/008862
32. Du P, Kibbe WA, Lin SM, lumi: a pipeline for processing Illumina microarray. Bioinformatics. 2008;24(13):1547–8. doi: 10.1093/bioinformatics/btn224 18467348.
33. Leek JT, Johnson WE, Parker HS, Jaffe AE, Storey JD, The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics. 2012;28(6):882–3. doi: 10.1093/bioinformatics/bts034 22257669; PubMed Central PMCID: PMCPMC3307112.