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

Authors:
Thomas SM, Kagan C, Pavlovic BJ, Burnett J, Patterson K, Pritchard JK, Gilad Y
In:
Source: PLoS Genet
Publication Date: (2015)
Issue: 11(5): e1005216
Research Area:
Stem Cells
Gene Expression
Cells used in publication:
LCL
Species: human
Tissue Origin: blood
Induced Pluripotent Stem Cell (iPS), human
Species: human
Tissue Origin:
Experiment
iPSC Generation and Validation: One million cells were transfected with 2 µg of each episomal plasmid encoding OCT3/4, shP53, Lin28, SOX2, L-MYC, KLF4, and GFP(Addgene plasmids 27077, 27078, 27080, 27082 [21]) using the Amaxa transfection program X-005. Transfected cells were grown in suspension for a week in hESC media (DMEM/F12 supplemented with 20% KOSR, 0.1mM NEAA, 2mM GlutaMAX, 1% Pen/Strep, 0.1 mM BME, and 12.5 ng/mL human bFGF) supplemented with 0.5mM sodium butyrate between days 2–12 post-nucleofection. Lonza Summary: The authors report that using reprogrammed LCL\\\'s can recover donor gene expression which were previously lost during long term LCL culture maintenance. Futhermore, the findings suggest that iPSCs generated from LCLs are useful in studies regarding the genetic basic for individual phenotypic variation.
Abstract
Renewable in vitro cell cultures, such as lymphoblastoid cell lines (LCLs), have facilitated studies that contributed to our understanding of genetic influence on human traits. However, the degree to which cell lines faithfully maintain differences in donor-specific phenotypes is still debated. We have previously reported that standard cell line maintenance practice results in a loss of donor-specific gene expression signatures in LCLs. An alternative to the LCL model is the induced pluripotent stem cell (iPSC) system, which carries the potential to model tissue-specific physiology through the use of differentiation protocols. Still, existing LCL banks represent an important source of starting material for iPSC generation, and it is possible that the disruptions in gene regulation associated with long-term LCL maintenance could persist through the reprogramming process. To address this concern, we studied the effect of reprogramming mature LCL cultures from six unrelated donors to iPSCs on the ensuing gene expression patterns within and between individuals. We show that the reprogramming process results in a recovery of donor-specific gene regulatory signatures, increasing the number of genes with a detectable donor effect by an order of magnitude. The proportion of variation in gene expression statistically attributed to donor increases from 6.9% in LCLs to 24.5% in iPSCs (P < 10-15). Since environmental contributions are unlikely to be a source of individual variation in our system of highly passaged cultured cell lines, our observations suggest that the effect of genotype on gene regulation is more pronounced in iPSCs than in LCLs. Our findings indicate that iPSCs can be a powerful model system for studies of phenotypic variation across individuals in general, and the genetic association with variation in gene regulation in particular. We further conclude that LCLs are an appropriate starting material for iPSC generation.