Regulatory network changes between cell lines and their tissues of origin

Abstract

BackgroundCell lines are an indispensable tool in biomedical research and often used as surrogates for tissues. Although there are recognized important cellular and transcriptomic differences between cell lines and tissues, a systematic overview of the differences between the regulatory processes of a cell line and those of its tissue of origin has not been conducted. The RNA-Seq data generated by the GTEx project is the first available data resource in which it is possible to perform a large-scale transcriptional and regulatory network analysis comparing cell lines with their tissues of origin.ResultsWe compared 127 paired Epstein-Barr virus transformed lymphoblastoid cell lines (LCLs) and whole blood samples, and 244 paired primary fibroblast cell lines and skin samples. While gene expression analysis confirms that these cell lines carry the expression signatures of their primary tissues, albeit at reduced levels, network analysis indicates that expression changes are the cumulative result of many previously unreported alterations in transcription factor (TF) regulation. More specifically, cell cycle genes are over-expressed in cell lines compared to primary tissues, and this alteration in expression is a result of less repressive TF targeting. We confirmed these regulatory changes for four TFs, including SMAD5, using independent ChIP-seq data from ENCODE.ConclusionsOur results provide novel insights into the regulatory mechanisms controlling the expression differences between cell lines and tissues. The strong changes in TF regulation that we observe suggest that network changes, in addition to transcriptional levels, should be considered when using cell lines as models for tissues.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4111-x) contains supplementary material, which is available to authorized users.

Effect of EBV-Transformation on Oxidative Phosphorylation Physiology in Human Cell lines

“…In the one of the first studies [20], EBVtransformation relative to whole blood had small but significant effects on mRNA expression and methylation patterns, yet LCLs recapitulate the naturally occurring gene expression variation in primary B cells [20]. Similarly in EBV-transformed LCLs cells, cell cycle genes have significantly greater expression compared to primary tissues, which is thought to be the result of less repressive transcription factor regulation [18]. These differences paired LCLs with whole blood and found that the regulatory changes were subtle; for example the levels of mRNA expression for the transcription factor Sp1 and Sp3 were not significantly different in transformed versus native cells, but the targets for these transcription factors differed [18].…”

“…Similarly in EBV-transformed LCLs cells, cell cycle genes have significantly greater expression compared to primary tissues, which is thought to be the result of less repressive transcription factor regulation [18]. These differences paired LCLs with whole blood and found that the regulatory changes were subtle; for example the levels of mRNA expression for the transcription factor Sp1 and Sp3 were not significantly different in transformed versus native cells, but the targets for these transcription factors differed [18]. Furthermore, mRNA expression substantially changed with passage [16,18,25].…”

“…These differences paired LCLs with whole blood and found that the regulatory changes were subtle; for example the levels of mRNA expression for the transcription factor Sp1 and Sp3 were not significantly different in transformed versus native cells, but the targets for these transcription factors differed [18]. Furthermore, mRNA expression substantially changed with passage [16,18,25]. In contrast, EBV-transformation had no significant effect on mitochondrial copy number, with nearly equal numbers of mitochondria among replicate EBV-transformations [20].…”

“…EBV-transformed LCLs and specifically cell lines from the 1,000 Human genome project have been used successfully to define sex bias in gene expression [16], statin-dependent QTL [17], cell specific networks [18], genetic variation in DNA replication [19] and epigenetics [20,21]. Overall, these and other studies have concluded that EBVtransformed LCLs continue to represent naturally occurring biological variation [22,23].…”

xMD-miRNA-seq to generate near in vivo miRNA expression estimates in colon epithelial cells

“…Therefore, it is wellestablished that cultured cells are good, but not ideal surrogates for in vivo expression. 9 This was nicely demonstrated for miRNAs in a study that compared primary endothelial cells directly harvested from umbilical cords to endothelial cells cultured for 3 passages. miR-126, a highly-expressed, mature endothelial cell miRNA, was over 2 fold less abundant at passage 3 versus passage 0.…”