Expression phenotype changes of EBV-transformed lymphoblastoid cell lines during long-term subculture and its clinical significance.
OBJECTIVE
The EBV-transformed lymphoblastoid cell line (LCL) is a useful resource for population-based human genetic and pharmacogenetic studies. The principal objective here was to assess expression phenotype changes during long-term subculture of LCLs, and its clinical significance.


METHODS
We searched for genes that were differentially expressed in 17 LCLs at late (p161) passage compared to early passage (p4) using microarray assay, then validated them by real-time RT-PCR analysis. In addition, we estimated correlations between expression phenotypes of 20 LCL strains at early passage and 23 quantitative clinical traits from blood donors of particular LCL strains.


RESULTS
Transcript sequences of 16 genes including nuclear factor-kappaB (NF-kappaB) pathway-related genes (such as PTPN13, HERC5 and miR-146a) and carcinogenesis-related genes (such as XAF1, TCL1A, PTPN13, CD38 and miR-146a) were differentially expressed (>2-fold change) in at least 15 of the 17 LCL strains. In particular, TC2N, FCRL5, CD180, CD38 and miR-146a were downregulated in all 17 of the evaluated LCL strains. In addition, we identified clinical trait-associated expression phenotypes in LCLs.


CONCLUSIONS
Our results showed that LCLs acquired expression phenotype changes involving expression of NF-kappaB pathway- and carcinogenesis-related genes during long-term subculture. These differentially expressed genes can be considered to be a gene signature of LCL immortalization or EBV-induced carcinogenesis. Clinical trait-associated expression phenotypes should prove useful in the discovery of new candidate genes for particular traits.
Lee
J-E
JE
Division of Biobank for Health Sciences, Center for Genome Science, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Seoul, Korea. jaepiljeon@hanmail.net
Nam
H-Y
HY
Shim
S-M
SM
Bae
G-R
GR
Han
B-G
BG
Jeon
J-P
JP
D001483:Base Sequence; D002460:Cell Line; D002461:Cell Line, Transformed; D004854:Herpesvirus 4, Human / Q000235:genetics* / Q000276:immunology* / Q000378:metabolism; D006801:Humans; D035683:MicroRNAs / Q000235:genetics / Q000276:immunology / Q000378:metabolism; D016328:NF-kappa B / Q000235:genetics / Q000276:immunology / Q000378:metabolism; D010641:Phenotype; D016133:Polymerase Chain Reaction; D054595:Protein Tyrosine Phosphatase, Non-Receptor Type 13; D011518:Proto-Oncogene Proteins; D020133:Reverse Transcriptase Polymerase Chain Reaction
D035683:MicroRNAs; D016328:NF-kappa B; D011518:Proto-Oncogene Proteins; C090851:TCL1A protein, human; C516742:PTPN13 protein, human; D054595:Protein Tyrosine Phosphatase, Non-Receptor Type 13