Genomic, transcriptional and proteomic clarification of fathead minnow and common carp composition in epithelioma papulosum cyprini (EPC) cell line.

Abstract

The epithelioma papulosum cyprini (EPC) cell line has been routinely used in various research, such as viral infection, transfection, and expression analysis in laboratory, although the contamination with fathead minnow cells has been indicated in a previous report. However, the exact genomic composition of the cell line has never been reported. In this study, the EPC cells were generically sequenced, and were further subjected to transcriptomic analyses following poly (I:C) and SVCV stimulations. In addition, proteomic analysis was also performed following the stimulations. In comparison with common carp and fathead minnow genomes, 98.69 % reads in EPC cells were matched to fathead minnow, while only 85.31 % reads could be matched to common carp. A total of 2077 genes were upregulated and 1903 genes were downregulated in EPC cells following poly (I:C) induction, and 1437 genes upregulated, and 1453 genes downregulated following SVCV infection. Transcriptome analyses revealed that 99.57 % sequences in unstimulated EPC cells were in concordance with fathead minnow, while only 0.43 % with common carp. Following poly (I:C) and SVCV stimulations, 98.97 % and 99.66 % sequences in EPC cells were consistent with fathead minnow, while 1.03 % and 0.34 % were consistent with common carp, respectively. It is thus indicated that genes from fathead minnow were responsive to viral stimulations, and when EPC cells are used in viral stimulation experiments, genes should be detected on the basis of fathead minnow, rather than common carp.