High variability of genomic instability and gene expression profiling in different HeLa clones.
The HeLa cell line is one of the most popular cell lines in biomedical research, despite its well-known chromosomal instability. We compared the genomic and transcriptomic profiles of 4 different HeLa batches and showed that the gain and loss of genomic material varies widely between batches, drastically affecting basal gene expression. Moreover, different pathways were activated in response to a hypoxic stimulus. Our study emphasizes the large genomic and transcriptomic variability among different batches, to the point that the same experiment performed with different batches can lead to distinct conclusions and irreproducible results. The HeLa cell line is thought to be a unique cell line but it is clear that substantial differences between the primary tumour and the human genome exist and that an indeterminate number of HeLa cell lines may exist, each with a unique genomic profile.
Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), via Fantoli 15/16, 20090 Milan, Italy.|Department of Clinical and Experimental Medicine (DMCS), University of Insubria, via J.H. Dunant 5, 21100 Varese, Italy.
Annalisa
A
Frattini
Department of Clinical and Experimental Medicine (DMCS), University of Insubria, via J.H. Dunant 5, 21100 Varese, Italy.
Marco
M
Fabbri
Department of Clinical and Experimental Medicine (DMCS), University of Insubria, via J.H. Dunant 5, 21100 Varese, Italy.
Roberto
R
Valli
Department of Clinical and Experimental Medicine (DMCS), University of Insubria, via J.H. Dunant 5, 21100 Varese, Italy.
Elena
E
De Paoli
Department of Clinical and Experimental Medicine (DMCS), University of Insubria, via J.H. Dunant 5, 21100 Varese, Italy.
Giuseppe
G
Montalbano
Institute for Health and Consumer Protection, European Commission, I Via Enrico Fermi 2749, 21027 Ispra (VA), Italy.
Laura
L
Gribaldo
Department of Clinical and Experimental Medicine (DMCS), University of Insubria, via J.H. Dunant 5, 21100 Varese, Italy.
Francesco
F
Pasquali
Department of Clinical and Experimental Medicine (DMCS), University of Insubria, via J.H. Dunant 5, 21100 Varese, Italy.
Emanuela
E
Maserati
D055028:Comparative Genomic Hybridization; D056915:DNA Copy Number Variations; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D018740:Genetic Heterogeneity; D005819:Genetic Markers; D015894:Genome, Human; D042822:Genomic Instability; D023281:Genomics; D006367:HeLa Cells; D006801:Humans; D000860:Hypoxia / Q000235:genetics; D017404:In Situ Hybridization, Fluorescence; D059785:Karyotype; D015203:Reproducibility of Results; D059467:Transcriptome
D005819:Genetic Markers