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Tumour-derived cell lines play an important role in tumour biology and genetic research. Across a wide array of studies, they have been tools of choice for the discovery of important genes involved in cancer and for the analysis of the cellular pathways that are impaired by diverse oncogenic events. They are also invaluable for screening novel anticancer drugs. The TP53 protein is a major component of multiple pathways that regulate cellular response to various types of stress. Therefore, TP53 status profoundly affects the phenotype of tumour cell lines and must be carefully determined in all experimental projects.
In 2008, we published a first report describing the TP53 mutation status of cell lines [Berglind et al., 2008]. We were deeply concerned by the finding that many cell lines had a controversial TP53 status, including popular cell lines such as those from the NCI-60 panels.
In 2012, we published a second paper showing that the situation has not changed.
The TP53 mutation cell line compendium is designed to provide strong and reliable information about the TP53 status of the most widely used cell lines.
The problem is not related to TP53 but to cell line misidentification, contamination and poor annotation as well as the methodology used to define the genotype of the cell line. Due to the heterogeneity of TP53 mutations, TP53 status has been used as a marker to differentiate various cell lines. Although not as sensitive as STR, it is can be very useful.
The problem of cell line cross-contamination and misidentification has been known for quite some time, as illustrated by the first—but not the last—warnings expressed by Nelson-Rees et al. (1981) more than thirty years ago. Today, this issue continues to be ignored. Indeed, recent studies have suggested that the "silent and neglected danger" of cross-contamination or misidentification may affect 10%–20% of cell lines [Drexler et al., 2000; MacLeod et al., 2002].
Cell line names are often published with inconsistent syntax, capitalization or use of different separators in the literature as well as in cell line repository catalogues.
Another potential source of cell line genotype discrepancies is related to the methodology used for analysis. Using either DNA or cDNA sequencing can lead to major differences with mutation miscalls obtained by RNA-based assays [Kropveld et al., 1999]. An initial problem is associated with splice mutations. , splice mutations may not be correctly detected on RNA sequencing as only the consequence of the mutation is identified, usually a deletion that starts close to the intron/exon boundary. This leads to misidentification of a missense mutation located at a splice site, since it is considered to be a deletion. Nonsense-mediated mRNA decay (NMD) is a second potential problem associated with RNA-based assays. Frameshift and nonsense mutations have been known to induce significant RNA instability via the NMD pathway. This instability could impair the detection of mutations and lead to a false wild-type genotype.
Using RNA-based assays has led to mutation discrepancies for the TP53 gene (MIM #191170) in numerous tumours and cell lines. Cell lines such as OVCAR-8 or HOP62 were previously described with an exon deletion, but more recent studies using genomic DNA sequencing have confirmed that these two cell lines have single-nucleotide mutations at splice sites.
TP53 mutation ID should never be used as a replacement for Short Tandem Repeat (STR), which is the most accurate way to validate cell line identity. For example, TP53 status will not detect contamination between two cell lines with wild-type status.
TP53 certification has been attributed to all cell lines with a TP53 status established by three independent studies. This very stringent selection ensures the validity of certification. In a few cases, certification has also been attributed when the discrepancy was only due to a nomenclature issue.
Cell lines with a similar status in the CCLE and COSMIC databases have been flagged, but due the high level of cell line misidentification, no certification has been attributed.
The "p53-null" status is used in many different ways in the literature. The most common meaning is a cell line with absent TP53 expression assessed by either RNA or protein analysis. Unfortunately, many events can result in absence of TP53 expression, including small insertions and deletions or nonsense and splice mutations because Nonsense-mediated mRNA decay (NMD) eliminates aberrant transcripts. HeLa cells that express wild-type TP53 and that present no mutations may nevertheless be identified as null when E6 protein expressed by an endogenous papillomavirus degrades TP53, thus leaving no protein to be detected by Western blot.
Recent identification of truncated TP53 isoforms suggests that some of these shorter proteins could be expressed in several cell lines.
To avoid problems due to residual TP53 sequences, only cell lines with deletion of the endogenous TP53 gene have been identified as "TP53-null." Several popular cell lines, such as Saos-2, HL-60, or H1299, are known to have a biallelic deletion of the TP53 gene.
Reports describing TP53 mutations in cell lines have been manually curated. Only data from publications that used TP53 sequencing are included. Publications reporting TP53 status via a reference or personal communication have not been included.
The TP53 status described in this paper is incorrect for more than one half of cell lines.
O'Connor, P. M., Jackman, J., Bae, I., Myers, T. G., Fan, S., Mutoh, M., Scudiero, D. A., Monks, A., Sausville, E. A., Weinstein, J. N., Friend, S., Fornace, A. J. J., and Kohn, K. W. (1997). Characterization of the p53 tumor suppressor pathway in cell lines of the National Cancer Institute anticancer drug screen and correlations with the growth-inhibitory potency of 123 anticancer agents. Cancer Res 57, 4285-4300.
A red flag is used as a warning to indicate that some publications have reported contradictory results. Nevertheless, a significant consensus has been reached by the scientific community to certify the TP53 status of these cell lines.
Feel free to contact us and we will modify the database accordingly.
We do not take stand on this matter. In many cases, the wt. status indicated in the CCLE database is a false-negative result (see Hudson et al. for more information). On the other hand, the mutation nomenclature used in the CCLE database is more accurate than that used in COSMIC.
Hudson, A. M., Yates, T., Li, Y., Trotter, E. W., Fawdar, S., Chapman, P., Lorigan, P., Biankin, A., Miller, C. J., and Brognard, J. (2014). Discrepancies in cancer genomic sequencing highlight opportunities for driver mutation discovery. Cancer Res 74, 6390-6396.
In many cases, the wild-type allele has been lost.
Check the origin of your cell line.
Feel free to contact us to resolve this problem.
Only human cell lines are included in the database. There are no plans to include non-human cell lines.
Only cell lines with published TP53 status are included in the database. If you have unpublished information that you are willing to share, please contact us.
It is planned to include the MDM2/MDM4 status in the next release. Stay tuned.