Following the publication of our recent article in BMC Genomics [1] a number of aspects were called to our attention. We have carefully reviewed the experiments reported in this manuscript, as well as additional data from our laboratories, and would like to make the following points:
SW-850, included in our paper as a bladder cancer cell line, has been reported by several authors to be a pancreatic cancer cell line [2–5]. This is unlikely to be the case given that most pancreatic cancers are KRAS-mutant and both our analysis and a previous publication [5] indicate that the cells used are KRAS-wild type. However, given the controversy we recommend that these cells are not be used as bladder cancer models.
The Materials and Methods section of our paper indicated that the following cell lines were obtained from ATCC: 253 J, 575A, 639 V, JON, MGH-U4, SW-800, SW-1710, VM-CUB-2. However, these cultures have never been distributed by the ATCC. Therefore, they are available from us if other investigators are interested in using them.
It has been reported that UM-UC-2 is a T24 contaminant (http://www.ncbi.nlm.nih.gov/biosample/SAMN03151953 ,http://web.expasy.org/cellosaurus/CVCL_8155, http://iclac.org/wp-content/uploads/Cross-Contaminations-v7_2.pdf). We have used fingerprinting analysis to confirm this fact and the genetic identity of the cells/DNAs used in our experiments (Table 1).
It has been reported that VM-CUB-3 is a VM-CUB-1 contaminant (http://iclac.org/wp-content/uploads/Cross-Contaminations-v7_2.pdf, http://www.ncbi.nlm.nih.gov/biosample/3152040, http://web.expasy.org/cellosaurus/CVCL_9830). Nevertheless, our data indicate that the two cultures we used as VM-CUB-1 and VM-CUB-3 are distinct at the genomic level. Furthermore, as shown in Table 1, fingerprinting analysis clearly indicates that VM-CUB-1, VM-CUB-2, and VM-CUB-3 are different from each other. The origin of the DNA/cells in our paper was as indicated in the Material and Methods section and, therefore, investigators interested in these cells could directly address the corresponding co-authors.
Table 1.
SNP fingerprint analysis of the bladder cancer cell lines suffering from an “identity crisis”
| Cell Line | Comments | D5S818 | D13S317 | D7S820 | D16S539 | VWA | TH01 | AM | TPOX | CSF1PO |
|---|---|---|---|---|---|---|---|---|---|---|
| VM- CUB-1 p29 | 11 | 10 | 8,11 | 11,12 | 18,19 | 9 | X | 8 | 11 | |
| VM-CUB-2 p112 | 11,13 | 12 | 8 | 9 | 14 | 7 | X,Y | 8,12 | 11,12 | |
| VM-CUB-3 p65 | 11 | 9,12 | 8,9 | 12 | 16 | 9.3 | X | 8 | 12 | |
| UM-UC-2 p264 | DNA fingerprinting data, same as T24 | 10,12 | 10,12 | 10,11 | 9 | 17 | 6 | X | 8,11 | 10,12 |
| T24 p8 | ATCC | 10,12 | 12 | 10,11 | 9 | 17,19 | 6 | X | 8,11 | 10,12 |
P passage
In the last few years there has been much emphasis on the need to accurately designate, identify, and characterize cancer cell lines as they are precious tools for cell biology studies [6, 7]. It is with this aim that we wish to make these comments and clarifications related to our recently published work.
Footnotes
The online version of the original article can be found under doi:10.1186/s12864-015-1450-3.
Competing interests
The authors declare no competing financial interests.
Contributor Information
Julie Earl, Email: jearl@ext.cnio.es.
Daniel Rico, Email: drico@cnio.es.
Enrique Carrillo-de-Santa-Pau, Email: ecarrillo@cnio.es.
Benjamín Rodríguez-Santiago, Email: benjamin.rodriguez@qgenomics.com.
Marinela Méndez-Pertuz, Email: mmendez@cnio.es.
Herbert Auer, Email: herbert.auer@irbbarcelona.org.
Gonzalo Gómez, Email: ggomez@cnio.es.
H. Barton Grossman, Email: hbgrossman@mdanderson.org.
David G. Pisano, Email: dgpisano@cnio.es
Wolfgang A. Schulz, Email: wolfgang.schulz@uni-duesseldorf.de
Luis A. Pérez-Jurado, Email: luis.perez@upf.edu
Alfredo Carrato, Email: acarrato@telefonica.net.
Dan Theodorescu, Email: dan.theodorescu@ucdenver.edu.
Stephen Chanock, Email: chanocks@mail.nih.gov.
Alfonso Valencia, Email: avalencia@cnio.es.
Francisco X. Real, Email: preal@cnio.es
References
- 1.Earl J, Rico D, Carrillo-de-Santa-Pau E, Rodríguez-Santiago B, Méndez M, Auer H, Gómez G, Grossman HB, Pisano DG, Schulz WA, Pérez-Jurado LA, Carrato A, Theodorescu D, Chanock S, Valencia A, Real FX. The UBC-40 Urothelial Bladder Cancer Cell Line Index: a genomic resource for functional studies. BMC Genomics. 2015;16:403. doi: 10.1186/s12864-015-1450-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Fogh J, Fogh JM, Orfeo T. One hundred and twenty-seven cultured human tumor cell lines producing tumors in nude mice. J Natl Cancer Inst. 1977;59(1):221–6. doi: 10.1093/jnci/59.1.221. [DOI] [PubMed] [Google Scholar]
- 3.Fogh J, Wright WC, Loveless JD. Absence of HeLa cell contamination in 169 cell lines derived from human tumors. J Natl Cancer Inst. 1977;58(2):209–14. doi: 10.1093/jnci/58.2.209. [DOI] [PubMed] [Google Scholar]
- 4.Kalthoff H, Schmiegel W, Roeder C, Kasche D, Schmidt A, Lauer G, Thiele HG, Honold G, Pantel K, Riethmüller G, et al. p53 and K-RAS alterations in pancreatic epithelial cell lesions. Oncogene. 1993;8(2):289–98. [PubMed] [Google Scholar]
- 5.Müller C, Bockhorn AG, Klusmeier S, Kiehl M, Roeder C, Kalthoff H, Koch OM. Lovastatin inhibits proliferation of pancreatic cancer cell lines with mutant as well as with wild-type K-ras oncogene but has different effects on protein phosphorylation and induction of apoptosis. Int J Oncol. 1998;12(3):717–23. doi: 10.3892/ijo.12.3.717. [DOI] [PubMed] [Google Scholar]
- 6.Freedman LP, Gibson MC, Ethier SP, Soule HR, Neve RM, Reid YA. Reproducibility: changing the policies and culture of cell line authentication. Nat Methods. 2015;12(6):493–7. doi: 10.1038/nmeth.3403. [DOI] [PubMed] [Google Scholar]
- 7.Yu M, Selvaraj SK, Liang-Chu MM, Aghajani S, Busse M, Yuan J, Lee G, Peale F, Klijn C, Bourgon R, Kaminker JS, Neve RM. A resource for cell line authentication, annotation and quality control. Nature. 2015;520(7547):307–11. doi: 10.1038/nature14397. [DOI] [PubMed] [Google Scholar]