The BT549 breast cancer cell line is a triple negative cell line of the Claudin-low sub-type. It was derived from a breast ductal carcinoma of a 72 year old woman. The STR profile along with other data and references pertinent to this cell line can be found here at Cellosaurus, or here at COSMIC, or here at DepMap portal.
The tables below were derived using the data mining tools on the SLKBase and are designed to provide rapid summaries of the oncogene signature of this cell line, and the best druggable targets for these cells. For a complete description of how this and other druggable signatures for these cell lines were derived, please consult my recent blog, here.
Oncogene Signature:Because this is a triple negative breast cancer cell line, the Oncogene Signature is simple and not terribly informative with respect to predicting a targeted drug strategy. As can be seen, the cell line is characterized by a TP53 mutation that is commonly observed in breast cancer, and a less common mutation in PTEN, which is associated with very low expression of the gene at the mRNA level. Interestingly, TP53 is actually overexpressed at the message level in this cell line, suggesting a dominant negative function of this gene, although it was not a hit in the screen.
| Gene | CRISPR score | Demeter score | Log fold change | DNA amp | mutation | occ. In Cosmic |
| TP53 | 0.062199367 | 1.947258373 | 0.4564 | p.R249S | 365 | |
| PTEN | 0.505326191 | -1.168576755 | 0.0518 | p.W274fs | 38 |
Druggable Targets in BT549. As will often (though not always) be the case with triple negative breast cancer cell lines, there are very few drugs that these cells were found to be sensitive to. Indeed, as can be seen below, there were no genes that were both hits in the screens and associated with sensitivity to targeted drugs. There is one drug that the cells are sensitive to in the Tier 3 category but even this level of sensitivity isn’t particularly striking. As indicated in the blog that goes with these drug sensitivity tables, we consider this sensitivity likely to be a correct on-target sensitivity and the reason that the gene did not score in the screen is because the drug inhibits both ROCK1 and ROCK2 and both genes are expressed in these cells.
| BT549T1 | ||||||||
| None | ||||||||
| BT549T2 | ||||||||
| None | ||||||||
| BT549T3 | ||||||||
| Drug Name | GeneSymbolHGNC | z_score_GDSC1 | z_score_GDSC2 | DNA_amp | lfc | mutation | achilles_score | demeter |
| GSK269962A | ROCK1 | -2.151074 | -1.73682 | -0.0221 | 0.290746139 | NULL | 0.198465564 | NULL |
| GSK269962A | ROCK2 | -2.151074 | -1.73682 | -0.5123 | -0.030278777 | NULL | 0.352205645 | NULL |
