I have been testing compounds for for their anti-cancer properties. The National Cancer Institute has 60 cell lines they test potential anti-cancer drugs on. If funding, and time, and lab space were not a problem, I would purchase all 60 cell lines... But....
My boss has suggested I consider getting three cell lines which could serve as a 'pre-NCI60' panel...
I'm hoping someone can point me in the direction of three cell lines that would work as a good panel.
The solution is a 3-cell line prescreen adopted by the NCI about 20 years ago. Analysis of historical screening results across 60 cancer cell lines showed that compounds that failed to show activity at 100 uM in 3 highly sensitive cell lines were unlikely to show activity against any of the remaining 57 cancer cell lines. Thus, all tested compounds were initially prescreened against those 3 cell lines, and only compounds demonstrating activity against at least one of them were subsequently tested in the full NCI60 panel at 5 concentration levels. The 3 cell lines were: MCF-7 breast cancer, NCI-H460 lung cancer, and SF-268 glioblastoma cell lines. The selection criteria have more recently changed and this 3-cell panel is no longer used.
may be you can try HL60, A549, HCT 116 as many natural and synthetic drugs are used as a target against these cell lines with good results. You can search literature's from pubmed
It is a very complicated questions, as each cell line has it's own specificity. If the compound mechanism of action is not known or it is not specific, then you could take any three most commonly used cell lines. Usually we use glioblastoma (U87), triple-negative breast cancer (MDA-MB-231), lung cancer (A549), melanoma (IGR39) or pancreatic cell line (BxPC-3). As you may notice, majority of my mentioned cell lines are derived from quite aggressive tumors, as there is a great need for anticancer drugs for their treatment. On the other hand, if you already know something about the mechanism of action of your compounds, you should look for such cancer cell lines that express the target for them.
You need to distinguish a target-directed screening, that would try to identify compounds with target-specific activities, and untargeted screening that aims to use just 3 cell lines to capture compounds that would have have high probability to score positive in at least one of the 60 NCI60 cell lines. This is how the problem was framed, and so the answer needs to be data-driven as opposed to mechanistic insight-driven. And there is no point in using just any common 3 cell lines, because commonality is not a good criterion for a cell line inclusion. Instead, it is meaningful to use 3 cell lines that can be, as a subset, most predictive of the response of the whole 60-cell line panel. These 3 cell lines have highest negative predictive value, which means that probability of a compound being inactive across NCI60 panel is high if the given compound is inactive in the 3 cell lines: MCF-7, NCI-H460, and SF-268. This approach has been taken by the Developmental Therapeutics Program of the National Cancer Institute as a pre-screening to save the resources and preselect compounds with highest probability of activity against cells in the full NCI60 panel.
Thank you, everyone, for you answers...
I've been doing some reading since I posted this question... and I find myself with MORE questions... (We never stop learning, do we?)
Roman, thank you so much. I downloaded the NCI-60 cell panel data set. I've decided to set up a panel of (perhaps) 7 to 11 cell lines. I will definitely start with the MCF-7, NCI-H460, and SF-268.
I already have PC-3, K562, A549, LnCAp, HCT 116, MDA-MB-231, and MDA-MB-435. I did not purchase these for this project. I just happen to have them store in liquid N2 from previous projects. They're all on the NCI-60 panel but it is just coincidental that I have them. I need to do some reading and wrap my mind around the negative predictive values.
I realize there must be a data set or table somewhere with the negative predictive values for each of these cell lines but I'm having trouble locating it. Could you steer me in the right direction?
where can i get NCI-60 cancer cell panel data set as used in https://arxiv.org/pdf/1304.4773.pdf page 17
Thank you
Ishaq Baba: The study used data that can be accessed through the CellMiner tool (https://discover.nci.nih.gov/cellminer/), or alternatively through the NCI Developmental Therapeutics Program website (https://dtp.cancer.gov/).
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