I am currently given a project to check on the cytotoxicity of a drug on 2 cell lines ( a liver cancer cell line and a breast cancer cell line) and then do a comparison of protein expression in the 2 cell lines that were affected by the drug.

What puzzled me is how could I compare two cell lines when the 2 of them are totally different cell lines? I tried asking this question to everyone in the lab, including the professor who assigned me the project but I could not get an answer.

Hope someone here can help me. Thank you very much.

I think comparison across several tumor cell lines can possibly identify lineage specific or common genetic expression
in response to treatment with drug in the context of identifying classes of affected genes. For example, if a certain protein/protein-family is up/downregulated in both the cell lines after the drug treatment, this means that it provides a more universal control.

On the other hand if the protein is up/downregulated in response to the drug only in one cell line and not the other, that may be because of the involvement of this protein in that particular cell line's response. Please take a look at the following paper:

J Neurooncol. 2003 Sep;64(3):219-25. Differential expression of bikunin (HAI-2/PB), a proposed mediator of glioma invasion, by demethylation treatment. Schuster JM, Longo M, Nelson PS.
http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=14558597&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum