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beta actin vs GAPDH as loading controls for Western blotting - (Sep/20/2008 )

Dear All
a friend of mine is testing the efficacy of a combination treatment on cancer cells. He got some results showing that antiapoptic proteins are like XIAP, survivin, cIAP1 were downregulated in addition Akt was also downregulated. Strangely, using beta actin as a loading control shows non-equal loading which explains the results obtained, but using GAPDH indiciates equal loading! this result was obtained in replicate analysis of different samples on different membranes. My friend decided to use GAPDH data as loading control and ignore beta actin data. Is this valid? Does this reflects, for example, some non specific toxicity of the treatment?
comments are welcome


It depends - could the treatments affect the loading control proteins indirectly or directly? Would this explain the result?