I am conducting a gene modulation on a cell line, which we hypothesize it to mediate the resistance of the cell line towards a certain drug. However, following the gene modulation, MTT assay shows no changes in IC50 of the drug and cell viability upon treatment with various concentrations of the drug but a significant lesser drug-mediated apoptotic cells (both late and early), with higher percentage of viable cells is observed via Apoptosis Assay.

This is quite puzzling to me, as usually people would see changes in cell viability/proliferation, followed with/without changes in percentage of apoptotic cells. But instead, I observed the other way around. The experiments has been independently repeated for three times. Now I'm not sure if there are any assays functionality that I missed to explain these observations.

Please help to give an input, I am in a desperate need of second (or perhaps, third) opinion(s). Thanks in advance!