You are asking for help with biological interpretation of differentially expressed genes. No one can provide specific help without knowing which genes you have actually found differentially expressed. If you just need a general guidance, you can check databases of gene perturbations, and see which genes were previously found to be associated with down-regulation of your genes, when they were over-expressed, down-regulated, knocked-out or mutated. One such database is free - GPA (http://biocc.hrbmu.edu.cn/GPA/); another is for fee (BaseSpace Correlation Engine, Illumina). Additional option is to build gene networks around your genes of interest to facilitate interpretation, and obviously, a systematic review of literature.

I agree that you need to tell which gene in order to help you better.. I believe from your description that it is a gene that inhibits apoptosis, let's say for instance caspace 8. If it is lower in CSC than cancer cells it means that CSC are more capable of surviving because they removed an inhibition. It is typical of CSC to be resistant to drugs and overcome apoptosis as well as being able to live without the presence of growth factors in the serum media. They are more powerful and harder to kill by conventional therapy. Therefore they are usually the prime promoters of recurrences in patients, accordingly to literature data published in Nature (to cite one of such papers: doi: 10.1038/nature11287 )