Potential misinterpretation of data on differential gene expression in normal and malignant cells in vitro

High throughput genomic and proteomic methods are often used for comparisons between expression of genes and proteins, respectively in normal cells and malignant counterparts for the identification of potential tumor markers for diagnosis and prognosis. Some experiments use normal and malignant cells cultured in vitro as a source of the mRNA or proteins for analysis. The conditions used for cell culture can exert major effects on the expression of genes and proteins. The interpretation of results of some such studies can be erroneous if normal cells and cancer cells are cultured in serum-free medium (SFM) and serum-supplemented media, respectively as recommended for their optimal growth. The reason for potential complications in the data interpretation is that serum contains different factors that affect gene expression. Likewise, SFM is usually supplemented with specific growth factors as well as bovine pituitary extract. Experimental examples demonstrating the issue include the stimulatory effects of serum on the expression of retinoic acid-inducible genes (e.g. GPRC5A) leading to the potentially erroneous conclusion that such genes are overexpressed in cancer cells. Potential remedy for this problem is to grow the normal and malignant cells in the same medium (serum-free or serum-containing) before analysis.