Quantitative proteomics investigates physiology at the molecular level by measuring relative differences in protein expression between samples under different experimental conditions. A major obstacle to reliably determining quantitative changes in protein expression is to overcome error imposed by technical variation and biological variation. In drug discovery and development the issue of biological variation often rises in concordance with the developmental stage of research, spanning from in vitro assays to clinical trials. In this paper we present case studies to raise awareness to the issues of technical variation and biological variation and the impact this places on applying quantitative proteomics. We defined the degree of technical variation from the process of two-dimensional electrophoresis as 20-30% coefficient of variation. On the other hand, biological variation observed experiment-to-experiment showed a broader degree of variation depending upon the sample type. This was demonstrated with case studies where variation was monitored across experiments with bacteria, established cell lines, primary cultures, and with drug treated human subjects. We discuss technical variation and biological variation as key factors to consider during experimental design, and offer insight into preparing experiments that overcome this challenge to provide statistically significant outcomes for conducting quantitative proteomic research.

The in vitro effects of prolactin (PRL) on lipoprotein lipase (LPL) activity and on LPL mRNA levels were studied in cultured mammary tissues derived from mid-pregnant mice. Mouse mammary gland tissues were initially incubated for 24 hr in M199 media containing 1 microg/ml insulin and 10(-7) M cortisol. A subsequent treatment of the tissues with 1 microg/ml PRL caused a 76% increase in heparin-releasable LPL (hrLPL) activity after 24 hr. A significant increase in LPL activity was detected 16 hr after PRL addition, but not at earlier times. PRL at 100 ng/ml elicited a maximum stimulation of LPL activity. When Northern hybridization techniques were employed, PRL was also found to increase the tissue content of LPL mRNA; this effect was initially detected after a 6-hr PRL treatment employing PRL concentrations of 50 ng/ml and above. Specificity studies revealed that only lactogenic hormones stimulated LPL activity and LPL mRNA accumulation in cultured mammary tissues. PRL also expressed a small (25% increase), but significant, effect on ATP citrate-lyase activity in mammary tissues cultured for more than 6 hr with the hormone.

The in vitro effects of rapamycin on prolactin (PRL)-stimulated S6 kinase activity and milk product synthesis were investigated in cultured mouse mammary tissues. Mouse mammary gland explants were initially incubated for 24 h in M199 media containing 1 microgram/ml insulin and 10(-7) M cortisol. A subsequent treatment of the tissues with 1 microgram/ml PRL for 12 h caused a 98% increase in S6 kinase activity in the cytosolic fraction; effects were not observed at earlier times. PRL at or above 500 ng/ml was needed to elicit a maximum stimulation of S6 kinase activity, and this response was specific for lactogenic hormones (PRL, hPL, hGH). Rapamycin, an inhibitor of 70 K S6 kinase, was employed to assess the possible physiological role of S6 kinase in the PRL stimulation of milk product formation. Rapamycin (25-100 ng/ml) impeded, in a dose-dependent fashion, the PRL stimulation of casein, lipid and lactose synthesis in concert with its inhibition of cytoplasmic S6 kinase activity. These results suggest a possible role for the activation of 70 K kinase in the signalling pathway for the PRL regulation of milk product synthesis in the mammary gland.

The in vitro effect of wortmannin, an inhibitor of P13 kinase, on prolactin (PRL) stimulated p70S6K, iodide transport, and milk product synthesis were investigated in cultured mouse mammary tissues. Mouse mammary gland explants were initially incubated for 24 hr in media M199 containing 1 microg/ml insulin and 10(-7)M cortisol. A subsequent treatment with wortmannin impeded, in a dose-dependent fashion, the PRL stimulation of casein, lipid, and lactose synthesis as well as the PRL stimulation of iodide transport. Rapamycin (25 ng/ml), an inhibitor of p70S6K, also inhibited the effect of PRL on iodide transport; this drug was earlier shown to inhibit PRL effects on milk product synthesis. These results suggest the possible involvement of p70S6K and P13-kinase in PRL-stimulated milk product formation and iodide transport in mouse mammary explants. Since wortmannin caused a diminished cellular content of p70S6K and a reduced extent of P70S6K migration in polyacrylamide gels (likely due to dephosphorylation), P13-kinase likely lies upstream in the PRL signaling pathway for p70S6K activation.