Characterization of p38 MAPK isoforms for drug resistance study using systems biology approach

Motivation: p38 mitogen-activated protein kinase activation plays an important role in resistance to chemotherapeutic cytotoxic drugs in treating multiple myeloma (MM). However, how the p38 mitogenactivated protein kinase signaling pathway is involved in drug resistance, in particular the roles that the various p38 isoforms play, remains largely unknown. Method: To explore the underlying mechanisms, we developed a novel systems biology approach by integrating liquid chromatography-mass spectrometry and reverse phase protein array data from human MM cell lines with computational pathway models in which the unknown parameters were inferred using a proposed novel algorithm called modularized factor graph. Results: New mechanisms predicted by our models suggest that combined activation of various p38 isoforms may result in drug resistance in MM via regulating the related pathways including extracellular signal-regulated kinase (ERK) pathway and (NFDB)-B-0 pathway. ERK pathway regulating cell growth is synergistically regulated by p38 delta isoform, whereas nuclear factor kappa B ((NFDB)-B-0) pathway regulating cell apoptosis is synergistically regulated by p38 alpha isoform. This finding that p38 delta isoform promotes the phosphorylation of ERK1/2 in MM cells treated with bortezomib was validated by western blotting. Based on the predicted mechanisms, we further screened drug combinations in silico and found that a promising drug combination targeting ERK1/2 and NF kappa B might reduce the effects of drug resistance in MM cells. This study provides a framework of a systems biology approach to studying drug resistance and drug combination selection. Availability and implementation: RPPA experimental Data and Matlab source codes of modularized factor graph for parameter estimation are freely available online at ext-link-type=uri xlink:href=http://ctsb.is.wfubmc.edu/publications/modularized-factor-graph.php xlink:type=simplehttp://ctsb.is.wfubmc.edu/publications/modularized-factor-graph.php