19 We extended the biological meaning of the profile of autoreactive proteins by integrating information about interactions between the proteins as well as their functional roles. Indeed, out of the 17 proteins

identified, 12 proteins could be organized in a network with a distinct biological profile involved in regulation of development and cellular communication (Fig. 1), both of which play a role in coordinating cellular proliferation. Comparing with expression levels in donor lungs as measured in two already published studies9,10 for the genes encoding 15 of the 17 proteins, we observed significant positive correlation with autoreactivity changes in the Alectinib clinical trial recipients. This correlation was observed even though the gene expressions and autoreactivity were measured in different patient cohorts. The interpretation of these correlated molecular events with respect

to PGD is not straightforward. Downstream signalling from both EGFR and IGF1R, which are central components in the protein network in Fig. 1, typically includes activation of the mitogen-activated protein kinase cascade and subsequent transcriptional activation of immediate-early genes such as the activating protein 1 (AP-1) transcription factor subunits FOS and JUN.20 Indeed, AP-1 is known Y-27632 nmr to regulate processes such as proliferation and transformation, which meshes well with the biological profile of the identified proteins (Fig. 1 and Table 2). Interrogation of FOS and JUN gene expression in the GSE8021 study showed that FOS displays almost two-fold lower expression and JUN 1.2-fold lower expression in donor lungs that later developed PGD compared with those that did not (both with P < 0·05). In clinical studies with lung biopsies, PGD has been associated with acute alveolar damage early and fibrosis later, leading to reduced

lung volumes.21 The fibrotic response in inflamed airways most probably manifests itself in part by increased airway epithelial cell proliferation rates.22 We hypothesize that such aberrant proliferation may in part be caused by growth-factor-mediated, proliferative signalling in the donor lung not in balance with the surrounding tissues and organs in the recipient, inferred by the differences in gene expression Montelukast Sodium that correlate with altered autoreactivity against the encoded proteins. The link between donor transcript levels and recipient autoantibody repertoires reported here is supported by significant statistical results on four biological levels: at the level of autoreactive protein selection, at the level of network size and biological process over-representation, at the level of classification accuracy in an independent validation cohort of nine patients, and at the level of correlation with gene expression changes in two other independent patient cohorts of 50 and 26 patients, respectively.