Network perturbation analysis of gene transcriptional profiles reveals protein targets and mechanism of action of drugs and influenza A viral infection

Noh, Heeju; Shoemaker, Jason E; Gunawan, Rudiyanto

Besides high AUROCs, ProTINA also provided accurate and specific indications on the MoA of the compounds. In the NCI-DREAM synergy study, roughly half of the compounds are known to induce DNA damage response, including DNA topoisomerase inhibitors (camptothecin, doxorubicin and etoposide), DNA crosslinker (mitomycin C), oxidative DNA damaging agent (methothrexate), and histone deacetylase (HDAC) inhibitors (trichostatin A). In demonstrating ProTINA's ability to reveal the compound MoA, we focused on the canonical p53 DNA damage response pathway (23) , as illustrated in Figure 3 . Here, the activation of p53 in response to DNA damage is expected to induce the transcription of Cyclin Dependent Kinase Inhibitor 1A (CDKN1A) and Growth Arrest and DNA Damage Inducible Alpha (GADD45A) (50, 51) . In turn, CDKN1A and GADD45A--through their interactions with Proliferating Cell Nuclear Antigen (PCNA)--regulate the DNA replication and repair process (52) . GADD45A also inhibits the catalytic activity of Aurora Kinase A (AU-RKA) (53), leading to a lowered activation of Polo-like Kinase 1 (PLK1) and Cyclin B1 (CCNB1) in a phosphorylation cascade (54, 55) . As shown in Figure 4A , except for trichostatin A, the six proteins in the canonical p53 pathway above were ranked highly by ProTINA among the genotoxic compounds in the study (median rank <500), consistent with their known MoA. Note that the same six proteins were ranked much lower among the non-DNA damaging compounds (median rank > 500), signifying a high specificity of ProTINA predictions (see also Supplementary Figure S1 ). Equally important, ProTINA was able to accurately identify the direction of the drug-induced alterations caused by the DNA damaging compounds. The signs of protein target scores from ProTINA indicated drug-induced enhancement (positive scores) of CDKN1A, PCNA and GADD45A, and attenuation (negative scores) of CCNB1, AURKA and PLK1 (see Supplementary Table S4) , consistent with the expected response of these proteins to DNA damage in Figure 3 .