Functional interpretation of genomic variation is critical to understanding human disease but it remains difficult to predict the effects of specific mutations on protein interaction networks and the phenotypes they regulate. We describe an analytical framework based on multiscale statistical mechanics that integrates genomic and biophysical data to model the human SH2-phosphoprotein network in normal and cancer cells. We apply our approach to data in The Cancer Genome Atlas (TCGA) and test model predictions experimentally. We find that mutations in phosphoproteins often create new interactions but that mutations in SH2 domains result almost exclusively in loss of interactions. Some of these mutations eliminate all interactions but many cause more selective loss, thereby rewiring specific edges in highly connected subnetworks. Moreover, idiosyncratic mutations appear to be as functionally consequential as recurrent mutations. By synthesizing genomic, structural, and biochemical data our framework represents a new approach to the interpretation of genetic variation.
Highlights d Torin2 causes death of TNBC cells by inhibiting several PI3Klike kinases d Live-cell imaging shows that Torin2 exploits vulnerabilities during DNA replication d Combined inhibition of mTOR and Chk1 with selective drugs mimics Torin2 d Computational models confirm the importance of mTOR inhibition in S phase
Rheumatoid arthritis (RA) is a chronic inflammatory disorder that causes joint pain, swelling, and loss of function. Development of effective new drugs has proven challenging, in part because of the complexities and interconnected nature of intracellular signaling networks, which complicate the effects of pharmacological interventions. Here, we characterized the signaling pathways that are activated in RA and evaluated the multivariate effects of targeted inhibitors. Synovial fluids from RA patients activated the kinase signaling pathways JAK, JNK, p38, and MEK in synovial fibroblasts (SFs), a stromal cell type that promotes RA progression. Kinase inhibitors enhanced signaling of “off-target” pathways in a manner dependent on stimulatory context. For example, p38 inhibitors, which have been widely explored in clinical trials for RA, resulted in undesirable increases in nuclear factor κB (NFκB), JNK, and MEK signaling in SFs in inflammatory, but not mitogenic, contexts. CREB, a transcription factor that functions in part within a negative feedback loop in MAPK signaling, emerged as a key regulator of this context-dependence. CREB activation was induced predominately by p38 in response to inflammatory stimuli but by MEK in response to mitogenic stimuli; the effects of drugs targeting p38 or MEK were therefore markedly different in SFs cultured in mitogenic or inflammatory conditions. Together these findings illustrate how stimulatory context can alter pathway cross-talk even for a fixed network topology, suggest cross-talk by p38 in inflammatory contexts limited the benefit of p38 inhibitors in RA, and furthermore demonstrate the need for careful consideration of p38-targeted drugs in inflammation-related disorders.
Frequent mutation of genes in the PI3K/AKT/mTOR signaling pathway in human cancers has stimulated large investments in therapeutic drugs but clinical successes have been rare. As a result, many cancers with high PI3K pathway activity such as triple-negative breast cancer (TNBC) are still treated primarily with conventional chemotherapy. By systematically analyzing responses of TNBC cells to a diverse collection of PI3K pathway inhibitors, we find that one drug, Torin2, is unusually effective because it inhibits both mTOR and PI3K-like kinases (PIKKs). In contrast to mTOR-selective inhibitors, Torin2 exploits dependencies on several kinases for progression of S-phase and for cell cycle checkpoints, thereby causing accumulation of single-stranded DNA and death by replication catastrophe or mitotic failure. Thus, Torin2 and its analogs represent a mechanistically distinct class of PI3K pathway inhibitors that are uniquely cytotoxic to TNBC cells. This insight could be translated therapeutically by further developing Torin2 analogs or combinations of existing mTOR and PIKK inhibitors. HIGHLIGHTS • Torin2-like dual mTOR/PIKK inhibitors are cytotoxic to PI3K-activated TNBC cells • Live-cell imaging shows that Torin2 exploits replicative and checkpoint vulnerabilities • Combined inhibition of mTORC1/2 and Chk1 with selective drugs mimics Torin2 • Computational models show the importance of S-phase drug interactions for cytotoxicity•
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