Abstract
As genomics advances reveal the cancer gene landscape, a daunting task is to understand how these genes contribute to dysregulated oncogenic pathways. Integration of cancer genes into networks offers opportunities to reveal protein-protein interactions (PPIs) with functional and therapeutic significance. Here, we report the generation of a cancer-focused PPI network, termed OncoPPi, and identification of >260 cancer-associated PPIs not in other large-scale interactomes. PPI hubs reveal new regulatory mechanisms for cancer genes like MYC, STK11, RASSF1 and CDK4. As example, the NSD3 (WHSC1L1)-MYC interaction suggests a new mechanism for NSD3/BRD4 chromatin complex regulation of MYC-driven tumours. Association of undruggable tumour suppressors with drug targets informs therapeutic options. Based on OncoPPi-derived STK11-CDK4 connectivity, we observe enhanced sensitivity of STK11-silenced lung cancer cells to the FDA-approved CDK4 inhibitor palbociclib. OncoPPi is a focused PPI resource that links cancer genes into a signalling network for discovery of PPI targets and network-implicated tumour vulnerabilities for therapeutic interrogation.
Publication types
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Research Support, N.I.H., Extramural
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Research Support, Non-U.S. Gov't
MeSH terms
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AMP-Activated Protein Kinase Kinases
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Cell Cycle Proteins
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Cell Line, Tumor
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Cell Survival / drug effects
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Cyclin-Dependent Kinase 4 / genetics
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Cyclin-Dependent Kinase 4 / metabolism
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Databases, Protein
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Gene Expression Regulation, Neoplastic / drug effects*
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Gene Expression Regulation, Neoplastic / genetics*
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Gene Regulatory Networks / drug effects*
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Gene Regulatory Networks / genetics*
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Genes, Tumor Suppressor / drug effects
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Genes, myc / genetics
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Genomics
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Histone-Lysine N-Methyltransferase / genetics
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Histone-Lysine N-Methyltransferase / metabolism
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Humans
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Lung Neoplasms / drug therapy
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Lung Neoplasms / genetics
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Lung Neoplasms / metabolism
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Molecular Targeted Therapy
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Neoplasm Proteins / genetics
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Neoplasm Proteins / metabolism
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Nuclear Proteins / genetics
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Nuclear Proteins / metabolism
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Oncogenes / drug effects*
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Oncogenes / genetics*
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Oncogenes / physiology
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Protein Interaction Domains and Motifs / drug effects*
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Protein Interaction Domains and Motifs / genetics*
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Protein Interaction Domains and Motifs / physiology
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Protein Interaction Mapping
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Protein Kinase Inhibitors / pharmacology
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Protein Serine-Threonine Kinases / genetics
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Protein Serine-Threonine Kinases / metabolism
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Protein Stability
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Signal Transduction / drug effects
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Signal Transduction / genetics
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Transcription Factors / genetics
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Transcription Factors / metabolism
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Tumor Suppressor Proteins / genetics
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Tumor Suppressor Proteins / metabolism
Substances
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BRD4 protein, human
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Cell Cycle Proteins
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Neoplasm Proteins
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Nuclear Proteins
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Protein Kinase Inhibitors
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RASSF1 protein, human
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Transcription Factors
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Tumor Suppressor Proteins
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Histone-Lysine N-Methyltransferase
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NSD3 protein, human
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Protein Serine-Threonine Kinases
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STK11 protein, human
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CDK4 protein, human
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Cyclin-Dependent Kinase 4
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AMP-Activated Protein Kinase Kinases