Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses

Joshua Broyde, David R. Simpson, Diana Murray, Evan O. Paull, Brennan W. Chu, Somnath Tagore, Sunny J. Jones, Aaron T. Griffin, Federico M. Giorgi, Alexander Lachmann, Peter Jackson, E. Alejandro Sweet-Cordero, Barry Honig, Andrea Califano

Research output: Contribution to journalArticlepeer-review

17 Scopus citations

Abstract

Tumor-specific elucidation of physical and functional oncoprotein interactions could improve tumorigenic mechanism characterization and therapeutic response prediction. Current interaction models and pathways, however, lack context specificity and are not oncoprotein specific. We introduce SigMaps as context-specific networks, comprising modulators, effectors and cognate binding-partners of a specific oncoprotein. SigMaps are reconstructed de novo by integrating diverse evidence sources—including protein structure, gene expression and mutational profiles—via the OncoSig machine learning framework. We first generated a KRAS-specific SigMap for lung adenocarcinoma, which recapitulated published KRAS biology, identified novel synthetic lethal proteins that were experimentally validated in three-dimensional spheroid models and established uncharacterized crosstalk with RAB/RHO. To show that OncoSig is generalizable, we first inferred SigMaps for the ten most mutated human oncoproteins and then for the full repertoire of 715 proteins in the COSMIC Cancer Gene Census. Taken together, these SigMaps show that the cell’s regulatory and signaling architecture is highly tissue specific.

Original languageEnglish
Pages (from-to)215-224
Number of pages10
JournalNature Biotechnology
Volume39
Issue number2
DOIs
StatePublished - Feb 2021

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