Abstract P6-06-01: Analyzing the physical and functional protein interaction landscape of breast cancer
Authors: Kim M , Kim K , Tutuncuoglu B , Soucheray M , Swaney D , Zheng F , Park J , O'Leary P , Coppé J-P , van 't Veer L , Ashworth A , Ideker T , Krogan N 
Published: May 2019

Abstract
A key unanswered question in cancer genetics is how different mutations, dispersed across a multitude of genes, elicit similar pathology and patient outcomes. The answer may lie in understanding the molecular networks and protein complexes (i.e. signaling pathways, chromatin architecture, etc) in cancer and mapping mutated genes into the complexes and pathways in which they function. Determining how systematic interaction networks are wired in cancer cells and how different mutations perturb these networks will guide the search for new cancer genes and provide a platform for integrating patient data to make biological and clinical predictions more accurate. The goal of this study is to uncover the comprehensive protein-protein interaction networks and pathways in various breast cancer subtypes to better understand how mutated cancer genes and genomes hijack and re-wire pathways and complexes during the course of breast tumorigenesis.
Here we catalog protein-protein interactions for 40 genes recurrently mutated in breast cancer, using affinity purification and mass spectrometry. To identify co-associated proteins, cDNA clones expressing each protein were tagged with 3xFLAG at either N or C-terminus and introduced into MCF10A (non-tumorigenic “healthy” control), MCF7 (luminal A subtype), and MDA-MB-231 (claudin-low) cells using doxycycline-inducible lentiviral vectors. For proteins with prevalent pathogenic mutations (e.g. PIK3CA-H1047R, BRCA1-C61G), mutant cDNA clones were also analyzed in parallel. Our interaction network reveals subtype and mutation-specific protein-protein interactions, many of which are not previously reported. Given that genes encoding components of a protein complex or a biological pathway often share similar phenotype upon genetic perturbation, we genetically knocked out genes interacting with DNA damage response (DDR) proteins using CRISPR/Cas9, and found multiple novel interacting genes whose knockout results in significant PARPi (olaparib) and/or cisplatin sensitivity. This result not only functionally validates the physical protein interactions, but also demonstrates that our interactome mapping approach can helps identify newdruggable vulnerabilities in cancer cells.
We anticipate the breast cancer interactome study will uncover aberrant pathways and protein complexes uniquely operating in breast cancer cells, and thus pinpoint proteins that may potentially serve as distinct biomarkers or therapeutic targets for tumors having the same or similar subtypes and/or genomic mutations.
Citation Format: Kim M, Kim K, Tutuncuoglu B, Soucheray M, Swaney D, Zheng F, Park J, O'Leary P, Coppé J-P, van 't Veer L, Ashworth A, Ideker T, Krogan N. Analyzing the physical and functional protein interaction landscape of breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P6-06-01.