Identification of clinically predictive metagenes that encode components of a network coupling cell shape to transcription by image-omics.
Date
2017-02-01ICR Author
Author
Sailem, HZ
Bakal, C
Type
Journal Article
Metadata
Show full item recordAbstract
The associations between clinical phenotypes (tumor grade, survival) and cell phenotypes, such as shape, signaling activity, and gene expression, are the basis for cancer pathology, but the mechanisms explaining these relationships are not always clear. The generation of large data sets containing information regarding cell phenotypes and clinical data provides an opportunity to describe these mechanisms. Here, we develop an image-omics approach to integrate quantitative cell imaging data, gene expression, and protein-protein interaction data to systematically describe a "shape-gene network" that couples specific aspects of breast cancer cell shape to signaling and transcriptional events. The actions of this network converge on NF-κB, and support the idea that NF-κB is responsive to mechanical stimuli. By integrating RNAi screening data, we identify components of the shape-gene network that regulate NF-κB in response to cell shape changes. This network was also used to generate metagene models that predict NF-κB activity and aspects of morphology such as cell area, elongation, and protrusiveness. Critically, these metagenes also have predictive value regarding tumor grade and patient outcomes. Taken together, these data strongly suggest that changes in cell shape, driven by gene expression and/or mechanical forces, can promote breast cancer progression by modulating NF-κB activation. Our findings highlight the importance of integrating phenotypic data at the molecular level (signaling and gene expression) with those at the cellular and tissue levels to better understand breast cancer oncogenesis.
Collections
Subject
Humans
Breast Neoplasms
NF-kappa B
Signal Transduction
Cell Shape
Transcription, Genetic
Gene Expression Regulation, Neoplastic
Female
Smad3 Protein
Transcription Factor RelA
Research team
Dynamical Cell Systems
Language
eng
Date accepted
2016-11-17
License start date
2017-02
Citation
Genome research, 2017, 27 (2), pp. 196 - 207
Publisher
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT