Abstract A18: Genetic elements of cancer cell survival in tumor microenvironment stresses
Authors: Keenan Melissa M. , Liu Beiyu , Wu Jianli , Cyr Derek , Lucas Joseph , Nevins Joseph , Kim So Young , Chi Jen-Tsan 
Published: August 2014

Abstract
As solid human cancer tumors form there are a number of physiological changes that occur within the tumor itself, including low oxygen levels (hypoxia) and an accumulation of lactic acid with concomitant lowered pH levels (lactic acidosis). In order to adapt to and survive in these tumor microenvironmental (TME) stresses, human cancer cells in solid tumors exhibit significant genetic and metabolic changes. While transcriptional responses and downstream signaling events are known under certain stresses, a systematic genome-wide investigation of which genes are critical or restrictive for cell survival in these TME stresses has not been examined. The central hypothesis of this research is that understanding the function of genes that modulate cell survival under TME stresses will allow for the development of treatments to specifically target cancer cells under these stress conditions.
To investigate this hypothesis, the concept of synthetic lethality was applied to cultured cancer cells by combining individual gene expression knockdown with the application of hypoxia or lactic acidosis. Specifically, we transduced lung cancer cells with the genome-wide, pSM2C short-hairpin RNA (shRNA) retroviral library before subjecting them to a hypoxic or lactic acidosis stress in culture. Genomic DNA was recovered from surviving cells and the resulting shRNAs amplified by PCR before de-convolution by microarray. A number of criteria were used to select top candidate hits, including a cut off of multiple shRNAs targeting a single gene needing to pass stringent statistical criteria.
We have successfully validated a number of candidate genes with multiple short-hairpin RNAs. For example, HIF2a was identified and validated as critical for these lung cancer cells to survive hypoxia. Other top candidate genes have a wide variety of unexpected biological functions, as could only be found in a genome-wide screen. A top gene candidate indicates that blocking lipid synthesis protects cells under hypoxia. This protection is HIF-independent and more specific to a low serum growth condition. Another top candidate gene reveals a new role for a transcription factor previously implicated in leukemias and lymphomas as important for cell survival under lactic acidosis. Detailed mechanistic studies of these findings are ongoing.
The goal of these studies is to realize how these genes impact the survival of cancer cells under TME stresses and how they play a role in the selection of somatic mutations under long-term stresses. Accomplishing this goal will allow for a better understanding of the genetic changes selected by the TME and improve therapies to target solid human cancers in the future.
Citation Format: Melissa M. Keenan, Beiyu Liu, Jianli Wu, Derek Cyr, Joseph Lucas, Joseph Nevins, So Young Kim, Jen-Tsan Chi. Genetic elements of cancer cell survival in tumor microenvironment stresses. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr A18.