Abstract 1110: Functional genomics reveals genetic dependencies in gastric cancer
Authors: Kulkarni Meghana M. , Gurumurthy Sushma , Schmidt-Kittler Oleg , Berglund Jason , Hulton Christopher H. , Wilson David J. , Jakubosky David , Michaud Daniel , Jones Robert E. , Sjoblom Nicole M. , McSweeney Russell , Zhou Hongwei , Venkatakrishnan Annapurna , Jensen Karin J. , Zhang Jingxin , Mankoo Parminder K. , Pollard Jack , Winter Christopher , Jänne Pasi A. , Wong Kwok-Kin , Richon Victoria M. , English Jessie M. , Bittinger Mark A. 
Published: August 2015

Gastric cancer is the second leading cause of cancer deaths in the world. The genomics of gastric cancers is unique in that they harbor significantly more copy number alterations compared to point mutations, yet the functional importance of these genetic alterations in tumor maintenance is not known. To better understand oncogenic drivers of gastric cancer and identify potential therapeutic targets we performed negative selection RNAi screens in ten well annotated gastric cancer cell lines. Screens were performed using two different but overlapping shRNA libraries. The first library was the Decipher Human Module I pool from Cellecta composed of 27500 shRNAs targeting 5043 genes. The second library was a custom designed focused pool with 6500 shRNAs targeting 608 genes. In addition to screening the two shRNA libraries in vitro, the focused pool was also screened in subcutaneous xenograft tumor models in eight of the gastric cancer cell lines. The screens revealed distinct genetic vulnerabilities that correlated with the corresponding genomic alteration in the specific cell lines. In particular we found that KRAS amplifications confer dependency to the same degree as activating KRAS mutations. This KRAS dependency was further validated with additional shRNAs in KRAS amplified and mutated cell lines. Furthermore, we identified AMPK which is focally amplified in 9% of gastric cancer as a critical oncogenic driver. Multiple subunits of the AMPK holoenzyme scored in the screen and dependency on AMPK alpha and beta subunits was demonstrated with independent shRNAs in two cell lines from the primary screen. Consistent with the screen results we find that LMSU, a gastric cancer cell line not part of the primary screen but annotated as amplified for the AMPK alpha subunit shows elevated expression levels and is sensitive to knockdown of AMPK. These observations have identified AMPK as a novel oncogenic driver in gastric cancer with therapeutic potential.

Citation Format: Meghana M. Kulkarni, Sushma Gurumurthy, Oleg Schmidt-Kittler, Jason Berglund, Christopher H. Hulton, David J. Wilson, David Jakubosky, Daniel Michaud, Robert E. Jones, Nicole M. Sjoblom, Russell McSweeney, Hongwei Zhou, Annapurna Venkatakrishnan, Karin J. Jensen, Jingxin Zhang, Parminder K. Mankoo, Jack Pollard, Christopher Winter, Pasi A. Jänne, Kwok-Kin Wong, Victoria M. Richon, Jessie M. English, Mark A. Bittinger. Functional genomics reveals genetic dependencies in gastric cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1110. doi:10.1158/1538-7445.AM2015-1110