Abstract A45: Investigation of efficacy of the NAE inhibitor MLN4924 across large-scale cell line panels reveals potentially sensitive cancer indications and candidate predictive biomarkers.
Authors: Li Bin , Schu Matthew , Blakemore Stephen J. , Trepicchio William , Smith Peter G. , Lightcap Eric , Mihollen Michael , Knight Ben , Benes Cyril , Milligan George 
Published: June 2012

Abstract
MLN4924 is an investigational inhibitor of NAE (Nedd8 Activating Enzyme). NAE mediates NEDD8 conjugation and thus regulates the cullin-RING ligase (CRL) proteasomal degradation pathway. MLN4924 is currently being tested in Phase 1 clinical trials of patients with hematological or solid tumors. To support future clinical development and identify potential biomarkers of tumor sensitivity or resistance, two large cancer cell line panels (Panel 1, N=653; Panel 2, N=240) were treated with MLN4924 and cell viability data (IC50, EC50, and POC - Percentage of Control) were generated. These data were used to correlate sensitivity/resistance with the cell line's tumor histology and with underlying genetic data for the specific cell lines. Overlapping cell lines from the two panels (114) showed consistent growth inhibition effects (Spearman Correlation coefficient = 0.72). Using Fisher's exact test and POC cutoffs at 25% and 50% quartiles on viability data, we identified bladder cancer and head and neck cancer lines as associated with MLN4924 sensitivity in both panels. Using median percentage of control values as cutoff, we applied Fisher's exact test to evaluate associations of individual mutations in the cell lines to MLN4924 sensitivity or resistance. Examples of mutations linked to sensitivity include KDM6A (p-value = 0.02, Panel 1; p-value = 0.06, Panel 2). APC mutation is associated with resistance to MLN4924 (p-value = 5.75 × 10−5, Panel 1; p-value = 0.04, Panel 2).
Combining cell viability and baseline gene expression data from cell line Panel 2, a PLSR predictive model was developed, identifying a gene signature (102 genes) for MLN4924 sensitivity and resistance. A median cutoff of PLSR scores was applied to separate predicted sensitive/resistant cell lines. Consistent with previous association of cell viability with histology, PLSR analysis of gene expression predicted that bladder cancer cell lines are particularly sensitive to MLN4924. Two pathway analysis approaches were applied to identify MLN4924 sensitivity related pathways using either whole genome information (GSEA) or the PLSR gene signature list. The two approaches consistently indicated an over-representation of signaling pathways including cell cycle, development hedgehog signaling and ErbB signaling. The over-represented cell cycle pathway is in good agreement with previous MLN4924 mechanism of action studies. In particular, this finding was independently validated via a whole genome siRNA screen that also identified the cell cycle pathway as associated with tumor sensitivity. The consistent observations from two large cell line panels and a siRNA screen support the utility of these approaches for clarifying sensitive and resistant tumor cell types and also potentially identifying candidate biomarkers.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr A45.