Functional Genomic Identification of Predictors of Sensitivity and Mechanisms of Resistance to Multivalent Second-Generation TRAIL-R2 Agonists

Functional Genomic Identification of Predictors of Sensitivity and Mechanisms of Resistance to Multivalent Second-Generation TRAIL-R2 Agonists

Grinkevitch, Vera (Wellcome Sanger Institute)
Wappett, Mark (Queen's University Belfast)
Crawford, Nyree (Queen's University Belfast)
Price, Stacey (Wellcome Sanger Institute)
Lees, Andrea (Queen's University Belfast)
McCann, Christopher (Queen's University Belfast)
McAllister, Katherine (Queen's University Belfast)
Prehn, Jochen (Royal College of Surgeons in Ireland)
Wessels, L.F.A. (TU Delft Pattern Recognition and Bioinformatics; Netherlands Cancer Institute)

2022

Multivalent second-generation TRAIL-R2 agonists are currently in late preclinical development and early clinical trials. Herein, we use a representative second-generation agent, MEDI3039, to address two major clinical challenges facing these agents: lack of predictive biomarkers to enable patient selection and emergence of resistance. Genome-wide CRISPR knockout screens were notable for the lack of resistance mechanisms beyond the canonical TRAILR2 pathway (caspase-8, FADD, BID) as well as p53 and BAX in TP53 wild-type models, whereas a CRISPR activatory screen identified cell death inhibitors MCL-1 and BCL-XL as mechanisms to suppress MEDI3039-induced cell death. High-throughput drug screening failed to identify genomic alterations associated with response to MEDI3039; however, transcriptomics analysis revealed striking association between MEDI3039 sensitivity and expression of core components of the extrinsic apoptotic pathway, most notably its main apoptotic effector caspase-8 in solid tumor cell lines. Further analyses of colorectal cell lines and patient-derived xenografts identified caspase-8 expression ratio to its endogenous regulator FLIP(L) as predictive of sensitivity to MEDI3039 in several major solid tumor types and a further subset indicated by caspase-8: MCL-1 ratio. Subsequent MEDI3039 combination screening of TRAIL-R2, caspase-8, FADD, and BID knockout models with 60 compounds with varying mechanisms of action identified two inhibitor of apoptosis proteins (IAP) that exhibited strong synergy with MEDI3039 that could reverse resistance only in BIDdeleted models. In summary, we identify the ratios of caspase-8: FLIP(L) and caspase-8:MCL-1 as potential predictive biomarkers for second-generation TRAIL-R2 agonists and loss of key effectors such as FADD and caspase-8 as likely drivers of clinical resistance in solid tumors.

http://resolver.tudelft.nl/uuid:c0a9df57-b127-4fa9-aaf2-3cdcc5dca58b

https://doi.org/10.1158/1535-7163.MCT-21-0532

1535-7163

Molecular Cancer Therapeutics, 21 (4), 594-606

Institutional Repository

journal article

© 2022 Vera Grinkevitch, Mark Wappett, Nyree Crawford, Stacey Price, Andrea Lees, Christopher McCann, Katherine McAllister, Jochen Prehn, L.F.A. Wessels, More Authors