Development of a protein signature to enable clinical positioning of IAP inhibitors in colorectal cancer

Abstract

Resistance to chemotherapy‐induced cell death is a major barrier to effective treatment of solid tumours such as colorectal cancer, CRC. Herein, we present a study aimed at developing a proteomics‐based predictor of response to standard‐of‐care (SoC) chemotherapy in combination with antagonists of IAPs (inhibitors of apoptosis proteins), which have been implicated as mediators of drug resistance in CRC. We quantified the absolute expression of 19 key apoptotic proteins at baseline in a panel of 12 CRC cell lines representative of the genetic diversity seen in this disease to identify which proteins promote resistance or sensitivity to a model IAP antagonist [birinapant (Bir)] alone and in combination with SoC chemotherapy (5FU plus oxaliplatin). Quantitative western blotting demonstrated heterogeneous expression of IAP interactome proteins across the CRC cell line panel, and cell death analyses revealed a widely varied response to Bir/chemotherapy combinations. Baseline protein expression of cIAP1, caspase‐8 and RIPK1 expression robustly correlated with response to Bir/chemotherapy combinations. Classifying cell lines into ‘responsive’, ‘intermediate’ and ‘resistant’ groups and using linear discriminant analysis (LDA) enabled the identification of a 12‐protein signature that separated responders to Bir/chemotherapy combinations in the CRC cell line panel with 100% accuracy. Moreover, the LDA model was able to predict response accurately when cells were cocultured with Tumour necrosis factor‐alpha to mimic a pro‐inflammatory tumour microenvironment. Thus, our study provides the starting point for a proteomics‐based companion diagnostic that predicts response to IAP antagonist/SoC chemotherapy combinations in CRC.

Efficacy of birinapant in combination with carboplatin in targeting platinum‑resistant epithelial ovarian cancers

“…McCann et al also reported that expression of IAP proteins alone could not be correlated to birinapant sensitivity in a panel of colorectal cancer cell lines (49). Similarly, in our study, we did not see a correlation between IAP protein levels and response to birinapant in the ovarian cancer cell lines tested.…”

“…One of the main challenges is to identify and develop biomarkers of response to birinapant. Several studies have assessed and demonstrated that IAP levels do not correlate with sensitivity to birinapant ( 48 , 49 ). Zinngrebe et al demonstrated that protein expression levels of cIAP1 and XIAP were similar in SMAC mimetic-sensitive and SMAC mimetic-insensitive primary B-cell acute lymphoblastic leukemia samples ( 48 ).…”

“…Zinngrebe et al demonstrated that protein expression levels of cIAP1 and XIAP were similar in SMAC mimetic-sensitive and SMAC mimetic-insensitive primary B-cell acute lymphoblastic leukemia samples ( 48 ). McCann et al also reported that expression of IAP proteins alone could not be correlated to birinapant sensitivity in a panel of colorectal cancer cell lines ( 49 ). Similarly, in our study, we did not see a correlation between IAP protein levels and response to birinapant in the ovarian cancer cell lines tested.…”

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

“…MEDI3039 sensitivity is significantly affected by FLIP(L). To further determine whether expression of caspase-8 at the protein level or other components of the apoptotic pathway could be used to predict response to MEDI3039, we next used a panel of 12 colorectal cancer (CRC) cell lines in which we have quantitatively measured protein levels of 18 major cell death regulatory proteins (23). CRC cell lines were selected because they exhibited variable sensitivity to MEDI3039 in the cell line screen and interestingly CASP8 mRNA expression alone did not predict for sensitivity to MEDI3039, despite a biomodal pattern of sensitivity (Figure 2B/D).…”

Increased sensitivity to SMAC mimetic LCL161 identified by longitudinal ex vivo pharmacogenomics of recurrent, KRAS mutated rectal cancer liver metastases

“…Single-sample gene set enrichment analyses of gene signatures of response and resistance to 5-fluorouracil (5-FU) [31], as well as the "hallmark" gene sets (n = 50; retrieved from the Molecular Signatures Database, v7.0 [32]) were performed by the gsva function (gene set variation analysis) in the R package GSVA [33]. Sensitivity to LCL161 was also analyzed in relation to log2 expression signals of previously suggested target genes encoding mediators of the TNF alpha pathway and apoptosis regulators [34].…”