The sum of gains and losses of genes encoding the protein tyrosine kinase targets predicts response to multi-kinase inhibitor treatment: Characterization, validation, and prognostic value

Abstract

Validated predictive biomarkers for multi-tyrosine kinase inhibitors (MTKI) efficacy are lacking. We hypothesized that interindividual response variability is partially dependent on somatic DNA copy number alterations (SCNAs), particularly those of genes encoding the protein tyrosines targeted by MTKI (called target genes). Genomic alterations were investigated in MTKI responsive and non responsive patients with different histological subtypes included in the ProfiLER protocol (NCT 01774409). From March 2013 to August 2014, 58 patients with advanced cancer treated with one of 7 MTKIs were included in the ProfiLER trial and split into one discovery cohort (n = 13), and 2 validation cohorts (n = 12 and 33). An analysis of the copy number alterations of kinase-coding genes for each of 7 MTKIs was conducted. A prediction algorithm (SUMSCAN) based on the presence of specific gene gains (Tumor Target Charge, TTC) and losses (Tumor Target Losses, TTL) was conceived and validated in 2 independent validation cohorts. MTKI sensitive tumors present a characteristic SCNA profile including a global gain profile, and specific gains for target genes while MTKI resistant tumors present the opposite. SUMSCAN favorable patients achieved longer progression-free and overall survival. This work shows that the copy number sum of kinase-coding genes enables the prediction of response of cancer patients to MTKI, opening a novel paradigm for the treatment selection of these patients.

Trial registration: ClinicalTrials.gov NCT01774409.

Keywords: biomarker; chromosomal instability; multi-kinase inhibitor; regorafenib.

Conflict of interest statement

CONFLICTS OF INTEREST

The authors declare no conflict of interest.

Figures

Figure 1

a. Copy-number alteration pattern of the 18 regorafenib target genes in the discovery cohor. The SCNA pattern of the 18 target genes was displayed as a heatmap. Top and bottom parts show the grouped results of the 6 regorafenib clinical benefit positive and the 7 regorafenib resistant tumors, respectively. The tumor/normal log2 ratios categories for different copy-number alterations levels were defined as in the online methods. b. Copy-number alteration pattern of the 18 regorafenib target genes in the validation cohort I. Top and bottom parts show the grouped results of the 5 tumors with regorafenib clinical benefit and the 7 tumors without clinical regorafenib benefits, respectively. c. Sum of total gains and deletions in the regorafenib clinical benefit positive and the clinical benefit negative tumors. There are significantly more gene gains in tumors having a clinical benefit than in the resistant ones (Top). d. Integral analysis of copy-number change pattern of the 18 regorafenib target genes in 25 patients. Gene gain events in red and gene deletion events in green. e. SUMSCAN Algorithm 1). TTC: tumor target charge, sum of gains on target genes; 2). Number of gains at target genes* versus number of losses at target genes 3) If there are more losses at target genes than gains, the tumor is predicted as resistant. All gain/loss events were equally considered. f. PFS and OS curve of 25 patients treated with regorafenib.

Figure 2. Differences concerning gain and loss frequencies between patients with regorafenib clinical benefits and those without clinical benefits

a. A significant difference in the gain frequencies was observed for the DDR2, NTRK1 and FLT4 genes. b. Specific loss on EPHA2 was remarkably frequent in the regorafenib resistant tumors.

Figure 3. Validation II in 33 patients treated by one of the 6 other MTKIs

a. Copy-number alteration pattern of the target genes of 6 MTKIs (Sorafenib, sunitinib, pazopanib, axitinib, vandetanib and cabozantinib) in the validation cohort: Top and bottom parts show the results of the 20 tumors with clinical benefits and the 13 tumors without clinical benefits, respectively. b. Sum of total gains and deletions in the validation cohort II. There are significantly less gene deletions and more gene gains in the tumors having the clinical benefits compared to those without clinical benefits. c. and d. PFS and OS curve of 33 patients treated with one of the 6 MTKIs in the first-line MTKI settings. The patients with a favorable SUMSCAN had a progression free survival benefit. e. and f. PFS and OS curve of 22 patients treated by MTKI in the second-line MTKI settings. Patients with a favorable SUMSCAN achieved a better PFS and OS.