Heterogeneity of kinase inhibitor resistance mechanisms in GIST

Abstract

Most GIST patients develop clinical resistance to KIT/PDGFRA tyrosine kinase inhibitors (TKI). However, it is unclear whether clinical resistance results from single or multiple molecular mechanisms in each patient. KIT and PDGFRA mutations were evaluated in 53 GIST metastases obtained from 14 patients who underwent surgical debulking after progression on imatinib or sunitinib. To interrogate possible resistance mechanisms across a broad biological spectrum of GISTs, inter-and intra-lesional heterogeneity of molecular drug-resistance mechanisms were evaluated in the following: conventional KIT (CD117)-positive GISTs with KIT mutations in exon 9, 11 or 13; KIT-negative GISTs; GISTs with unusual morphology; and KIT/PDGFRA wild-type GISTs. Genomic KIT and PDGFRA mutations were characterized systematically, using complementary techniques including D-HPLC for KIT exons 9, 11-18 and PDGFRA exons 12, 14, 18, and mutation-specific PCR (V654A, D820G, N822K, Y823D). Primary KIT oncogenic mutations were found in 11/14 patients (79%). Of these, 9/11 (83%), had secondary drug-resistant KIT mutations, including six (67%) with two to five different secondary mutations in separate metastases, and three (34%) with two secondary KIT mutations in the same metastasis. The secondary mutations clustered in the KIT ATP binding pocket and kinase catalytic regions. FISH analyses revealed KIT amplicons in 2/10 metastases lacking secondary KIT mutations. This study demonstrates extensive intra-and inter-lesional heterogeneity of resistance mutations and gene amplification in patients with clinically progressing GIST. KIT kinase resistance mutations were not found in KIT/PDGFRA wildtype GISTs or in KIT-mutant GISTs showing unusual morphology and/or loss of KIT expression by IHC, indicating that resistance mechanisms are fundamentally different in these tumours. Our observations underscore the heterogeneity of clinical TKI resistance, and highlight the therapeutic challenges involved in salvaging patients after clinical progression on TKI monotherapies.

Concordance of c‐kit Mutational Status in Matched Primary and Metastatic Cutaneous Canine Mast Cell Tumors at Baseline

“…As a consequence, the ongoing acquisition of these alterations can result in the emergence of neoplastic subclones with varying genotypes and, consequently, phenotypes,32 leading to discordance between the primary tumor and its metastases. In people, several tumors including melanoma,33 gastrointestinal stromal tumor,34 and lung cancer35 show intratumor and intertumor heterogeneity, indicating the presence of more than one clone of cancer cells within a given neoplastic mass, and the presence of different genetic alterations in different metastatic sites from a single patient, respectively. Therefore, determining if there is homogeneous mutational status between primary tumor and its metastatic sites has important clinical implications, overall to select the appropriate treatment.…”

Gastrointestinal stromal tumors: what do we know now?

“…135,137 Additional studies using more sensitive assays have identified secondary mutations in 480% of drug-resistant GIST lesions. [141][142][143] More sobering is that there is significant heterogeneity of resistance across different lesions, and even within different areas of the same lesion. For example, there are reports of up to five different drug resistance mutations in different portions of an individual lesion and up to seven different secondary resistance mutations across multiple tumors in the same patient.…”

“…For example, there are reports of up to five different drug resistance mutations in different portions of an individual lesion and up to seven different secondary resistance mutations across multiple tumors in the same patient. 141 This heterogeneity of resistance significantly impacts the efficacy of salvage TKI therapy after frontline imatinib, because the diversity of resistant, minority clones precludes the systemic suppression of GIST cells by any particular TKI.…”

Frequent expression of KIT in endometrial stromal sarcoma with YWHAE genetic rearrangement

“…Polymerase chain reaction using primer sets for KIT exons 9, 11, 13 and 17 were performed using the extracted genomic DNA as described previously. 9 The primers are shown in Table 1.…”