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KIT in Gastrointestinal Stromal Tumours (GIST): ESMO Biomarker Factsheet

ESMO Factsheets on Biomarkers


The KIT proto-oncogene maps to 4q12 and encodes the 145-kDA transmembrane receptor tyrosine kinase, KIT (CD117), the cellular homolog of the Hardy–Zuckerman 4 feline sarcoma viral oncogene, v-kit[1, 2]. KIT is a member of the type III tyrosine kinase receptor family, which also includes the platelet derived growth factor receptor-alpha (PDGFRA)[2]. KIT is activated through binding of its ligand, stem cell factor, to its extracellular domain, which initialises downstream signalling cascades, including the JAK–STAT3, phosphatidylinositide-3- kinase (PI3K)–AKT–mTOR, and RAS–MAPK pathways, important in regulating cellular functions such as proliferation and apoptosis, chemotaxis and adhesion[1, 3]. Normal expression of KIT is critical for the development and maintenance of different cell types, including interstitial cells of Cajal involved in gastrointestinal pacemaker activity[1, 3].

In 1998 a critical discovery showed that gain-of-function mutations in KIT are a key oncogenic driver in most gastrointestinal stromal tumours (GISTs)[4]. These mutations are present in over 80% of GISTs and lead to constitutive, ligand-independent activation of the KIT receptor and its downstream pathways, ultimately increasing cell proliferation and inhibiting apoptosis[2].

KIT mutations in GIST

Mutations in KIT mainly affect those exons that encode the functional domains of the tyrosine kinase receptor, namely exons 9, 11, 13 and 17[3].

Exon 11, which encodes the juxtamembrane domain of KIT, is the most frequently mutated region, affecting 70–75% of GIST[5, 6]. The conformational changes in KIT due to exon 11 mutations disrupt the autoinhibitory domain of the receptor and permit continuous kinase activation[7]. Deletions affecting codons 557-558 of exon 11 are the most common KIT mutation, detected in 23-28% of GISTs[2]. Point mutations, duplications and homo/hemizygous exon 11 mutation status have also been identified[2]. The vast majority (>80%) of exon 11-mutated GISTs are located in the stomach, although they may arise essentially anywhere in the GI tract[1].

Mutations in exon 9, which encodes the extracellular domain of KIT, occur in 7–15% of GIST cases[2]. These mutations are believed to mimic the conformational change that the extracellular KIT receptor undergoes when ligand is bound, thus leading to dimerisation and constitutive activation[1]. The majority of exon 9 mutations are duplications of codons 502 and 503 and are almost exclusively associated with GISTS of small intestinal origin[3, 8]

Mutations in exons 13 and 17 are not common, occurring in 1-2% of GISTs[2, 9, 10]. Mutations in exon 13 encoding the ATP-binding region of KIT are speculated to interfere with the physiological auto-inhibitory function of the juxtamembrane domain, and usually arise in the stomach[1, 10]. Mutations in exon 17 encoding the activation loop of the kinase seem to stabilize the active conformation[10], and appear to arise twice as frequently in the small intestine as in the stomach[1, 2]. Mutations in KIT can also appear after treatment, termed secondary mutations, and are usually in exons 13, 14, and 17 accompanied by a primary KIT mutation[11]

KIT mutations as a diagnostic biomarker in GIST

KIT (CD117) expression is detected immunohistochemically in >95% of GISTs, making it a key diagnostic marker, together with anoctamin1 (DOG1)[11]. KIT detection by immunohistochemistry is unrelated to the existence of underlying KIT mutations, which have been identified in a proportion of GISTs that stain negative for CD117[11, 12]. Inclusion of mutational analysis for known mutations in genes such as KIT in the diagnostic work-up of GIST is paramount for the selection of appropriate therapy (see below) but may also help confirm the diagnosis of suspect GIST that do not exhibit positive immunoreactivity for CD117/DOG1[13]

KIT mutations as a prognostic biomarker in GIST

Exon 11 deletions affecting codons 557/558 have been associated with an aggressive, metastasising phenotype and indicate an overall poorer prognosis in both high-risk and non­high-risk gastric GIST[2, 14-16]. In contrast, gastric GISTs harbouring exon 11 duplications or point mutations have been linked with a more favourable clinical course[2, 15, 16]

KIT exon 9 duplications have been associated with a poor clinical prognosis as compared with other mutations[16]. However, the worse prognosis of KIT exon 9 mutants seems to be related to the almost exclusive high-risk extra-gastric tumour location of these GISTs rather than to an intrinsic aggressive biologic behaviour[2]

KIT mutations as a predictive biomarker in GIST

As a key oncogenic driver expressed in the majority of GISTs, KIT is a key therapeutic target. KIT mutational status holds predictive value for GIST sensitivity to targeted treatments and routine genotyping has become an integral part of management of GISTs undergoing tyrosine kinase inhibitor therapy[2].

Imatinib (Glivec®, Novartis Pharmaceuticals), a tyrosine kinase inhibitor that competitively binds the ATP-binding domain of KIT has demonstrated pronounced clinical efficacy in GISTs [17-19].  Imatinib 400 mg/day was licensed over 15 years ago for the treatment of adult patients with KIT (CD 117) positive, unresectable and/or metastatic malignant GIST and for the adjuvant treatment of adult patients who are at significant risk of relapse following resection of KIT (CD117)-positive GIST[19].

In the adjuvant setting, studies demonstrate that patients with KIT exon 11 mutations benefit most from imatinib[20, 21].  In the ACOSOG Z 9001 trial of 645 patients receiving one year adjuvant imatinib or placebo after resection of primary GIST, imatinib therapy was associated with longer recurrence-free survival in patients with a exon 11 deletion of any type[20]. In another study, patients with exon 11 mutations benefited from longer 3-year adjuvant treatment, whereas no significant improvement over 12 months of imatinib was found in the subsets of patients whose GIST harboured an exon 9 or PDGFRA mutation, or patients who had no mutation in either gene, although patient numbers were small in these latter groups[21].

In the advanced GIST setting, improved treatment outcomes with imatinib have been observed for patients with KIT exon 11 mutations compared with patients with exon 9 mutations or wild-type KIT[22, 23]. In the North American Phase III SWOG S0033 study, the presence of exon 11 mutation (n = 283) correlated with improved treatment outcome when compared with exon 9 mutation (n = 32) and wild-type (n = 67) genotypes for objective response (71.7% v 44.4% [P=0.007]; and 44.6% [P=0.0002], respectively); time to tumour progression (median 24.7 months v 16.7 and 12.8 months, respectively); and overall survival (OS) (median 60.0 months v 38.4 and 49.0 months, respectively)[23]. In the joint analysis of the S0033 and European Organisation for Research and Treatment of Cancer 62005 trials comparing standard 400 mg once daily imatinib dose versus 400 mg twice daily, the sole predictive factor of response was the presence of a KIT exon 9 mutation[24]. The estimated risk of progression or death was reduced by 42% in the high-dose arm (compared with the standard-dose arm) in patients with KIT exon 9 mutated tumours. The study concluded that for most patients, the recommended imatinib dose is 400 mg daily, with exception of KIT exon 9 mutated tumours for which the 400 mg twice daily dose can be considered[24].

Although 80–85% patients with advanced GIST benefit from imatinib treatment, all will subsequently develop secondary resistance, which is frequently associated with secondary KIT mutations[2]. Imatinib can only bind to the inactive conformation of KIT, and both primary and secondary resistance to imatinib can be partially explained by a conformational shift in the kinase domain of KIT that favours the activated state[2, 25]. Activation loop mutations (i.e. those affecting exon 17) indirectly induce imatinib resistance by stabilising the active receptor conformation[7]. In a Phase I/II study, half of the patients progressing on imatinib had a secondary KIT mutation detected in either exon 13, 14 or 17[26]. Secondary mutations were more likely to be found in patients who initially harboured KIT exon 11 mutations (73%) as compared with KIT exon 9 mutations (19%), likely due to the longer exposure to imatinib of the primary exon 11 mutant subgroup[2, 26].

In 2006 a second tyrosine kinase inhibitor, Sunitinib (Sutent®, Pfizer), was approved for use in imatinib-resistant GIST[27]. Sunitinib (50 mg/day over 4 weeks followed by 2-week rest period) is licensed for the treatment of unresectable and/or metastatic malignant GIST in adults after failure of imatinib treatment due to resistance or intolerance [27, 28].

Response to sunitinib appears to be influenced by both primary and secondary KIT mutations.  Patients harbouring primary exon 9 mutations appear to achieve better outcomes than those with exon 11 mutation or wild-type KIT/PDGFRA[26, 29]. In a worldwide, open-label treatment-use study of patients resistant or intolerant to imatinib a median progression-free survival (PFS) of 7.1 months was reported for patients who received sunitinib[29]. The PFS in patients with a primary exon 9 mutation was significantly better as compared with those with a primary exon 11 mutation (12.3 vs. 7.0 months, respectively), which also translated to longer overall survival (OS) and higher objective response rate ORR. Regarding secondary mutations, in a study including primarily KIT-mutated GIST patients, the median PFS and OS with sunitinib was significantly longer for secondary KIT exon 13 or 14 mutations (which involve the KIT-ATP binding pocket) than for those with secondary exon 17 or 18 mutations (which involve the KIT activation loop) (PFS 7.8 vs. 2.3 months, respectively; OS 13.0 vs. 4.0 months, respectively[26].

A third tyrosine kinase inhibitor, Regorafenib (Stivarga®, Bayer), is indicated for patients with unresectable or metastatic GIST who progressed on or are intolerant to prior treatment with imatinib and sunitinib[30, 31]. There is little evidence available of the predictive power of mutational status in third-line regorafenib treatment of GISTs, but and similar benefits have been observed for patients with primary KIT exon 11 or exon 9 mutations[30].

KIT mutation analysis in GIST

Mutation analysis should be performed using an appropriate, validated, technique, and performed by specifically trained personnel and results should always specify the type of analysis performed, the region or mutations evaluated, and the sensitivity of the detection method used[11].  

The most widely used method for detecting KIT mutations is amplification of the exons of interest by polymerase chain reaction (PCR) followed by direct sequencing (Sanger method) of amplification products. Due to limitations in the sensitivity of this technique it is essential that the methodology is appropriately optimised and controlled and performed only on samples containing ≥50% tumour cells[11]. Next-generation sequencing can provide greater sensitivity with several GIST-specific gene panels now commercially available[11].

Patient selection

Given its diagnostic, prognostic and predictive value, mutational analysis of KIT should be included in the diagnostic work-up of all GISTs as standard practice for optimal management[13].


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Last update: 05 Jul 2018

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