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Dr. Michael Heinrich

This is part one of a two-part series on “KIT and PDGFRA kinase mutations in GIST: from A to Z”. In this newsletter, Dr. Heinrich will provide a background on the role of kinase mutations in GIST, focusing largely on the biological and clinical implications of these mutations. In part two (which will be featured in the July 2007 edition of the newsletter, following the special “Five-year anniversary” edition), Dr. Christopher Corless will provide a practical, clinically-based commentary on these mutations. In particular, Dr. Corless’ article will focus on practical aspects of mutation testing as it applies to routine clinical decisions.

In 1988, Dr. Seiichi Hirota and his scientific team in Japan discovered that GISTs express the KIT protein (aka c-Kit or CD117). In addition, they found that in most GISTs the KIT protein has been mutated so that it provides an inappropriately high level of growth stimulation to the tumor cells. These observations revolutionized the field of GIST in two ways: 1) they provided pathologists a new test (immunohistochemical staining for KIT protein) that allowed the distinction of GISTs from other tumors of the GI tract;1 and 2) they explained what made GIST cells grow. The finding that most GISTs have a mutant, activated KIT enzyme (kinase) immediately raised the possibility that drug treatments that could inhibit KIT enzyme activity would be an effective treatment for malignant GISTs. In the nine years since Dr. Hirota’s initial report, there have been huge advances in GIST diagnosis and treatment. Notably, two different kinase inhibitors (imatinib and sunitinib) have now been FDA-approved for treatment of GIST and numerous other inhibitors are being tested for treatment of imatinib- and/or sunitinib-resistant tumors.

Figure 1: KIT and PDGFRA MutationsOne of the advances was the 2003 discovery that a subset of GISTs have mutations in a sister kinase called PDGFRA.2 This observation, the result of a collaboration between Drs. Jonathan Fletcher and George Demetri in Boston and our labs at OHSU, helped to explain the origin of at least some of the GISTs that lack KIT mutations. Several lines of evidence support the hypothesis that activating mutations of KIT or PDGFRA are the initiating event in most adult GISTs: 1) KIT mutations are common in small, incidentally discovered GISTs; 2) KIT mutation status does not correlate pathologic grade; 3) inherited KIT or PDGFRA mutations are associated with familial GIST syndromes (in humans); 4) expression of mutant KIT in mice results in GISTs; 5) KIT mutations precede other genetic abnormalities that contribute to GIST growth and malignancy. Overall, KIT or PDGFRA mutations are found in 80 to 85 percent and five percent of GISTs, respectively. These mutations are mutually exclusive (i.e., there are no reported cases of both KIT and PDGFRA mutations in the same tumor). What accounts for the growth of GISTs lacking kinase mutations (so-called “wildtype” GISTs), remains unknown but is the subject of intense investigation. From the standpoint of standard pathology tools such as immunohistochemistry and light microscopy, these tumors are indistinguishable from GISTs with kinase mutations.

The KIT and PDGFRA genes are contained in a large section of DNA on chromosome 4. Like most genes in our DNA, the KIT and PDGFRA genes are comprised of approximately twenty exons (if a gene is a book, an exon is a chapter). Each exon consists of a string of words (codons), and each word is represented by three DNA letters (bases A, T, G or C). The precise sequence of the letters/bases in the exons represents the blueprint for production of normal KIT or PDGFRA protein, assembled from building blocks called amino acids.

Mutations of KIT or PDGFRA found in GISTs are localized to certain exons (exons 8, 9, 11, 13 or 17 in KIT; 12, 14, or 18 in PDGFRA). In addition, within a given exon, only certain mutations can result in abnormal kinase enzyme activation. These mutations can be as simple as substitution of one DNA letter/base with another, or more complicated alterations involving deletion or insertion of a whole string of DNA bases. Figure 1 depicts the reported frequency and location of KIT and PDGFRA mutations in GIST, based on work in the Heinrich-Corless laboratory.

In addition to the presumed role of kinase mutations in giving rise to GISTs, there is also strong evidence of a correlation between tumor biology and the presence and/or type of kinase mutation. For example, 98 percent of GISTs with KIT exon 9 mutations arise from the small bowel or colon, whereas most GISTs with PDGFRA mutations arise from the stomach. In contrast, GISTs with KIT exon 11 mutations can arise from any portion of the GI tract. Additionally, the type of mutation correlates with global changes in the pattern of genes expressed in GISTs, as assessed by sophisticated “gene chip” technology in the laboratories of Dr. Antonescu and Dr. van de Rijn. Finally, the underlying malignant potential of GISTs may be influenced not only by the presence or absence of a mutation, but potentially by the class of mutation (e.g. exon involved, deletion vs. single base substitution).

The above commentary refers to GISTs arising in adult patients. In contrast, GISTs arising in children, adolescents, or young adults have a much lower frequency of mutations in KIT or PDGFRA (less than 10% of cases).3 As detailed in the literature and other LRG newsletters, GISTs arising in younger patients have other distinctive features when compared to GISTs arising in adult patients. Based on the above considerations, a molecular classification of GISTs has been developed (See Table 1).

Table 1. Molecular Classification of GISTsOne of the notable features of the clinical studies of imatinib for treatment of GIST is the consistent observation that genotypically-defined subsets of GIST have different outcomes during treatment with this drug. Listed in Table 2 are the correlations between tumor genotype and tumor response (complete and partial responses) in four trials (phases 1- 3). Based on 509 genotyped GISTs, the response rate for KIT exon 11 mutant, KIT exon 9 mutant, and wildtype GISTs is 74 percent, 38 percent, and 22 percent, respectively. Likewise, the probability of primary resistance to imatinib for KIT exon 11, KIT exon 9, and wildtype GISTs is 4 percent, 16 percent and 25 percent, respectively. An even more striking observation is that kinase genotype correlates with progression-free and overall survival, with superior survival seen for patients whose GIST harbors a KIT exon 11 mutation. For example, the median time to tumor progression for patients whose GIST has an associated KIT exon 11 mutation is more than one year longer than patients whose tumors have KIT exon 9 or wildtype kinase genotypes. A similar overall survival benefit is seen for patients with KIT exon 11 mutations versus the other common genotypic subsets.4-6

The above results reflect pooled data from clinical studies in which imatinib doses ranged from 400-800 mg per day. In a recent subset analysis of the EORTC/AustralAsia phase III trial, Dr. Debiec-Rychter and colleagues found that the progression-free survival of GIST patients with KIT exon 9 mutations was significantly better when they were treated with 800 mg per day as compared with 400 mg.6 In contrast, patients whose GIST had KIT exon 11 mutations had a similar progression-free survival on either dose. Many GIST experts now recommend routine tumor genotyping and dose selection based on the presence or absence of a KIT exon 9 mutation. Similar correlative analyses are underway using genotyping data and outcomes from the North American phase III study. A meta-analysis (statistical aggregation) of data from both trials will be completed in late 2007.

A minority of patients experience continued tumor growth on imatinib within the first six months of treatment, which is referred to as primary resistance. Compared with patients who have KIT exon 11-mutant tumors, those with exon 9-mutant or wildtype tumors are overrepresented in this group. Amongst patients who benefit from treatment beyond six months, a significant fraction will show growth in one or more tumors between 12 and 36 months of treatment. This is called secondary resistance.Table 2: Relationship between Kinase Genotype Response and Outcome Recent studies from a number of laboratories have established that in most such tumors there are new, acquired mutations in KIT or PDGFRA that directly interfere with the ability of imatinib to block the kinase.7-10 This phenomenon is similar to bacteria becoming resistant to an antibiotic, and it tells us that we need to be smarter in the design of new drugs and that we must consider combinations of drugs in the future.

Sunitinib is FDA-approved for the treatment of GIST patients who are intolerant of, or resistant to, imatinib. Based on an extended phase II trial, it appears that the best responses to this drug are in patients with KIT exon 9- mutant or wildtype tumors.11 There is a lesser benefit to patients whose tumors have acquired imatinib-resistance mutations associated with secondary kinase mutations, as many of these mutations (particularly those in exon 17) confer cross-resistance to sunitinib. Predictably, patients who initially respond well to sunitinib may develop secondary resistance, and preliminary studies in our laboratories indicate that sunitinib-specific resistance mutations occur in this setting.

Based on the fundamental importance of kinase mutations to GIST pathogenesis, biology, and response to kinase inhibitors, it is expected that basic science and translational research efforts will continue to devote substantial resources to understanding how such mutations may be further exploited as therapeutic targets. As noted above, characterization of these mutations is increasingly important for routine clinical diagnosis and management.


  1. Hirota S, Isozaki K, Moriyama Y, Hashimoto K, Nishida T, Ishiguro S, Kawano K, Hanada M, Kurata A, Takeda M, Muhammad Tunio G, Matsuzawa Y, Kanakura Y, Shinomura Y, Kitamura Y: Gain-offunction mutations of c-kit in human gastrointestinal stromal tumors. Science 279:577- 580, 1998
  1. Heinrich MC, Corless CL, Duensing A, McGreevey L, Chen CJ, Joseph N, Singer S, Griffith DJ, Haley A, Town A, Demetri GD, Fletcher CD, Fletcher JA: PDGFRA Activating Mutations in Gastrointestinal Stromal Tumors. Science 299:708-710, 2003
  1. Prakash S, Sarran L, Socci N, DeMatteo RP, Eisenstat J, Greco AM, Maki RG, Wexler LH, LaQuaglia MP, Besmer P, Antonescu CR: Gastrointestinal stromal tumors in children and young adults: a clinicopathologic, molecular, and genomic
  1. Heinrich MC, Corless CL, Demetri GD, Blanke CD, von Mehren M, Joensuu H, McGreevey LS, Chen CJ, Van den Abbeele AD, Druker BJ, Kiese B, Eisenberg B, Roberts PJ, Singer S, Fletcher CD, Silberman S, Dimitrijevic S, Fletcher JA: Kinase mutations and imatinib response in patients with metastatic gastrointestinal stromal tumor. J Clin Oncol 21:4342-4349, 2003
  1. Debiec-Rychter M, Dumez H, Judson I, Wasag B, Verweij J, Brown M, Dimitrijevic S, Sciot R, Stul M, Vranck H, Scurr M, Hagemeijer A, van Glabbeke M, Van Oosterom AT: Use of c-KIT/PDGFRA mutational analysis to predict the clinical response to imatinib in patients with advanced gastrointestinal stromal tumours entered on phase I and II studies of the EORTC Soft Tissue and Bone Sarcoma Group. Eur.J Cancer 40:689-695, 2004
  1. Debiec-Rychter M, Sciot R, Le CA, Schlemmer M, Hohenberger P, Van Oosterom AT, Blay JY, Leyvraz S, Stul M, Casali PG, Zalcberg J, Verweij J, van GM, Hagemeijer A, Judson I: KIT mutations and dose selection for imatinib in patients with advanced gastrointestinal stromal tumours. Eur.J.Cancer 42:1093-1103, 2006
  1. Heinrich MC, Corless CL, Blanke CD, Demetri GD, Joensuu H, Roberts PJ, Eisenberg BL, von Mehren M, Fletcher CD, Sandau K, McDougall K, Ou WB, Chen CJ, Fletcher JA: Molecular correlates of imatinib resistance in gastrointestinal stromal tumors. J.Clin Oncol 24:4764-4774, 2006
  1. Wardelmann E, Merkelbach-Bruse S, Pauls K, Thomas N, Schildhaus HU, Heinicke T, Speidel N, Pietsch T, Buettner R, Pink D, Reichardt P, Hohenberger P: Polyclonal evolution of multiple secondary KIT mutations in gastrointestinal stromal tumors under treatment with imatinib mesylate. Clin.Cancer Res. 12:1743-1749, 2006
  1. Antonescu CR, Besmer P, Guo T, Arkun K, Hom G, Koryotowski B, Leversha MA, Jeffrey PD, Desantis D, Singer S, Brennan MF, Maki RG, DeMatteo RP: Acquired resistance to imatinib in gastrointestinal stromal tumor occurs through secondary gene mutation. Clin.Cancer Res. 11:4182-4190, 2005
  1. Debiec-Rychter M, van OA, Marynen P: Mechanisms of resistance to imatinib mesylate in gastrointestinal stromal tumors and activity of the PKC412 inhibitor against imatinib-resistant mutants. Gastroenterology 128:270-279, 2005
  1. Heinrich M, Maki G, Corless C et al: Sunitinib (SU) response in imatinib-resistant (IM-R) GIST correlates with KIT and PDGFRA mutation status. 2006 ASCO Annual Meeting Proceedings24:520S, 2006 (abstr)

Due to space limitations, we could not cite all relevant publications related to this topic.