Mutations In KIT Exons Research Articles

Prognostic relevance of genetic aberrations in gastrointestinal stromal tumors.

49 Background: Gastrointestinal stromal tumours (GISTs) contain oncogenic KIT or PDGFRA tyrosine kinase (TK) mutations leading to disturbance of downstream signaling pathways that contribute to GIST pathogenesis. Additional genetic aberrations were found in GISTs, demonstrating the involvement of other genes important in tumor progression. The aim of the study was to evaluate the prognostic relevance of different TK mutations in GISTs and to analyze the additional genetic aberrations in GISTs according to mutational status. Methods: 180 GIST patients were examined for KIT (9, 11, 13, 17 exons) and PDGFRA mutations (12, 14, 18 exons) by direct sequencing of DNA obtained from microdissected tumor sections. Tumor tissue DNA from 44 GISTs patients was screened for loss of heterozygosity (LOH) at 11 microsatellite loci on 1p, 9p, 14q, 15q and 22q arms. Results: KIT and PDGFRA mutations were identified in 76.1% and 10% of GISTs, respectively. 13.9% GISTs had no mutations (wild type). Most of KIT mutations were located in exon 11 (65%) and exon 9 (9.4%). Prognostic significance of TK mutations was evaluated. There was a trend of better survival for patients with PDGFRA mutation then with KIT mutation or wild type GISTs. The higher overall survival prior to target therapy was shown for patients with duplication or point mutation in KIT exon 11 in comparison to exon 11 deletion. Analysis of LOH revealed allelic deletions in 85% of GISTs, more frequently at 14q arm. There was a different LOH pattern in subgroups of GISTs. GISTs with PDGFRA mutation and with KIT exon 11 point mutation had LOH at 14q, while GISTs with KIT exon 11 deletions revealed high LOH frequency also on 22q, 15q and 1p arms. LOH in wild type GISTs occurred on all chromosomes with low frequency. LOH on 9p was found exclusively in metastatic and recurrent GISTs. Specific gene loci of frequent LOH were identified on 9p, 15q and 22q that may be contributed to GIST progression. Conclusions: Specific mutations are associated with GISTs prognosis. Tumors with point mutations and duplications in KIT exon 11 are associated with a better survival then GISTs with other KIT mutations. Specific pattern of allelic deletions was identified in subgroups of GISTs according to type of mutation and tumor progression. No significant financial relationships to disclose.

A quality control program for mutation detection in KIT and PDGFRA in gastrointestinal stromal tumours

Although most gastrointestinal stromal tumours (GIST) carry oncogenic mutations in KIT exons 9, 11, 13 and 17, or in platelet-derived growth factor receptor alpha (PDGFRA) exons 12, 14 and 18, around 10% of GIST are free of these mutations. Genotyping and accurate detection of KIT/PDGFRA mutations in GIST are becoming increasingly useful for clinicians in the management of the disease. To evaluate and improve laboratory practice in GIST mutation detection, we developed a mutational screening quality control program. Eleven laboratories were enrolled in this program and 50 DNA samples were analysed, each of them by four different laboratories, giving 200 mutational reports. In total, eight mutations were not detected by at least one laboratory. One false positive result was reported in one sample. Thus, the mean global rate of error with clinical implication based on 200 reports was 4.5%. Concerning specific polymorphisms detection, the rate varied from 0 to 100%, depending on the laboratory. The way mutations were reported was very heterogeneous, and some errors were detected. This study demonstrated that such a program was necessary for laboratories to improve the quality of the analysis, because an error rate of 4.5% may have clinical consequences for the patient.

Association of Merkel cell polyomavirus infection with tumor p53, KIT, stem cell factor, PDGFR‐alpha and survival in Merkel cell carcinoma

Most Merkel cell carcinomas (MCCs) contain Merkel cell polyomavirus (MCPyV) DNA, and the virus likely has a pivotal role in tumor pathogenesis. p53 and the KIT receptor tyrosine kinase have also been implicated in MCC pathogenesis, but little is known about their association with MCPyV infection. We identified 207 patients diagnosed with MCC in Finland in 1979-2004 and reviewed the histological diagnoses. Adequate clinical information, tumor tissue and DNA were available from 87 confirmed MCC cases. Presence of MCPyV DNA was assessed using quantitative PCR; p53, KIT, phospho-KIT, stem cell factor (SCF) and PDGFRα expression using immunohistochemistry and presence of mutations in KIT exons 9, 11, 13 and 17 and PDGFRA exons 10, 12, 14 and 18 using DNA sequencing. Most (77.0%) of the 87 tumors contained MCPyV DNA and 37 (42.5%) expressed KIT, whereas PDGFRα, p53, SCF and pKIT expression was less common (31.9, 22.8, 8.6 and 4.8%, respectively). No KIT or PFGFRA mutations were detected, but 10 (12.5%) of the 80 tumors studied harbored common PDGFRA exon 10 S478P substitution. Tumor p53 and KIT expression were associated with absence of MCPyV DNA (p = 0.01 and 0.009, respectively). Tumor p53 expression was associated with unfavorable MCC-specific survival (p = 0.021) and overall survival (p = 0.046), but tumor KIT expression only when stratified by presence of MCPyV DNA. The results suggest that p53 and KIT expression are associated with absence of MCPyV DNA in MCC, and that the molecular pathogenesis of MCC is multifactorial.

Expression profiling of GIST: CD133 is associated with KIT exon 11 mutations, gastric location and poor prognosis

In gastrointestinal stromal tumors (GISTs), KIT exon 11 deletions are associated with poor prognosis. The aim of this study was to determine the gene expression profiles of GISTs carrying KIT exon 11 deletions and to identify genes associated with poor prognosis. Expression profiling was performed on nine tumors with KIT exon 11 deletions and 7 without KIT exon 11 mutations using oligonucleotide microarrays. In addition, gene expression profiles for 35 GISTs were analyzed by meta-analysis. Expression of CD133 (prominin-1) protein was examined by tissue microarray (TMA) analysis of 204 GISTs from a population-based study in western Sweden. Survival analysis was performed on patients subjected to R0 resection (n=180) using the Cox proportional hazards model. Gene expression profiling, meta-analysis, and qPCR showed up regulation of CD133 in GISTs carrying KIT exon 11 deletions. Immunohistochemical analysis on TMA confirmed CD133 expression in 28% of all tumors. CD133 positivity was more frequent in gastric GISTs (48%) than in small intestinal GISTs (4%). CD133 positivity was also more frequent in GISTs with KIT exon 11 mutations (41%) than in tumors with mutations in KIT exon 9, platelet-derived growth factor receptor α (PDGFRA), or wild-type tumors (0-17%). Univariate survival analysis showed a significant correlation between the presence of CD133 protein and shorter overall survival (hazard ratio=2.23, p=0.027). Multivariate analysis showed that CD133 provided additional information on patient survival compared to age, sex, National Institutes of Health (NIH) risk group and mutational status. CD133 is expressed in a subset of predominantly gastric GISTs with KIT exon 11 mutations and poor prognosis.

QPCR in gastrointestinal stromal tumors: Evaluation of reference genes and expression analysis of KIT and the alternative receptor tyrosine kinases FLT3, CSF1-R, PDGFRB, MET and AXL

BackgroundGastrointestinal stromal tumors (GIST) represent the most common mesenchymal tumors of the gastrointestinal tract. About 85% carry an activating mutation in the KIT or PDGFRA gene. Approximately 10% of GIST are so-called wild type GIST (wt-GIST) without mutations in the hot spots. In the present study we evaluated appropriate reference genes for the expression analysis of formalin-fixed, paraffin-embedded and fresh frozen samples from gastrointestinal stromal tumors. We evaluated the gene expression of KIT as well as of the alternative receptor tyrosine kinase genes FLT3, CSF1-R, PDGFRB, AXL and MET by qPCR. wt-GIST were compared to samples with mutations in KIT exon 9 and 11 and PDGFRA exon 18 in order to evaluate whether overexpression of these alternative RTK might contribute to the pathogenesis of wt-GIST.ResultsGene expression variability of the pooled cDNA samples is much lower than the single reverse transcription cDNA synthesis. By combining the lowest variability values of fixed and fresh tissue, the genes POLR2A, PPIA, RPLPO and TFRC were chosen for further analysis of the GIST samples. Overexpression of KIT compared to the corresponding normal tissue was detected in each GIST subgroup except in GIST with PDGFRA exon 18 mutation. Comparing our sample groups, no significant differences in the gene expression levels of FLT3, CSF1R and AXL were determined. An exception was the sample group with KIT exon 9 mutation. A significantly reduced expression of CSF1R, FLT3 and PDGFRB compared to the normal tissue was detected. GIST with mutations in KIT exon 9 and 11 and in PDGFRA exon 18 showed a significant PDGFRB downregulation.ConclusionsAs the variability of expression levels for the reference genes is very high comparing fresh frozen and formalin-fixed tissue there is a strong need for validation in each tissue type. None of the alternative receptor tyrosine kinases analyzed is associated with the pathogenesis of wild-type or mutated GIST. It remains to be clarified whether an autocrine or paracrine mechanism by overexpression of receptor tyrosine kinase ligands is responsible for the tumorigenesis of wt-GIST.

KIT and PDGFRA mutations and PDGFRA immunostaining in gastrointestinal stromal tumors

In the present study, we investigated the association of PDGFRA and KIT mutations as well as PDGFRA immunohistochemical expression with clinicopathologic features and prognosis in a series of gastrointestinal stromal tumors (GISTs). Tumor DNA from 40 GISTs was sequenced for the presence of mutations in KIT exons 9, 11, 13 and 17, and in PDGFRA exons 12 and 18. Tissue sections were stained with polyclonal anti-PDGFRA antibody. KIT mutations occurred in 26 cases. There were 13 deletions, 6 substitutions, 3 deletion-substitutions, 3 duplications and 1 insertion. Tumors with KIT deletions/insertion were large with a high mitotic index (MI), and were associated with a high rate of symptoms at diagnosis, invasion into adjacent organs, distant metastasis, relapse and a short disease-free survival (DFS). PDGFRA mutations occurred in 6 gastric GISTs. There were 4 deletions and 2 substitutions. Tumors with PDGFRA mutations were small, with a low MI and Ki67 score, and were associated with a very low rate of symptoms at diagnosis, invasion into adjacent organs and distant metastasis. PDGFRA immunopositivity was found in 23 cases: a peculiar 'dotlike' staining was found in 5 out of 6 PDGFRA mutated cases. Patients with positive PDGFRA immunostaining had a longer DFS than those with negative staining. Our data confirm that the type of KIT mutation is associated with various clinicopathologic features of GISTs, and indicate that PDGFRA mutations are associated with rather indolent tumors. PDGFRA immunopositivity reflects PDGFRA mutational status and is associated with a favorable outcome.

Phase II trial of nilotinib as third-line therapy for gastrointestinal stromal tumor (GIST) patients in Japan.

10015 Background: Patients with GIST resistant to both imatinib (IM) and sunitinib (SU) have a poor prognosis and few therapeutic options. The objective of this study is to investigate efficacy and safety of nilotinib as a third line therapy for Japanese GIST pts who have shown resistance and/or intolerance to imatinib and sunitinib. Methods: A single arm, open-label trial was conducted in 8 hospitals in Japan. The key eligibility criteria included histologically confirmed KIT-positive GIST and progression on or intolerance to both imatinib and sunitinib treatment. Pts were treated with nilotinib 400 mg b.i.d. The primary endpoint was disease control rate defined as rates of CR + PR + SD (lasting at least 24 weeks) assessed by central reviewers based on RECIST criteria. Registered with Clinical Trials.gov, number NCT00718562 and sponsored by Novartis Pharmaceuticals. Results: Among the 35 pts enrolled between Sep 2008 and Apr 2009, 26 (74.3%) were resistant to both IM and SU, 6 (17.1%) IM-resistant and SU-intolerant, 2 (5.7%) IM- intolerant and SU-resistant, and the remaining 1 (2.9%) intolerant to both. The median prior maximum doses were 400 mg (≥600 mg for 16/35 pts) for IM and 50 mg (50 mg for 34/35 pts) for SU. The median age was 57 years (range 26 - 76) and 22 (62.9%) pts were male. The most common primary sites of GIST were the small intestine (21 [60.0%] pts) and stomach (11 [31.4%] pts). The median exposure to nilotinib was 120 days (range 5-316) at the time of data cut-off (02Oct2009). Disease control rate at 24 weeks was 28.6% (90% CI ; [16.4%, 43.6%]). The median PFS was 113 days. The median OS was 310 days. The objective response rate was obtained for 2.9% with 1 PR pt who carried GIST with KIT mutations in exon 11 (dup 567 - 576) and exon 17 (D820G) after resistance to both imatinib and sunitinib, and 23 pts (65.7%) had SD as the best response. Nilotinib was well tolerated; the most common treatment-related AEs of any grade were nausea, vomiting, hyperbilirubinemia and appetite loss (28.6% each). No patients developed grade 3-4 hematological toxicities except for anemia (5.7%). Conclusions: These results suggest that nilotinib is effective in Japanese GIST pts who failed both imatinib and sunitinib and well tolerated. Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Chugai Pharmaceutical, Novartis, Pfizer, sanofi-aventis Tsumura Co. Daiichi Sankyo, Kyowa Hakko Kirin, Novartis, Taiho Pharmaceutical, Wyeth, Yakult Honsha

Clinical responses observed with imatinib or sorafenib in melanoma patients expressing mutations in KIT

Background:Mutations in KIT are more frequent in specific melanoma subtypes, and response to KIT inhibition is likely to depend on the identified mutation.Methods:A total of 32 patients with metastatic acral or mucosal melanoma were screened for mutations in KIT exons 11, 13 and 17.Results:KIT mutations were found in 38% of mucosal and in 6% of acral melanomas. Three patients were treated with imatinib and one with sorafenib. All four patients responded to treatment, but three have since progressed within the brain.Conclusion:The observed clinical responses support further investigation of KIT inhibitors in metastatic melanoma, selected according to KIT mutation status.

Melanoma Hyperpigmentation Is Strongly Associated With KIT Alterations

KIT alterations have been identified in melanoma and treatment with imatinib has met with some success. However, the relationship between KIT and melanoma histology remains uncharacterized, and its role in melanoma pathogenesis unknown. We evaluated 70 melanomas from 70 patients seen at a single institution from 1997 to 2008. Cases were analyzed for KIT protein expression relative to histologic variables: subtype, sun damage, tumor infiltrating lymphocytes, melanoma in situ, vertical growth phase (VGP), location, and hyperpigmentation. Twenty-eight cases demonstrated 3+ membranous staining. Univariate analysis revealed 5 significant variables: sun damage (inverse, P = 0.015), tumor location (trunk>extremities>head and neck, P = 0.005), subtype (epithelioid>spindle, mixed>desmoplastic, P < 0.001), VGP (inverse, P = 0.024), and hyperpigmentation [22/26 (85% hyperpigmented cases) and 6/44 (14% nonhyperpigmented cases), P < 0.001]. Upon multivariate analysis, only hyperpigmentation and VGP remained statistically significant (P = 0.002, P = 0.019). Mutational analyses for KIT exons 9 and 11, and BRAF were performed on cases with 3+ labeling. Two of 27 of cases contained mutations in KIT exon 11, whereas only 1 case contained a V600E BRAF mutation, suggesting that KIT and BRAF mutations may be redundant events. Although KIT mutations were uncommon overall, pigmentation in conjunction with immunohistochemistry and nodular growth phase raised their frequency to 2 (40%) of 5 cases. We expand the context of KIT aberrations to involve areas other than acral and mucosal sites and demonstrate an inverse relationship between KIT abnormalities and sun damage. There is a strong correlation to hyperpigmentation that overrides factors including sun damage, tumor location, and histologic subtype, which may be used to identify cases with KIT aberrations.

Low-grade Epithelial-Myoepithelial Carcinoma of Bartholin Gland: Report of 2 Cases of a Distinctive Neoplasm Arising in the Vulvovaginal Region

We report 2 cases of a distinctive neoplasm arising from Bartholin gland and presenting as a vulval or vaginal mass. The tumors occurred in patients aged 44 and 51 years and were 2 and 3 cm in maximum dimension. In both cases, normal Bartholin gland tissue was identified adjacent to the lesion. The neoplasms were unencapsulated and largely well circumscribed but with a focally infiltrative edge. They were composed of tubular, trabecular, or insular arrangements with a double layer of inner cuboidal cells with round nuclei and outer cells with ovoid nuclei and clear cytoplasm, corresponding to epithelial and myoepithelial cells, respectively. Luminal eosinophilic colloid-like material was present. In both cases, a minor proportion of the neoplasm consisted of cribriform arrangements, creating an appearance reminiscent of adenoid cystic carcinoma, although the overall morphology was not typical of that lesion. Mitotic figures were identified in both cases, the mitotic count being 1 and 5/10 high-power fields. Immunohistochemically, the inner cells were positive with epithelial markers, including broad-spectrum cytokeratins and epithelial membrane antigen, and the outer cell layer was positive with myoepithelial markers p63, calponin, and alpha-smooth muscle actin. Both neoplasms exhibited diffuse strong immunoreactivity of the epithelial cells with c-kit. Activating mutations in KIT exons 9, 11, 13, and 17 and in platelet-derived growth factor receptor alpha exons 12, 14, and 18 were searched for by polymerase chain reaction and direct sequencing but were not identified. We believe this represents a low-grade carcinoma arising from Bartholin gland composed of a dual population of epithelial and myoepithelial cells and closely resembling the salivary gland neoplasm termed epithelial-myoepithelial carcinoma. We propose the term low-grade epithelial-myoepithelial carcinoma of Bartholin gland.

Laparoscopic resection of sporadic synchronous gastric and jejunal gastrointestinal stromal tumors: Report of a case

Multicentricity of gastrointestinal stromal tumors (GISTs) has been described only in patients with neurofibromatosis type 1 (NF1) or within the small intestine, and different pathogenetic mechanisms are involved. We report a case of synchronous sporadic gastric and jejunal GISTs, which were resected laparoscopically in a 67-year-old man. Immunohistochemical analysis revealed that both lesions were KIT (CD117)-positive, but that the gastric lesion was CD34-positive, whereas the jejunal one was Vimentin-, S-100-, and SMA-positive. Molecular analysis of mutations in KIT exons 9, 11, 13, and 17, and in PDGFRA exons 12 and 18 revealed the presence of a gastric sporadic GIST with a KIT mutation of the exon 11 and a jejunal sporadic GIST without KIT or PDGFRA mutations. To our knowledge, this is the first report of laparoscopically resected synchronous sporadic gastric and jejunal GISTs.

Analysis of a case with disappearance of the primary gastrointestinal stromal tumor and progressive liver metastases under long-term treatment with tyrosine kinase inhibitors

The response of gastrointestinal stromal tumors (GISTs) to tyrosine kinase receptor inhibitors (TKR-I) has been a breakthrough for small molecular therapy. We report here on the very different long-term outcome of a synchronous metastatic GIST with complete remission of the primary tumor and progressive liver metastases under TKR-I therapy. In 2003, a 52-year-old patient was diagnosed with gastric GIST and synchronous multiple liver metastases. Therapy with imatinib, 400 mg daily, was started immediately. Fifteen months later, the primary was no longer detectable by endoscopy. In 2006, progression of the liver metastases was observed. Mutation analysis of the initial biopsy specimen from the primary, as well as the biopsy from the three main liver metastases after 3 years of imatinib treatment, revealed the common KIT exon 11 deletion (W557_K558del) in all tumor samples. Two of the metastases had a separate secondary mutation in KIT exon 14 and 17, respectively, while the largest cystic metastatic lesion had no other mutation. Imatinib was then increased to a daily dose of 800 mg, and in April 2007 the treatment was changed to sunitinib. Fifty-two months after initial diagnosis, the patient died of liver failure. At no time point, relapse of the gastric primary tumor was observed. Whilst TKR-Is are commonly very effective in treating GISTs, the present case illustrates their varying effects regarding the clinical behavior and genetic variations within different tumors of the same patient after long-term treatment.

KIT/PDGFRA Expression and Mutation in Testicular Seminoma and Ovarian Dysgerminoma

Background : KIT and PDGFRA are tyrosine kinase receptors. Stem cell factor/KIT-mediated signaling plays a role in normal spermatogenesis, and the alteration of KIT is important in the pathogenesis of seminomas/dysgerminomas (SD). Methods : To determine the role of expression and mutation of the KIT and PDGFRA genes, we analyzed 16 seminoma cases, 4 spermatocytic seminoma (SS) cases and 8 dysgerminoma cases for KIT and PDGFRA expression and mutation of KIT (exons 9, 11, 13, and 17) and PDGFRA (exons 12 and 18) using PCR-SSCP methods. Results : KIT was immunohistochemically positive in all 24 SD cases, and one of four (25%) SS cases. PDGFRA was immunohistochemically evident in 16 of the 24 (66.6%) SD cases, and two of the four (50%) SS cases. KIT expression was significantly reduced in SS compared with seminoma (p=0.0035). Four cases (14.3%) displayed mutation in KIT exon 17 or PDGFRA exon 12. Distant metastasis was present in three cases (10.7%), one of which had a nonsense mutation in KIT. Conclusions : These results indicate that KIT is expressed in the majority of SD cases, but not in most SS cases. However, there was no significant correlation between the clinicopathologic features and mutation or expression of KIT and PDGFRA.

KIT gene mutations and copy number in melanoma subtypes.

We recently identified a KIT exon 11 mutation in an anorectal melanoma of a patient who had an excellent response to treatment with imatinib. To determine the frequency of KIT mutations across melanoma subtypes, we surveyed a large series of tumors. One hundred eighty-nine melanomas were screened for mutations in KIT exons 11, 13, and 17. KIT copy number was assessed by quantitative PCR. A subset of cases was evaluated for BRAF and NRAS mutations. Immunohistochemistry was done to assess KIT (CD117) expression. KIT mutations were detected in 23% (3 of 13) of acral melanomas, 15.6% (7 of 45) of mucosal melanomas, 7.7% (1 of 13) of conjunctival melanomas, 1.7% (1 of 58) of cutaneous melanomas, and 0% (0 of 60) of choroidal melanomas. Almost all the KIT mutations were of the type predicted to be imatinib sensitive. There was no overlap with NRAS mutations (11.1% of acral and 24.3% of mucosal tumors) or with BRAF mutations (absent in mucosal tumors). Increased KIT copy number was detected in 27.3% (3 of 11) of acral and 26.3% (10 of 38) of mucosal melanomas, but was less common among cutaneous (6.7%; 3 of 45), conjunctival (7.1%; 1 of 14), and choroidal melanomas (0 of 28). CD117 expression, present in 39% of 105 tumors representing all melanoma types, did not correlate with either KIT mutation status or KIT copy number. Our findings confirm that KIT mutations are most common in acral and mucosal melanomas but do not necessarily correlate with KIT copy number or CD117 expression. Screening for KIT mutations may open up new treatment options for melanoma patients.

Multiple Sporadic Gastrointestinal Stromal Tumors (GISTs) of the Proximal Stomach are Caused by Different Somatic KIT Mutations Suggesting a Field Effect

Multifocal gastrointestinal stromal tumors (GISTs) are observed in patients with germline KIT or PDGFRA mutations, and in those with neurofibromatosis 1. However, the pathogenesis of apparently sporadic multifocal gastric GISTs in adults is poorly understood. We analyzed 27 GISTs from 11 patients (mean age, 75 y) with 2 to 4 tumors each. All tumors represented incidental findings in surgical (n=8) and autopsy (n=3) specimens and were located in the gastric body or fundus within < or =4 cm distance from each other. The 8 surgical cases represented 10% of GISTs involving the proximal stomach in our case material. Tumor size ranged from 1.5 mm to 45 mm (mean, 9 mm). Histology revealed a uniform spindle cell morphology with a variable sclerosis/calcification and a low mitotic activity (<5 mitoses/50 high-power fields). All tumors were KIT+/CD34+. Nineteen of 22 tumors (79%) revealed mutations in KIT exon 11 (13 deletions and 6 point mutations). Individual lesions from the same patient displayed different mutations in all, but 1 case, thus ruling out germline mutations and neurofibromatosis 1. Our findings indicate that multifocal gastric GISTs in elderly patients are unrelated to hereditary GIST syndromes. Clustering of these lesions in the proximal stomach, their close proximity, and the demonstration of different KIT mutations in individual lesions from the same patient point to the existence of distinct subsets of interstitial cells of Cajal with a higher propensity for different somatic KIT exon 11 mutations, possibly as a result of a field effect involving premutational epigenetic alterations or yet unidentified etiologic factors.

Heterogeneity of kinase inhibitor resistance mechanisms in GIST

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 wild-type 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.

Novel approaches to imatinib-and sunitinib-resistant GIST

Gastrointestinal stromal tumors (GISTs) generally arise from primary activating mutations in the KIT or PDGFRA genes that result in constitutive activation of receptor tyrosine kinase activity. Imatinib provides targeted therapy for GIST by inhibiting the KIT and PDGFR-alpha tyrosine kinases. Clinical benefit is achieved in approximately 85% of patients with unresectable or metastatic disease, with a median progression-free survival of 20 to 24 months. The mechanisms of acquired resistance to imatinib are heterogeneous, with most involving the emergence of secondary mutations in KIT exons 13, 14, or 17. In patients failing or intolerant to imatinib, the multitargeted agent sunitinib achieves durable disease control in approximately 50% of cases. Experimental treatment options beyond those currently available consist of other KIT-targeting tyrosine kinase inhibitors, such as nilotinib, or agents targeting alternative pathways, such as antiangiogenic agents, mammalian target of rapamycin, RAF kinase, and chaperone inhibitors.

Genomic alterations of KIT in acral and mucosal melanomas

9016 Background: KIT gene mutations have recently been reported in mucosal and acral melanomas. While the KIT inhibitor imatinib is ineffective in the treatment of cutaneous melanoma, we observed a dramatic clinical response in a patient with a rectal melanoma harboring a KIT mutation. We therefore surveyed a series of melanoma subtypes for genomic alterations in KIT, BRAF and NRAS to determine what fraction of tumors might be amenable to kinase inhibitor therapy. Design: DNA from archival melanomas was amplified by PCR and the products were screened by denaturing HPLC for mutations in KIT exons 11, 13, 17; BRAF exon 15; and NRAS exons 1 & 2. Mutations were confirmed by direct sequencing. Immunohistochemistry for CD117 was performed on a subset of cases. KIT copy number was assessed by quantitative PCR assay in some cases. Results: KIT mutations included substitutions in exons 11 (W557R, K558N, V559A/D, L576P) or 17 (Y823D), and size-altering mutations in exon 11 (del 554–559; ins PYDHKWE at E583). Notably, all of these mutations occur in GI stromal tumors and nearly all (except Y823D) are sensitive to imatinib. Among mucosal melanomas, KIT mutations were more common in anorectal/vaginal melanomas (4/8; 50%) than in tumors of the head & neck (3/36; 8.3%). KIT mutations were rare in conjunctival and cutaneous tumors, and absent in choroidal tumors. There was no correlation between CD117 staining and KIT mutation status. There was a trend for KIT-mutant melanomas to have increased copy number (4/8; 50%) compared with KIT wild-type tumors (8/39; 20.5%). Conclusion: Our findings confirm that KIT mutations of the type known to be sensitive to imatinib occur in mucosal and acral melanomas. In addition, a substantial minority of these tumors have increased KIT copy number. NRAS mutations are also common in these tumors and would be predicted to be unresponsive to KIT inhibitor therapy. BRAF mutations are found in acral but not in mucosal melanomas. Genotyping can play an important role in the clinical management of these rare melanomas. Genomic Abnormalities in Melanoma Subtypes KIT mutations BRAF mutations NRAS mutations KIT copy number increase Acral 23% (3/13) 16.7% (2/12) 11.1% (1/9) 27.3% (3/11) Mucosal 15.2% (7/46) 0% (0/47) 26.3% (10/38) 25.0% (10/40) Cutaneous 1.8% (1/57) 30.3% (20/66) 10% (6/60) 9.1% (2/22) Conjunctival 7.7% (1/13) 26.7% (4/15) 0% (0/11) Not done Choroidal 0% (0/60) 0% (0/60) 0% (0/60) 0% (0/5) Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Expert Testimony Other Remuneration Novartis, Pfizer MolecularMD Novartis, Pfizer Novartis, Pfizer

KIT, PDGFRα and EGFR analysis in nephroblastoma

Nephroblastoma prognosis has dramatically improved, but an unfavourable prognostic subgroup warrants development of novel therapeutic strategies. Selective KIT, PDGFRalpha and epidermal growth factor receptor (EGFR) tyrosine kinase inhibition evolved as powerful targeted therapy for gastrointestinal stromal tumours and non-small-cell lung cancer. To investigate a potential role for tyrosine kinase inhibition, we analyzed 209 nephroblastomas for immunohistochemical KIT and EGFR expression, 63 nephroblastomas for mutations in KIT exons 9, 11, 13, EGFR exons 18, 19, 20 and 21, and all 209 nephroblastomas for PDGFRalpha exons 12, 14 and 18. Twenty-two tumours (10.5%) expressed KIT, 31 (14.8%) EGFR, and 10 (4.8%) both KIT and EGFR, respectively. KIT expression was relatively more common among high-risk tumours (6/27; 22.3%) compared to low-/intermediate-risk tumours (26/181; 14.4%). Nine patients deceased, four of which had high-risk tumours with KIT expression in two of four and EGFR expression in one of four. There were no KIT, PDGFRalpha or EGFR mutations. Our results suggest no significant contribution of KIT, EGFR or PDGFRalpha mutations to nephroblastoma pathogenesis. Despite a trend towards association of immunohistochemical KIT and EGFR expression with poor outcome in high-risk nephroblastomas, statistical analysis did not yield significant correlations in this subgroup. Therefore, it remains open if KIT, PDGFRalpha or EGFR tyrosine kinase inhibition constitute a therapeutic target in nephroblastoma in the absence of KIT, PDGFRalpha or EGFR mutations.

KIT and PDGFRα mutations in 104 patients with gastrointestinal stromal tumors (GISTs): a population-based study

BackgroundThe prognostic significance of KIT or platelet-derived growth factor receptor α (PDGFRα) mutations in gastrointestinal stromal tumors (GISTs) is still controversial. Patients and methodsIn all, 104 patients were diagnosed with GISTs by KIT immunoreactivity; tumor DNA was sequenced for the presence of mutations in KIT exons 9, 11, 13 and 17 and in PDGFRα exons 12 and 18. Disease-free survival (DFS) was analyzed in 85 radically resected patients. ResultsKIT mutations occurred in exon 11 (69), in exon 9 (11) and in exon 17 (1). PDGFRα mutations were detected in exon 18 (10) and in exon 12 (3). Ten GISTs were wild type. Exon 11 mutations were as follows: deletions in 42 cases and point mutations in 20 cases and insertions and duplications, respectively, in 2 and 5 cases. A better trend in DFS was evident for duplicated and point-mutated exon 11 KIT GISTs. There was a significant association between PDGFRα mutations, gastric location and lower mitotic index. Moreover, PDGFRα-mutated GISTs seemed to have a better outcome. ConclusionsPoint mutations and duplications in KIT exon 11 are associated with a better clinical trend in DFS. PDGFRα-mutated GISTs are preferentially localized in the stomach and seem to have a favorable clinical behavior.