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JMD 2004, Vol. 6, No. 3
Copyright © 2004 American Society for Investigative Pathology & Association for Molecular Pathology

Association of Platelet-Derived Growth Factor Receptor Mutations with Gastric Primary Site and Epithelioid or Mixed Cell Morphology in Gastrointestinal Stromal Tumors

Eva Wardelmann^*, Aksana Hrychyk, Sabine Merkelbach-Bruse^*, Katharina Pauls^*, Jennifer Goldstein^*, Peter Hohenberger, Inge Losen^*, Christoph Manegold, Reinhard Büttner^* and Torsten Pietsch

From the Departments of Pathology * and Neuropathology, University of Bonn Medical Center, Bonn, Germany; the Division of Surgery and Surgical Oncology, Robert Roessle Hospital and Tumor Institute at the Max Delbrueck Center for Molecular Medicine, Charite, Campus Berlin-Buch, Humboldt University at Berlin, Berlin, Germany; and Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany

	Abstract

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Most gastrointestinal stromal tumors (GISTs) carry activating mutations of the KIT gene encoding the receptor tyrosine kinase KIT. In a previous study we were able to show an association between the lack of KIT mutations (wild-type GISTs) and the presence of a significant epithelioid tumor component. A very recent study described the occurrence of PDGFR mutations in KIT wt GISTS. Therefore, we studied a panel of 87 GISTs for mutations in the hot spot regions of the PDGFR gene with single strand conformation polymorphism analysis and sequencing and correlated the PDGFR status with pathomorphological data. We detected 20 cases with exon 18 mutations but none with exon 12 mutations. The mutations were located in the second kinase domain of PDGFR with 16 point mutations, and four larger deletions of 9 to 12 bp. All cases with mutations in the PDGFR gene revealed wild-type KIT in common regions of mutation, ie, exons 9 and 11. Most interestingly, the occurrence of PDGFR mutations was significantly associated with a higher frequency of epithelioid or mixed morphology (18 of 20 cases, P < 0.0001) and gastric location (all cases, P = 0.0008). Our data indicate that GISTs represent distinctive entities, differing in genetic, biological, and morphological features.

	Introduction

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Gastrointestinal stromal tumors (GISTs) are the most frequent mesenchymal tumors in the digestive tract.¹ They are characterized by the expression of the type III receptor tyrosine kinase KIT encoded by the KIT proto-oncogene.² The latter carries gain-of-function mutations in the majority of cases leading to a ligand-independent autoactivation of the KIT receptor.^{3, 4, 5, 6} However, a subset of GISTs is lacking any KIT mutations which is particularly critical as these tumors may be less sensitive to treatment with imatinib (Glivec), a tyrosine kinase inhibitor,⁷ than KIT mutation-positive tumors.

Very recently, activating mutations of the platelet-derived growth factor receptor (PDGFR) gene were described in a subset of KIT wild-type GISTs (wt GISTs).^{8, 9} PDGFR is a member of the subfamily of type III receptor tyrosine kinases, which includes KIT receptor, PDGF receptor ß, FLK-3, and CSF-1 receptor. All members are characterized by high sequence homologies especially in the juxtamembranous (JM) and the tyrosine kinase (TK) domains. KIT mutations in GISTs are preferentially found in exon 11 encoding the JM domain, less often in exon 9 (extracellular domain) and rarely in exon 13 and 17 (TK domains).^{3, 6, 10, 11} According to the first description of Heinrich et al⁸ PDGFR mutations seem to cluster in analogous regions known for KIT mutations with exon 12 mutations in the JM domain and exon 18 mutations in the TK domain.

In the present study, we investigated the occurrence of PDGFR mutations in 87 GISTs and compared 41 tumors with known KIT mutations with 46 GISTs without detectable KIT mutations in exons 9 or 11. We found PDGFR mutations in 20 cases (43.5% in the group of wt GISTs), all of them without KIT mutations in the most frequently mutated exons 11 and 9. None of the GISTs with KIT mutations carried PDGFR mutations. We evaluated clinicopathological data, histomorphological subtypes, and immunohistochemical expression patterns for PDGFR and KIT receptor and compared PDGFR-mutation-positive GISTs, KIT mutation-positive tumors and those without detectable KIT or PDGFR mutations.

	Materials and Methods

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Tissues and Clinical Data
In 87 cases from the files of the Department of Pathology, University of Bonn Medical Center, including 43 cases sent from other institutions for reference opinion, DNA was extracted from formalin-fixed, paraffin-embedded tissue for mutational analysis. KIT mutational status has been published in part previously.^{3, 12}

Criteria for GIST Diagnosis and Classification
GIST diagnosis was confirmed by immunohistochemical analysis using antibodies against CD117 (KIT receptor), CD34, bcl-2, -actin, desmin, S-100 protein, vimentin (all DAKO, Hamburg, Germany), and Ki-67 (MIB-1, Dianova, Hamburg, Germany) as previously described.³ Additionally, PDGFR-expression was evaluated using a monoclonal antibody (Santa Cruz Biotechnologies, Santa Cruz, CA, USA; C-20, dilution 1:50). Specificity of the antibody against PDGFR was controlled by peptide blocking (Santa Cruz Biotechnologies; blocking peptide, sc-338 P) and by Western blot analysis showing a specific band of approximately 185 kd (not shown). Immunohistochemical results were assessed in a semi-quantitative manner using the categories strong, intermediate, weak, or negative. The categories were defined as follows: strong, strong or intermediate positivity in more than 75% of tumor cells; intermediate, strong or intermediate positivity in more than 10% of tumor cells or weak positivity in more than 75% of tumor cells; weak, any positivity in less than 10% of tumor cells; and negative, no positivity. Proliferative activity was evaluated by counting mitoses per 50 high-power fields (HPFs). MIB1-index was determined by counting stained nuclei in 1000 tumor cells and is given in %.

Histomorphologically, GISTs were subtyped according to Fletcher et al¹³ into three categories: spindle cell type, epithelioid type, or mixed type. Potential risk for aggressive behavior was evaluated according to Fletcher et al (Table 1) .¹³

Analysis of PDGFR Mutations in Exons 12 and 18 and KIT Mutations in Exons 9 and 11
For PDGFR mutational analysis, tumor tissue for DNA extraction was marked on H&E-stained slides and microdissected from serial sections (10 µm). Tissue slides were deparaffinized by xylene. Total DNA was extracted after pretreatment with proteinase K and absorption on silica-gel-membranes (Qiagen, Hilden, Germany) and analyzed by single strand conformational polymorphism analysis (SSCP). Therefore, intronic PCR primers were designed to amplify exons 12 and 18. PDGFR DNA was amplified by PCR using the following primers: exon 12A forward: 5'-ttcaccagttacctgtcctg-3' and reverse: 3'-ccatctgggctgattgattc-5', product size 84 bp; exon 12B forward: 5'-gaatcaatcagcccagatgg-3' and reverse: 3'-accaagcactagtccatctc-5', product size 102 bp; exon 18 forward: 5'-cttttccatgcagtgtgtcc-3' and reverse: 3'-cactgcctttcgacacatag-‘5, product size 137 bp.

PCR was performed in 10-µl reactions containing 1.0 µl DNA, 10 mmol/L Tris-HCl (pH 8.3), 40 mmol/L KCl, 1.0 to 1.5 mmol/L MgCl₂, 200 mmol/L of each dNTP, 20 pM of each primer, and 0.25 U Platinum Taq polymerase (Life Technologies, Invitrogen GmbH, Karlsruhe, Germany). PCR reaction was carried out on an Uno II Thermoblock (Biometra, Göttingen, Germany). Initial denaturation at 94°C for 3 minutes was followed by 41 cycles and a final extension step (5 minutes at 72°C). The cycles included denaturation at 94°C for 40 seconds, annealing at 55 to 57°C for 40 seconds, and extension at 72°C for 35 seconds. PCR products were diluted with formamide, denaturated at 94°C for 10 minutes, and single strands were separated on polyacrylamide gels under two different conditions. Single and double strands of the PCR products were visualized by silver staining as described previously.¹⁴ DNA single strand bands showing an altered mobility in comparison to reference products were excised from the wet gel. DNA was eluted in H₂O for 2 hours at 50°C, precipitated by centrifugation at 12000 x g for 30 minutes and re-amplified. The products were purified using spin columns (QIAquick PCR Purification kit, Qiagen). Cycle sequencing (ABI PRISM Dye Terminator Sequencing Ready Reaction kit, Applied Biosystems, Weiterstadt, Germany) was done on a TC 9600 thermocycler (Perkin Elmer, Rodgau-Jügesheim, Germany) with 20 ng of PCR product as template according to the protocol of the manufacturer. The sequencing products were separated on an 6%, 1:19 bisacrylamide:acrylamide gel on an ABI 373A sequencer (Applied Biosystems). All sequence alterations were confirmed by an independent PCR amplification followed by SSCP, re-amplification, and sequencing to exclude PCR artifacts. Analysis of KIT mutations in exons 9 and 11 was performed as previously described.^{3, 12}

Sample Composition
We evaluated all available GISTs lacking KIT mutations in a larger series and compared them with a defined subset of previously described GISTs^{3, 12} with known KIT mutational status. Therefore, the data do not represent the incidence of specific mutations in an unselected cohort of GISTs.

Statistics
Statistical analysis was carried out using a commercially available computer program (SAS for Windows, release 8.01, SAS Institute Inc., Cary, NC, USA). For comparison of frequency counts the Chi-square test or the Fisher’s exact test were used, where appropriate. Correlations of quantitative variables were assessed by the method of Spearman. Logistic regression was used to investigate a possible influence of covariates on binominal or ordinal parameters. In general, backward elimination with a covariate removal criteria of P = 0.05 was used.

	Results

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PDGFR Mutations
In 20 of 46 (43.5%) GISTs without detectable KIT mutation in exons 9 or 11, shifts in the SSCP for exon 18 of the PDGFR gene were observed in comparison with the control (blood of a healthy person), whereas no SSCP shifts were detected for exon 12. None of the tumors with known KIT mutation showed SSCP shifts in exon 12 or 18 of PDGFR.

All tumors were sequenced on both strands of exon 12 and 18 PDGFR gene independently of the detection of SSCP shifts. Whereas all cases with altered bands in the SSCP showed mutations in exon 18, none showed mutations in exon 12. Three cases (numbers 42, 46, and 57) carried a 12 bp-deletion in codons 843 to 846 resulting in the loss of the amino acids isoleucine, methionine, histidine, and asparagine. Sixteen cases (numbers 43–45, 47–54, 56, and 58–61) showed a point mutation in codon 842 leading to an amino acid exchange from asparagine to valine. One case (number 55) carried a 9-bp deletion leading to an amino acid change in codon 842 from asparagine to alanine and to a loss of codons 843 to 845 (isoleucine, methionine, and histidine). Examples for SSCP shifts and sequence analysis in exon 18 of PDGFR are shown for GIST 47 (point mutation; Figure 1A ) and GIST 55 (9-bp deletion; Figure 1B ).

View larger version (39K): [in this window] [in a new window]   Figure 1. SSCP and sequence analysis in exon 18 of PDGFR. A: GIST 47: Point mutation (T -> A) leading to an amino acid exchange from asparagine to valine; DNA fragment with altered mobility marked by an arrow. B: GIST 55: Deletion of 9 bp leading to an amino acid change in codon 842 from asparagine to alanine and to a loss of codons 843 to 845 (isoleucine, methionine, and histidine; DNA fragment with altered mobility marked by an arrow).

View this table: [in this window] [in a new window]   Table 2. Clinicopathologic Data and Types of 41 KIT Mutation Positive, PDGFR Mutation Negative GISTs

View this table: [in this window] [in a new window]   Table 3. Clinicopathologic Data and Types of 20 KIT Mutation Negative, PDGFR Mutation Positive GISTs

View this table: [in this window] [in a new window]   Table 4. Clinicopathologic Data and Types of 26 KIT and PDGFR Mutation Negative GISTs

Interestingly, all GISTs with PDGFR mutation were located in the stomach, whereas tumors with KIT mutation or with wild-type status in both genes were found also in the small bowel (P = 0.0008).

Risk Assessment
Comparing the risk of aggressive behavior according to Fletcher et al¹³ KIT mutation-positive GISTs and tumors lacking any mutations belonged more frequently to the high-risk group (42% and 38%) than those with PDGFR mutation (20%; P = 0.0983, Table 5 ). However, the differences according to the Fletcher risk assessment did not reach statistical significance.

View this table: [in this window] [in a new window]   Table 5. Risk Assessment According to Fletcher et al.13 in Relation to Mutational Status in KIT and PDGFR Gene

Immunohistochemistry of KIT Receptor and PDGFR
A stronger PDGFR-expression was found in PDGFR mutation-positive tumors compared to the lesions lacking mutations in both genes (OR 9.259, P = 0.0068) but was not significantly higher than in KIT mutation-positive GISTs (OR 3.194, P = 0.1586). Figure 2 shows two examples of GISTs (numbers 47 and 55) with PDGFR mutation in exon 18 both exhibiting a strong PDGFR expression and a rather weak or only focal KIT-receptor expression.

View larger version (169K): [in this window] [in a new window]   Figure 2. Histomorphology and expression of KIT and PDGFR receptors in two PDGFR-mutated GISTs: Both tumors exhibited a mixed phenotype (GIST 55 in A, GIST 47 in B; H&E). GIST 55 showed a weak KIT receptor expression (C) and a strong membranous and dot-like cytoplasmatic PDGFR receptor expression (E). GIST 47 showed a strong, but only focal KIT receptor expression (D) and a strong membranous and cytoplasmatic PDGFR receptor expression (F). (Original magnification, x400, A–F).

View this table: [in this window] [in a new window]   Table 6. Immunohistochemical Expression Profiles in Relation to Mutational Status in KIT and PDGFR Gene

	Discussion

Top Abstract Introduction Materials and Methods Results Discussion References

Recently, Heinrich et al⁸ described mutations in the PDGFR gene in 14 of 40 GISTs (35%) with wild-type sequence in KIT. They could demonstrate that these mutations lead to autophosphorylation of the receptor protein in the same way as shown for the KIT receptor. Hirota et al⁹ could confirm these data in 5 of 8 KIT wt GISTs. PDGFR belongs to the same type III receptor tyrosine kinase subfamily as KIT with a similarity of 35% of amino acids between both proteins. Both genes are located on the long arm of chromosome 4 in close vicinity and both are believed to be derived from a common ancestor during evolution.

In the present study we found mutations in exon 18 of the PDGFR gene in 20 of 46 GISTs without detectable KIT mutation. In contrast to the results of Heinrich et al⁸ and Hirota et al⁹ we could not detect activating mutations in exon 12 of the PDGFR gene despite direct sequencing of all cases independently of our SSCP results. This result suggests that exon 12 mutations might be less frequent than exon 18 mutations. Furthermore, it cannot be ruled out that different genetic backgrounds of the populations studied may exist. All 41 GISTs with known KIT mutation showed a wild-type sequence in exons 12 and 18 of the PDGFR gene. Thus, PDGFR mutations seem to be an alternative cause for GIST development. Clarification is necessary as to whether mutant PDGFR transforms by itself or if it needs to form heterodimers with wt KIT to transform GIST precursors, as proposed by Hirota et al.⁹ In 26 tumors, mutations could not be detected in either exon 9 and 11 of KIT or in the PDGFR gene, suggesting a third subgroup with a still unknown pathogenesis. It cannot be ruled out completely that single cases in this group may harbor a KIT mutation in exon 13 or 17. However, detection rate in these two exons encoding the tyrosine kinase domains I and II is extremely low in other series. Lasota et al¹¹ found KIT exon 13 mutations in 2 of 200 tumors and Rubin et al.¹⁰ in 2 of 48 GISTs. The latter group described KIT exon 17 mutations in 2 of 48 GISTs, Heinrich et al¹⁶ found KIT exon 17 mutations in 2 of 127 GISTs.

Our data indicate that GISTs with PDGFR mutation in exon 18 differ from tumors with KIT mutations and from those lacking mutations in both genes according to their location, their histomorphological features, their immunohistochemical expression pattern, and their proliferative activity.

Surprisingly, all tumors carrying a PDGFR mutation were located in the stomach. In contrast, GISTs with KIT mutations occurred also in the small bowel (12 of 36) with tumors carrying exon 9 mutations even predominating in the small bowel (8 of 10). This suggests that GISTs are also genetically heterogeneous with respect to their site of origin. The progenitor cells giving rise to gastric GISTs seem to undergo different genetic hits compared to GISTs in other locations. There are different explanations for this finding. First, specific genotoxic events may only occur in the specific microenvironment of the stomach. However, the nature of such external factors is not known. Second, the progenitor cells leading to GISTs of the stomach may be different from those at other sites, or they may represent another stage of progenitor differentiation prone to be transformed by PDGFR mutations.

Interestingly, the vast majority of GISTs with PDGFR mutation (90%) displayed a mixed or epithelioid phenotype whereas KIT mutation-positive GISTs exhibited almost always a spindled histomorphology (85.4%) and also the majority (65.4%) of tumors lacking any mutations were composed of spindle cells. The occurrence of PDGFR mutations may indicate an alternative activation mechanism that has similar, but not identical, functional consequences. Activated PDGFR induces redistribution of cellular filaments, cell ruffling, and motility responses.¹⁷ Therefore, the epithelioid phenotype may be a direct consequence of the mutation. The fact that two cases had a spindle cell phenotype although they carry a PGRFR mutation indicates that additional signals may influence the cellular architecture.

Comparing the levels of KIT receptor and PDGFR expression, there was an association of mutational status and expression level. KIT receptor expression was lower in PDGFR-mutation-positive GISTs than in tumors carrying KIT mutations and vice versa. Heinrich et al⁸ showed that activated KIT and PDGFR receptors regulate a similar but not identical signaling cascade. They found phosphorylated STAT5 only in cells transfected with mutant KIT but not in cells transfected with mutant PDGFR. This argues against the possibility that mutated PDGFR simply dimerize wild-type KIT receptor and induce an identical activation response.

It is remarkable that differences between KIT and PDGFR-mutated GISTs are observed not only on the level of location and morphology but also when comparing the mitotic count and the resulting classification and risk of aggressive behavior. These findings should be confirmed in longitudinal clinical studies.

In summary, our finding of PDGFR mutations in KIT wild-type GISTs support the findings of Heinrich et al⁸ that these mutations may represent an alternative event in GIST pathogenesis. Furthermore, our analysis provides evidence that although these events are not equivalent, they define different genetic, phenotypic, and prognostic subsets of GISTs. Very recently, Heinrich et al¹⁶ demonstrated that PDGFR mutations in GISTs may lead to resistance to tyrosine kinase inhibitors, such as imatinib mesylate, underlining the impact of mutational analysis in Kit and PDGFR for therapeutic approaches. Further studies will be needed to dissect the functional consequences of these genetic events that are of particular interest in relation to GIST treatment with tyrosine kinase inhibitors.

	Acknowledgments

 
We thank Susanne Steiner, Barbara Reddemann, Ellen Pagen, Dorota Denkhaus, and Gerrit Klemm for technical assistance.

	Footnotes

 
Address reprint requests to Eva Wardelmann, M.D., Department of Pathology, University of Bonn Medical School, P.O. Box 2120, D-53011 Bonn, Germany. E-mail: eva.wardelmann{at}ukb.uni-bonn.de.

E.W. and A.H. contributed equally to this paper.

Accepted for publication March 30, 2004.

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This Article Abstract Full Text (PDF) Purchase Article View Shopping Cart Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Wardelmann, E. Articles by Pietsch, T. Search for Related Content PubMed PubMed Citation Articles by Wardelmann, E. Articles by Pietsch, T.