A Tyrosine Kinase Created by Fusion of the PDGFRA and FIP1L1 Genes as a Therapeutic Target of Imatinib in Idiopathic Hypereosinophilic Syndrome
Jan Cools, Ph.D., Daniel J. DeAngelo, M.D., Ph.D., Jason Gotlib, M.D., Elizabeth H. Stover, M.Phil., Robert D. Legare, M.D., Jorges Cortes, M.D., Jeffrey Kutok, M.D., Ph.D., Jennifer Clark, M.D., Ilene Galinsky, R.N., James D. Griffin, M.D., Nicholas C.P. Cross, Ph.D., Ayalew Tefferi, M.D., James Malone, M.D., Rafeul Alam, M.D., Ph.D., Stanley L. Schrier, M.D., Janet Schmid, M.D., Michal Rose, M.D., Peter Vandenberghe, M.D., Ph.D., Gregor Verhoef, M.D., Ph.D., Marc Boogaerts, M.D., Ph.D., Iwona Wlodarska, Ph.D., Hagop Kantarjian, M.D., Peter Marynen, Ph.D., Steven E. Coutre, M.D., Richard Stone, M.D., and D. Gary Gilliland, M.D., Ph.D.
Background Idiopathic hypereosinophilic syndrome involves aprolonged state of eosinophilia associated with organ dysfunction.It is of unknown cause. Recent reports of responses to imatinibin patients with the syndrome suggested that an activated kinasesuch as ABL, platelet-derived growth factor receptor (PDGFR),or KIT, all of which are inhibited by imatinib, might be thecause.
Methods We treated 11 patients with the hypereosinophilic syndromewith imatinib and identified the molecular basis for the response.
Results Nine of the 11 patients treated with imatinib had responseslasting more than three months in which the eosinophil countreturned to normal. One such patient had a complex chromosomalabnormality, leading to the identification of a fusion of theFip1-like 1 (FIP1L1) gene to the PDGFR (PDGFRA) gene generatedby an interstitial deletion on chromosome 4q12. FIP1L1-PDGFRis a constitutively activated tyrosine kinase that transformshematopoietic cells and is inhibited by imatinib (50 percentinhibitory concentration, 3.2 nM). The FIP1L1-PDGFRA fusiongene was subsequently detected in 9 of 16 patients with thesyndrome and in 5 of the 9 patients with responses to imatinibthat lasted more than three months. Relapse in one patient correlatedwith the appearance of a T674I mutation in PDGFRA that confersresistance to imatinib.
Conclusions The hypereosinophilic syndrome may result from anovel fusion tyrosine kinase FIP1L1-PDGFR thatis a consequence of an interstitial chromosomal deletion. Theacquisition of a T674I resistance mutation at the time of relapsedemonstrates that FIP1L1-PDGFR is the target of imatinib. Ourdata indicate that the deletion of genetic material may resultin gain-of-function fusion proteins.
The hypereosinophilic syndrome is a rare hematologic disorderwith sustained overproduction of eosinophils in the bone marrow,eosinophilia, tissue infiltration, and organ damage. The diagnosisis based on the criteria of Chusid et al.1: sustained eosinophilia(more than 1500 eosinophils per cubic millimeter) for more thansix months; the absence of other causes of eosinophilia, includingparasitic infections and allergies; and signs and symptoms oforgan involvement, most frequently the heart, the central andperipheral nervous system, the lungs, and the skin. The syndromeis more common in men than women (ratio, 9:1) and occurs predominantlybetween the ages of 20 and 50 years. Total leukocyte countsare usually less than 25,000 per cubic millimeter, with 30 to70 percent eosinophils. Bone marrow eosinophils are increased(30 to 60 percent), but myeloblasts are usually not.2 It hasbeen difficult to assess the clonality of the hypereosinophilicsyndrome, but some cases are clonally derived, as demonstratedby clonal karyotypic abnormalities and X-inactivation assays.3,4
Treatment of the hypereosinophilic syndrome attempts to limitorgan damage by controlling the eosinophil count and includesprednisone, hydroxyurea, interferon alfa, and cytotoxic chemotherapy.In most cases, however, the disorder is fatal. Recently, itwas reported that four of five cases responded to imatinib mesylate(Gleevec, Novartis).5 Imatinib, a 2-phenylaminopyrimidinebasedtyrosine kinase inhibitor,6 has been approved for the treatmentof BCR-ABLpositive chronic myeloid leukemia (CML) andacute lymphoblastic leukemia.7,8 Besides the ABL tyrosine kinase,imatinib also inhibits the type III transmembrane receptorsKIT and platelet-derived growth factor receptor (PDGFR) .6,9,10Hence, imatinib is also a promising new treatment for gastrointestinalstromal tumors, which frequently harbor activating mutationsin the KIT gene,11,12 and chronic myeloproliferative diseaseswith rearrangements of the gene for PDGFR (PDGFRB).13 The clinicalresponse to imatinib suggests that the hypereosinophilic syndromemay also be associated with constitutive activation of ABL,KIT, PDGFR, or an as yet unidentified target. Therefore, weevaluated the response to imatinib in patients with the hypereosinophilicsyndrome and the molecular basis of the response.
Methods
Patients and Treatment
The study was conducted from June 2001 to October 2002. We studied16 patients who had received a diagnosis of the hypereosinophilicsyndrome and 1 who had acute myelogenous leukemia with marrowfibrosis that developed from a rapidly progressive hypereosinophilicmyeloproliferative disorder (Table 1). Only Patients 1 through11, who had symptomatic disease, were treated with imatinib,at a dose of 100 to 400 mg per day. Patients 12 through 17 werenot treated with imatinib. No patient concurrently receivedcytotoxic therapy.
Table 1. Characteristics of 17 Patients with the Hypereosinophilic Syndrome (HES).
Written informed consent was obtained for the prospective accrualof clinical data and the collection of biologic specimens foranalysis of genes known to be inhibited by imatinib. Completehematologic remission was defined by a white-cell count of lessthan 10,000 per cubic millimeter, a platelet count of more than100,000 per cubic millimeter, the presence of fewer than 5 percenteosinophils in the peripheral blood and bone marrow, the absenceof blasts and promyelocytes in the peripheral blood, and theabsence of extramedullary involvement.
Fluorescence in Situ Hybridization
Fluorescence in situ hybridization was performed as describedpreviously.14 Probes were obtained from the Roswell Park CancerInstitute libraries RPCI6 and RPCI11 (http://www.chori.org/BACPAC).
Rapid Amplification of Complementary DNA Ends
Trizol (Invitrogen) was used to extract RNA from white cells.DNA was extracted with use of the QIAmp DNA blood Maxi Kit (Qiagen).First-strand complementary DNA (cDNA) was synthesized from 2µg of total RNA with the use of the Superscript first-strandsynthesis system (Invitrogen) with a gene-specific primer orrandom primers. Rapid amplification of cDNA ends was performedas previously described15 with primers PDGFRA-R1 for cDNA synthesisand PDGFRA-R2 and PDGFRA-R3 for a nested polymerase chain reaction(PCR).
PCR Assay
Fusion of the Fip1-like 1 (FIP1L1) gene to the PDGFR (PDGFRA)gene was confirmed on cDNA by nested PCR with the use of primerpairs FIP1L1-F4 and PDGFRA-R1 and FIP1L1-F5 and PDGFRA-R2. Thereciprocal fusion was detected with the use of primer pairsPDGFRA-F5 and FIP1L1-R1 and PDGFRA-F3 and FIP1L1-R2. Amplificationof the fusion gene at the DNA level was performed with use ofthe Expand Long template PCR system (Roche). For mutation analysisof the FIP1L1-PDGFRA fusion gene in Patient 5, the gene wasamplified with primers FIP1L1-F5 and PDGFRA-R12. Exon 15 ofPDGFRA was amplified with primers PDGFRA-F14 and PDGFRA-R15.PCR products were cloned in a pGEM-T-easy plasmid (Promega)and sequenced with use of an ABI sequencer (Perkin Elmer). Long-distanceinverse PCR was performed as previously described,16 with useof an AseI digest (New England Biolabs) and primer pairs LDI1and PDGFRA-R2 in the first PCR and LDI2 and PDGFRA-R3 in thenested PCR.
Constructs
The open reading frame of the FIP1L1-PDGFRA fusion gene wasamplified by PCR from cDNA from Patient 1 with use of the proofreadingenzyme HF-2 (Clontech) and primers FIP1L1-Fc and PDGFRA-Rc.This PCR product was cloned in the retroviral vector MSCV-EGFP(kindly provided by W. Pear, University of Pennsylvania). Constructswith point mutations, constructs with deletion mutations, andepitope-tagged constructs were obtained by PCR from the FIP1L1-PDGFRAclone and cloned into MSCV-EGFP. Similarity searches were performedwith use of the BLAST program (http://www.ncbi.nlm.nih.gov/BLAST).
Cell Culture
293T cells were grown in Dulbecco's modified Eagle's mediumwith 10 percent fetal-calf serum, and Ba/F3 cells were grownin RPMI medium with 10 percent fetal-calf serum and 1 ng ofmouse interleukin-3 per milliliter. Production of retroviralsupernatant and transduction have been described previously.17Interleukin-3independent growth was assessed by platingtransduced Ba/F3 cells in interleukin-3free medium, afterthe cells were washed three times in phosphate-buffered saline.Imatinib was stored as a 10 mM stock solution in water and dilutedin RPMI medium for use. For Western blotting, Ba/F3 cells wereincubated in the presence of imatinib for 90 minutes beforelysis. For doseresponse curves, Ba/F3 cells were incubatedfor 24 hours in the presence of imatinib, and the number ofviable cells at the start and at the end was determined withthe Celltiter96AQueousOne solution proliferation assay (Promega).Doseresponse curves were fitted with use of OriginPro6.1 software (OriginLab).
Western Blotting
Immunoprecipitation was performed with use of anti-MYC antibody(Cell Signaling) and protein G agarose (Roche). Each procedureinvolved 6 million Ba/F3 cells with stable expression of MYC-taggedwild-type FIP1L1-PDGFR fusion protein or the T674I mutant. Cellswere lysed in lysis buffer (Cell Signaling) containing 1 mMsodium orthovanadate, 20 µM phenylarsine oxide (Calbiochem),and protease inhibitors (complete tablets, Roche). For Westernblotting, Ba/F3 cells were collected, lysed in loading buffer(Cell Signaling), separated by sodium dodecyl sulfatepolyacrylamide-gelelectrophoresis, and transferred to membranes. The followingantibodies were used: anti-phospho-ERK1/2, anti-phospho-STAT5and antiphosphotyrosine (P-Tyr-100/102, Cell Signaling), anti-PDGFR(Upstate), anti-STAT5b (Santa-Cruz), antimouse peroxidase, andantirabbit peroxidase (Amersham Pharmacia Biotech). Detectionwas performed with use of the Western Lightning system (PerkinElmer).
Response to Imatinib in Patients with Hypereosinophilic Syndrome
The median age of the 11 patients (9 men and 2 women) who receivedimatinib was 46 years (range, 28 to 61) (Table 1). Prior therapiesincluded corticosteroids in 9, hydroxyurea in 10, interferonalfa in 5, cytotoxic chemotherapy in 2, cyclosporine in 1, andradiotherapy for extramedullary disease in 2. Patients had oneor more of the following: endomyocardial fibrosis or restrictivecardiomyopathy, gastrointestinal involvement, central nervoussystem or paraspinal disease, pulmonary involvement, skin involvement,hepatosplenomegaly, and thrombosis. The median eosinophil countat presentation was 14,500 per cubic millimeter (range, 4960to 53,000). Nine patients had a normal karyotype; one patienthad t(1;4)(q44;q12), and the patient with leukemia had trisomy8, trisomy 19, add2q, and del6q. All patients were BCR-ABLnegativeon cytogenetic analysis or fluorescence in situ hybridization.Imatinib was initiated at doses ranging from 100 to 400 mg daily.A complete hematologic remission was achieved in 10 of 11 patientsafter a median of 4 weeks (range, 1 to 12), although 1 of the10 had only a transient response, which lasted several weeks,and had no response to an increased dose of imatinib. The responselasted more than 3 months in the other nine patients (medianduration, 7 months; range, 3 to 15). Analysis of a bone marrowaspirate and biopsy specimen obtained before therapy from Patient5, who had a response, showed hypereosinophilia, with the largehypolobated eosinophils characteristic of the hypereosinophilicsyndrome. After therapy, there was extensive necrosis, CharcotLeydencrystals, and patchy, normal hematopoiesis. This patient relapsedat five months, with recurrent cytogenetic abnormalities.
Cloning of FIP1L1-PDGFRA
Patient DNA was analyzed for activating mutations in known targetsof imatinib: PDGFRA, PDGFRB, and KIT.6,9,10 No mutations werefound in exons encoding the activation loops or juxtamembranedomains (data not shown). One patient (Patient 1) had t(1;4)(q44;q12). The combination of this patient's response to imatiniband translocation at 4q12, a region where PDGFRA and KIT arelocated, prompted investigation of their involvement. Fluorescencein situ hybridization showed that a probe spanning the KIT locus(586A2) was translocated to the der(1) chromosome, indicatingthat the break point was centromeric to KIT. A probe at theCHIC2 locus (200D9), centromeric to PDGFRA,18 was deleted (Figure 1B).Taken together, these results indicated the presence ofa translocation associated with a deletion on 4q12 with a breakpoint near PDGFRA.
Figure 1. Detection of the Fusion Gene Formed by the Genes for Fip1-like 1 (FIP1L1) and Platelet-Derived Growth Factor Receptor (PDGFRA).
Panels A and B show the results of fluorescence in situ hybridization with a probe at the KIT locus (586A2, red signal) and a probe at the CHIC2 locus (200D9, green signal). In normal cells in metaphase (Panel A), these probes colocalize on chromosome 4q12. In cells in metaphase from Patient 1 (Panel B), colocalization is observed on the normal chromosome 4, but only the red signal (KIT) is detected on the der(1) chromosome. No green signal (CHIC2) was observed on the der(4) or any other chromosome, indicating that this chromosomal region was deleted. Panel C shows the results of fluorescence in situ hybridization with probe 120K16, located directly centromeric to FIP1L1. The presence of this probe on the der(1) (green signal) confirms that the translocation break point is separate from the deletion break points. Panel D shows the results of reverse-transcriptasepolymerase chain reaction indicating a fusion of FIP1L1 to PDGFRA in RNA from Patients 1, 4, 5, 6, 13, 14, and 17. The different bands represent splice variants. GAPDH was used as a control. Panel E shows the sequence of one in-frame splice variant for each patient with the fusion gene. FIP1L1 sequences are shown in lowercase and in blue or green, and PDGFRA sequences are shown in uppercase and in black. Sequences shown in green are derived from introns of FIP1L1.
To determine whether a chimeric PDGFRA transcript was present,we performed 5' rapid amplification of cDNA ends on the sequence,encoding the kinase domain of PDGFRA.19 Sequence analysis ofthe resultant products revealed that the kinase domain of PDGFRAwas fused to an uncharacterized gene (GenBank accession numberNM_030917), encoding a putative 520-amino-acid protein thatmost closely resembled Fip1, an essential component of the Saccharomycescerevisiae polyadenylation machinery.20 Therefore, we namedthe human gene FIP1L1 (Fip1-like 1). According to data fromExpressed Sequence Tags (http://www.ncbi.nlm.nih.gov/dbEST)and Ensembl (http://www.ensembl.org), FIP1L1 is widely expressedand undergoes alternative splicing. The FIP1L1-PDGFRA fusiongene was in-frame and fused the first 233 amino acids of FIP1L1to the last 523 amino acids of PDGFR (Figure 1 and Figure 2).
Figure 2. The Fip1-like 1 (FIP1L1)Platelet-Derived Growth Factor Receptor (PDGFR) Fusion Protein (Panel A) and the Resistance Mutation in Patient 5 (Panels B and C).
Panel A shows the FIP1L1, PDGFR, and FIP1L1-PDGFR proteins. The position of the break points is indicated by arrowheads. The position of the T674I mutation is indicated by the star. NLS denotes nuclear localization signal, TM transmembrane, and JM juxtamembrane region. Panel B shows the resistance mutation in Patient 5 T674I identified by sequencing of the PDGFRA kinase domain from samples obtained before (DNA) and after (RNA) imatinib treatment. Panel C shows the position of the threonine at position 315 in ABL relative to that of the threonine at position 674 in PDGFR.
Surprisingly, FIP1L1 was not located on chromosome 1, as mighthave been expected owing to a reciprocal translocation, butwas approximately 800 kb upstream of PDGFRA on 4q12 (NCBI contigNT_022853) (Figure 3). Taken together, this information indicatedthat the fusion gene was created by either del(4)(q12) or t(4;4)(q12;q12)rather than t(1;4)(q44;q12). The fusion of FIP1L1 and PDGFRAwas confirmed by reverse-transcriptasePCR on RNA andPCR on DNA from Patient 1 (Figure 1D and Figure 4A). The reciprocalPDGFRA-FIP1L1 fusion gene was not detected in RNA or DNA, stronglysuggesting that the fusion was the consequence of an interstitialdeletion (Figure 1D and Figure 4A).
Figure 3. Genomic Structure of the 4q12 Chromosomal Region.
Panel A shows the region of chromosome 4q12 between the Fip1-like 1 (FIP1L1) and KDR genes, indicating the deleted region between FIP1L1 and platelet-derived growth factor receptor (PDGFRA) (approximately 800 kb in size). Panels B and C show the break points (indicated by arrows) in FIP1L1 and PDGFRA, based on the results of reverse transcriptasepolymerase chain reaction and genomic polymerase chain reaction. The exact position of the exon 12 PDGFRA break points is indicated in the lower part of Panel C for patients for whom the genomic break points were cloned and sequenced. Exon numbering in FIP1L1 is based on a complementary DNA (cDNA) clone (GenBank accession number NM_030917); alternative exons 1a, 7a, 7b, 8a, and 10a, which are present in other cDNA clones or were identified in this study, are also shown. TM denotes transmembrane, and JM juxtamembrane region. The splice acceptor sites are underlined.
Figure 4. Genomic Break Points (Panels A and B) and Splicing (Panel C) of the Gene for Fip1-like 1 (FIP1L1) to the Gene for Platelet-Derived Growth Factor Receptor (PDGFRA).
Panel A shows amplification of the genomic break points by long-range polymerase chain reaction in Patients 1, 4, 6, 9, 12, 14, and 17. The reciprocal fusion gene PDGFRA-FIP1L1 could not be amplified, suggesting that it does not exist and that fusion of FIP1L1 to PDGFRA is caused by a deletion. Panel B shows the sequence of the FIP1L1-PDGFRA fusion gene for the five patients. In Panel C, comparison of the genomic sequences of FIP1L1 and PDGFRA with the sequence from the corresponding complementary DNAs reveals that splicing occurs by means of cryptic splice sites present in introns of FIP1L1 or exon 12 of PDGFRA. Splice donor acceptor sites are underlined in Panels B and C.
Incidence of FIP1L1-PDGFRA in the Hypereosinophilic Syndrome
An additional four of nine patients for whom pretreatment RNAor DNA was available had the FIP1L1-PDGFRA fusion gene. Fourof six patients with the hypereosinophilic syndrome who didnot receive imatinib were also found to have the gene on thebasis of RNA or DNA analysis (Figure 1 and Figure 4). Thus,the FIP1L1-PDGFRA fusion gene occurred in 9 of our 16 patients(56 percent).
Sequence analysis of DNA from peripheral-blood samples fromseven of nine patients with the fusion gene confirmed that allbreak points in PDGFRA occurred in exon 12 and that crypticsplice sites were used within introns of FIP1L1 or within exon12 of PDGFRA, to allow splicing between exons of FIP1L1 andthe interrupted exon 12 of PDGFRA (Figure 4). Attempts to amplifythe reciprocal fusion genes on RNA and DNA were unsuccessful,indicating that all fusions were the result of a deletion on4q12 and not of t(4;4) (Figure 1 and Figure 4).
Relapse during Imatinib Treatment Associated with an Acquired Mutation in PDGFRA
Patient 5, who relapsed during imatinib treatment, harboredthe FIP1L1-PDGFRA fusion gene initially and at the time of relapse.We hypothesized that relapse might be attributable to mutationsin the PDGFR moiety that conferred resistance to imatinib. Sequenceanalysis of the PDGFR kinase domain at the time of relapse showedthat the fusion protein had acquired a T674I mutation (Figure 2B).This mutation occurred in the ATP-binding region of PDGFRat the same position as the T315I mutation in BCR-ABL21,22 (Figure 2C),which is known to confer resistance to imatinib in thatcontext.21,22,23
Effect of FIP1L1-PDGFR
The expression of FIP1L1-PDGFR transformed the murine hematopoieticcell line Ba/F3 to interleukin-3independent growth (Figure 5B)and was constitutively tyrosine-phosphorylated in thesecells (Figure 5D). Deletion of the FIP1L1 moiety (amino acids4 to 233) abrogated this type of growth, indicating that thispart of the fusion protein was essential for the activationof the chimeric kinase. Further mutational analysis showed thatthe first 29 amino acids of FIP1L1 (encoded by exon 1) werenecessary and sufficient to activate the PDGFR kinase domain(Figure 5B). Analysis of the phosphorylation status of ERK1or ERK2 and STAT5 indicated that STAT5, but not ERK, was a downstreamtarget of FIP1L1-PDGFR (Figure 5E, and data not shown).
Figure 5. Transformation, Inhibition, and Signal Transduction Properties of the Fusion Tyrosine Kinase Formed by Fip1-like 1 (FIP1L1) and Platelet-Derived Growth Factor Receptor (PDGFR).
Panel A shows the retroviral constructs used in the study. MSCV denotes murine stem-cell virus, IRES internal ribosomal entry site, EGFP enhanced green fluorescent protein, LTR long terminal repeat, and F/P FIP1L1-PDGFR. The star indicates the position of the mutation. In Panel B, Ba/F3 cells retrovirally transduced with these constructs were grown in the absence or presence of interleukin-3, and their mean (±SD) growth was recorded over a period of three days. Panel C shows the doseresponse curves and cellular 50 percent inhibitory concentration (IC50) of imatinib for Ba/F3 cells expressing FIP1L1-PDGFR, FIP1L1-PDGFR with the T674I mutation, or BCR-ABL. The IC50 was 3.2 nM for FIP1L1-PDGFR, 582 nM for BCR-ABL, and 7498 nM for FIP1L1-PDGFR T674I. Panels D, E, F, and G show the phosphorylation status of PDGFR and STAT5 in Ba/F3 cells expressing either the wild type or the mutant (T674I) FIP1L1-PDGFR. Panels D and F show phosphorylation of PDGFR detected with an antiphosphotyrosine antibody or anti-PDGFR antibody (Control) after immunoprecipitation. Panels E and G show phosphorylation of STAT5 detected with an antiphospho-STAT5specific antibody or anti-STAT5 antibody (Control) with the use of whole-cell lysates.
Inhibition of FIP1L1-PDGFR Kinase Activity and Resistance to Imatinib
To confirm that FIP1L1-PDGFR was a target of imatinib, we testedthe effect of imatinib on the growth of Ba/F3 cells expressingFIP1L1-PDGFR or FIP1L1-PDGFR harboring the T674I mutation (Figure 5C).Ba/F3 cells expressing FIP1L1-PDGFR were efficiently inhibitedby much lower concentrations of imatinib than Ba/F3 cells expressingBCR-ABL. The concentration of imatinib required to inhibit cellstransformed by FIP1L1-PDGFR by 50 percent (IC50) was 3.2 nM,whereas the IC50 for BCR-ABL was 582 nM.23 These data indicatethat FIP1L1-PDGFR is more sensitive to inhibition by imatinibthan is BCR-ABL and correlate with the findings that the effectivedose of imatinib is lower in patients with the hypereosinophilicsyndrome (100 mg per day) than in patients with BCR-ABLpositiveCML (300 to 400 mg per day). As compared with Ba/F3 cells expressingwild-type FIP1L1-PDGFR, Ba/F3 cells expressing the FIP1L1-PDGFRT674I mutant were more than 1000 times as resistant to imatinib,with a cellular IC50 of 7498 nM (Figure 5C).
Consistent with these findings, imatinib inhibited tyrosinephosphorylation of FIP1L1-PDGFR and its downstream target STAT5with an IC50 of approximately 5 nM (Figure 5D and Figure 5E,respectively), whereas inhibition of the T674I mutant requiredconcentrations of imatinib that were at least 1000 times ashigh (10,000 and 5000 nM, respectively) (Figure 5F and Figure 5G).STAT5 phosphorylation was restored by the addition of interleukin-3(Figure 5E and Figure 5G), demonstrating the specificity ofimatinib in this context. Taken together, these data demonstratethat the PDGFR kinase domain is a direct target of imatinibin patients with the hypereosinophilic syndrome.
Discussion
Constitutive activation of tyrosine kinases is a key elementin the pathogenesis of myeloproliferative diseases. In mostcases the mutant kinases have been identified by cloning recurrentchromosomal translocation break points. Examples include theBCR-ABL,24 ETV6-PDGFR,25 HIP1-PDGFR,26 ETV6-JAK2,27 and H4-PDGFR28fusion proteins. The hypereosinophilic syndrome is a myeloproliferativesyndrome, but most patients present with an apparently normalkaryotype. We found a gene rearrangement, which is not evidenton standard karyotyping, that results in a novel FIP1L1-PDGFRfusion protein.
The FIP1L1-PDGFRA gene rearrangement is a clonal abnormalitythat raises several questions about the classification of eosinophilicsyndromes. World Health Organization (WHO) criteria indicatethat patients with clonally derived eosinophils should be classifiedas having chronic eosinophilic leukemia rather than the hypereosinophilicsyndrome. On the basis of these criteria, at least seven ofour patients with the hypereosinophilic syndrome should be reclassifiedas having chronic eosinophilic leukemia. Furthermore, it isplausible that most patients with the hypereosinophilic syndrome,or at least those with imatinib-sensitive disease, will haveclonally derived eosinophils. It may therefore be appropriateto reevaluate the WHO classification in the light of our observations.
Several lines of evidence argue that the FIP1L1-PDGFR fusionprotein is a cause of the hypereosinophilic syndrome. First,it was found in a majority of our patients and has the biologicproperties of other tyrosine kinase fusion proteins that areimplicated in the pathogenesis of myeloproliferative disease.Second, most patients with the hypereosinophilic syndrome hada response to imatinib, a potent inhibitor of PDGFR, PDGFR,KIT, and ABL.10 Most such patients have a response to lowerdoses of imatinib than those required for the induction of hematologicand cytogenetic responses in patients with BCR-ABLpositiveCML (e.g., 100 mg daily vs. 400 mg daily).8 This differencecorrelates with the lower IC50 of FIP1L1-PDGFR than BCR-ABL.Third, clinical relapse and resistance to imatinib in a patientwith the hypereosinophilic syndrome were associated with theacquisition of a point mutation in the ATP-binding domain ofthe FIP1L1-PDGFR fusion protein that confers resistance to imatinib.The T674I substitution is analogous to the T315I mutation inthe ABL kinase that occurs in some patients with BCR-ABLpositiveCML in whom resistance to imatinib develops21 and thus demonstratesthat FIP1L1-PDGFR is the therapeutic target of imatinib in thehypereosinophilic syndrome.
Nine of 11 patients with the hypereosinophilic syndrome hadresponses to imatinib that lasted more than three months, butonly 5 of these 9 had a detectable FIP1L1-PDGFRA fusion. Thebasis for a response to imatinib in the other four patientsis not known, but there are several possibilities. First, breakpoints for the deletion may be widely distributed within theFIP1L1 gene. Our biochemical data indicate that a deletion thatincorporated only the first exon of FIP1L1 would be sufficientto activate the PDGFR kinase domain. However, reverse-transcriptasePCRscreening for such FIP1L1-PDGFRA variants was negative in thesepatients. Second, another gene near FIP1L1 could form a fusionprotein with PDGFR. Detailed fluorescence in situ hybridizationwith probes that span the deleted region will resolve this question,but we have not yet identified alternative fusion partners forPDGFRA. Third, in some patients with the hypereosinophilic syndrome,the KIT gene, located approximately 400 kb downstream of PDGFRA,may be fused to FIP1L1. KIT is also sensitive to imatinib10;thus, a FIP1L1-KIT fusion protein in patients with the hypereosinophilicsyndrome should also result in a clinical response. However,we have been unable to identify such a FIP1L1-KIT fusion genein the four patients who had a response to imatinib but whodid not have the FIP1L1-PDGFRA fusion gene. Fourth, a similar,cytogenetically silent gene rearrangement may occur, involvingeither ABL or PDGFR in some patients. Finally, an as yet unidentifiedkinase that is inhibited by imatinib may be constitutively activatedby a mutation. Further analysis will be required to evaluatethese possibilities.
Cloning of the FIP1L1-PDGFRA gene rearrangement identified chromosomalinterstitial deletion as a novel molecular mechanism for a gain-of-functionfusion gene. Most investigations of the loss of heterozygosityin human tumors have focused on the loss of function of oneor both alleles of a putative tumor-suppressor gene. Our datasuggest that a comprehensive analysis of human tumors for smalldeletions that may result in gain-of-function fusion genes shouldbe undertaken.
Supported in part by grants from the National Institutes ofHealth (CA66996 and DK50654, to Dr. Gilliland; T32GMO7753-24,to Ms. Stover; and K23HL04409, to Dr. Gotlib); by a grant fromthe Leukemia and Lymphoma Society (to Dr. Gilliland); by a grantfrom the Fonds voor Wetenschappelijk Onderzoek-Vlaanderen (G.0121.00,to Dr. Marynen); and by the Belgian American Educational Foundationand the Commission for Educational Exchange between the UnitedStates and Belgium. Dr. Cools is a postdoctoral researcher andDr. Vandenberghe is a senior clinical investigator of the Fondsvoor Wetenschappelijk Onderzoek-Vlaanderen. Dr. Gilliland isan Associate Investigator of the Howard Hughes Medical Institute.
We are indebted to Ursula Pluys, Riet Somers, and Alexis Bywaterfor technical and administrative assistance, and to Marie Maerevoet,M.D., Lucienne Michaux, M.D., and Achiel Vanhoof, M.D. for contributionof patient samples and clinical care.
Source Information
From Brigham and Women's Hospital and Harvard Medical School, Boston (J. Cools, E.H.S., J.K., J. Clark, D.G.G.); the DanaFarber Cancer Institute, Boston (D.J.D., J. Clark, I.G., J.D.G., R.S., D.G.G.); Stanford University School of Medicine, Stanford, Calif. (J.G., J.M., S.L.S., S.E.C.); Women and Infants Hospital, Brown University School of Medicine, Providence, R.I., and Westerly Hospital, Westerly, R.I. (R.D.L.); M.D. Anderson Cancer Center, Houston (J. Cortes, H.K.); the Wessex Regional Genetics Laboratory, Salisbury, United Kingdom (N.C.P.C.); Mayo Clinic, Rochester, Minn. (A.T.); National Jewish Medical and Research Center, Denver (R.A.); Tulane University School of Medicine, New Orleans (J.S.); Yale University School of Medicine, New Haven, Conn. (M.R.); University Hospital Leuven, Leuven, Belgium (P.V., G.V., M.B.); Flanders Interuniversity Institute for Biotechnology, Leuven, Belgium (J. Cools, P.M.); Center for Human Genetics, Leuven, Belgium (I.W.); and Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston (D.G.G.). Drs. Cools and DeAngelo contributed equally to this article.
Address reprint requests to Dr. Gilliland at the Harvard Institutes of Medicine, 4 Blackfan Cir., Rm. 418, Boston, MA 02115 (gilliland{at}hihg.med.harvard.edu) or to Dr. Stone at the DanaFarber Cancer Institute, 44 Binney St., Boston, MA 02115 (rstone{at}partners.org).
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Hypereosinophilic Syndrome
Roufosse F. E., Goldman M., Cogan E., Gilliland D. G., Stone R. M., Coutre S. E.
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N Engl J Med 2003;
348:2687, Jun 26, 2003.
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