KIAA1509 is a novel PDGFRB fusion partner in imatinib-responsive
myeloproliferative disease associated with a t(5;14)(q33;q32)
Ross L. Levine1,2,5, Martha Wadleigh2,5, David W. Sternberg3, Iwona Wlodarska4, Ilene
Galinsky2, Richard M. Stone2, Daniel J. DeAngelo2, D. Gary Gilliland1, and Jan Cools4
1Division of Hematology, Brigham and Women’s Hospital and Howard Hughes Medical
Institute, Harvard Medical School, Boston, MA; 2Division of Medical Oncology, Dana-
Farber Cancer Institute, Boston, MA; 3Division of Hematology/Oncology, Mount Sinai
School of Medicine, New York, NY; and 4Department of Human Genetics – Flanders
Interuniversity Institute for Biotechnology (VIB), University of Leuven, Leuven,
5These authors contributed equally to this article.
Supported in part by National Institute of Health grants DK50654 and CA66996 to
D.G.G., grant CA82261 to D.W.S, and by the Leukemia and Lymphoma Society. D.G.G.
is a Doris Duke Foundation Distinguished Clinical Scientist and an Investigator of the
Howard Hughes Medical Institute
Reprints: D. Gary Gilliland, Division of Hematology, Brigham and Women’s Hospital,
75 Francis Street, Boston, MA 02115. Phone (617) 355-9092. Fax (617) 355-9093. E-
Running Title: KIAA1509 is a novel fusion partner to PDGFRB
We report the cloning of a novel PDGFRB fusion gene partner in a patient with a chronic
myeloproliferative disorder characterized by t(5;14)(q33;q32) who responded to
treatment with imatinib mesylate. Fluorescence in situ hybridization demonstrated that
PDGFRB was involved in the translocation. Long distance inversion PCR identified
KIAA1509 as the PDGFRB fusion partner. KIAA1509 is an uncharacterized gene with a
predicted coiled-coil oligomerization domain with homology to the HOOK family of
proteins. The predicted KIAA1509-PDGFRβ fusion protein contains the KIAA1509
coiled-coil domain fused to the cytoplasmic domain of PDGFRβ that includes the
tyrosine kinase domain. Imatinib therapy resulted in rapid normalization of the patient’s
blood counts, and subsequent bone marrow biopsies and karyotypic analysis were
consistent with sustained complete remission.
Fusion genes that result in constitutive activation of tyrosine kinases characterize
a subset of chronic myeloproliferative disorders. These fusion genes are the result of
chromosomal translocations or interstitial deletions.1, 2 In chronic myelomonocytic
leukemia (CMML) a subset of patients have balanced translocations involving the
platelet derived growth factor receptor beta (PDGFRB) gene. To date eight PDGFRB
fusion partners (ETV6, CEV14, HIP1, H4/D10S170, RABEP1, Myomegalin/PDE4DIP,
NIN, and HCMOGT-1) have been identified.3-10 In each case, chromosomal translocation
results in fusion of the 3’ region of PDGFRB encoding the kinase domain to a 5’ fusion
partner with a putative oligomerization domain. It has been demonstrated in most of
these that the PDGFRβ tyrosine kinase is constitutively activated as a consequence of
fusion to a dimerization or oligomerization motif in the amino-terminal partner. For
example, fusion of the ETV6 PNT oligomerization domain to PDGFRβ results in self
association and constitutive tyrosine kinase activity, and both the oligomerization and
kinase domains are required for transformation of hematopoetic cells.11 Mice engineered
to express the ETV6-PDGFRβ fusion protein using a lymphoid specific promoter
developed T and B cell lymphomas, and treatment with imatinib results in prolonged
survival in these mice.11, 12 There are additional reports of translocations involving
PDGFRB in MPDs where the fusion partner is not yet known.13
Imatinib mesylate (Gleevec; Novartis, Basel, Switzerland) is a specific tyrosine
kinase inhibitor with clinical activity in chronic myelogenous leukemia,
hypereosinophilic syndrome, and gastrointestinal stromal tumors.2, 14, 15 Based on the
observation that imatinib inhibits the growth of ETV6-PDGFRB transformed cells,
imatinib has been administered to three CMML patients with the ETV6-PDGFRB fusion;
durable responses were seen in all three cases.16 Similar responses to imatinib have been
reported in patients with the PDE4DIP-PDGFRB and NIN-PDGFRB fusion genes, and in
a patient with the RABEP1-PDGFRB fusion gene with a molecular relapse after
allogeneic bone marrow transplantation. 8, 9, 17
In this report we describe a patient with a myeloproliferative disorder
characterized by the chromosomal abnormality t(5;14)(q33;q32). The consequence of
the chromosomal translocation is fusion of the coiled-coil domain of KIAA5109 to the
tyrosine kinase domain of PDGFRβ. Imatinib therapy resulted in a rapid, complete, and
durable hematologic and cytogenetic response.
Materials and Methods
In July, 2002 a 42 year old man was incidentally noted to have a white blood cell
count of 64,900/µl with 41% bands, 21% neutrophils, 7% lymphocytes, 5% eosinophils,
12% monocytes, and 4% metamyelocytes. His platelet count was 176,000/µl and his
hemoglobin was 9.0 g/dL. Physical examination revealed no lymphadenopathy or
splenomegaly. Bone marrow biopsy revealed a hypercellular marrow with granulocytic
hyperplasia. Cytogenetic analysis revealed t(5;14)(q31;q32) and inv(9)(p23;q13) in all
cells analyzed. The BCR-ABL fusion gene was not detected. The patient was enrolled in
a clinical trial using imatinib mesylate in patients with CMML, which was defined as a
t(9;22) negative myeloproliferative disorder associated with a peripheral blood
monocytosis greater than 1,000/µL. Patients on this trial were treated with a daily oral
dose of 400 mg imatinib and were monitored with weekly blood counts and bone marrow
examinations every three months.
Fluorescence in Situ Hybridization
Fluorescence in situ hybridization (FISH) was performed as described previously.18
Cosmid probes c4-6, c4-1, and c12 spanning the PDGFRB gene were kindly provided by
Dr. M. Dixon.
Molecular Cloning of the Genomic Breakpoint
Long distance inversion PCR (LDI-PCR) was performed as previously described.19 The
sequence of the LDI-PCR product was analyzed using the BLAST program
(http://www.ncbi.nlm.nih.gov/BLAST). The genomic breakpoint was amplified from
patient DNA using primers KIAA1509-F3 (5’-cttatttgggatggagccct) and PDGFRB-R1
(5’-accaggtagggtactcggct). The fusion transcript was amplified using primers
KIAA1509-RTF1 (5’-ccgggacacagataaga) and PDGFRB-RTR1 (5’-
Results and Discussion
Response to Imatinib
The patient initiated treatment with imatinib in October, 2002; by that time his
white blood cell count had increased to 168,000/µL, his spun hematocrit had decreased to
25%, and his platelet count was 178,000/µL. After one month of therapy he was in a
hematologic remission with a normal complete blood count and differential (Figure 1).
After three months of therapy a bone marrow biopsy showed a hypocellular marrow with
one focus of hypercellularity and fibrosis. Cytogenetic analysis did not identify the
t(5;14)(q33;q32) in any cells analyzed, though inv(9)(p23;q13) was again identified in all
cells analyzed, suggesting a constitutional origin of inv(9). At 18 months of follow-up,
the patient remains in a cytogenetic remission; his most recent bone marrow examination
revealed a normo-cellular marrow with a normal myeloid to erythroid ratio. He has
tolerated therapy well with only grade 1 periorbital edema, and he continues on imatinib
400 mg daily.
Molecular Cloning of the t(5;14)(q33;q32)
FISH analysis (Figure 2) confirmed that the breakpoint involved the PDGFRB
locus. We used LDI-PCR to amplify the translocation breakpoint in genomic DNA.
Sequence analysis revealed a fusion between intron 9 of KIAA1509 and intron 10 of
PDGFRB. The fusion was confirmed by PCR on patient DNA and RNA (Figure 3).
KIAA1509 is a predicted gene (XM_029353) located on chromosome band 14q32,
and a partial cDNA has been cloned in a large scale cloning project.20 Based on data
from GeneNote (http://genecards.weizmann.ac.il/cgi-bin/genenote/home_page/pl)
KIAA1509 is widely expressed, with highest levels of expression in bone marrow, spleen
and thymus. The predicted mRNA encodes a 1935 amino acid protein with 73% amino
acid homology to the mouse 0610010D24Rik (Daple) protein. Daple was identified
based on its interaction with Dvl, and Daple has been shown to inhibit Wnt-3a dependent
accumulation of ß-caternin.21
The in-frame fusion transcript encodes a 934 amino acid protein composed of the
N-terminal 355 amino acids of the putative KIAA1509 protein and the C-terminal 579
amino acids of PDGFRβ (Figure 3). The breakpoint within PDGFRB is within intron 10,
which is identical to the location of the genomic breakpoints of all known PDGFRB
fusion genes except for NIN-PDGFRB.3-10, 22 There is 45% homology between the N-
terminal region of KIAA1509 and the central coiled coil domain of the HOOK family of
proteins.23 The coiled coil domain is highly conserved between the Drosophila hook
protein and the human HOOK proteins, and the Drosophila hook coiled coil domain
mediates dimerization.24 Analysis using the pepcoil program (http://www.emboss.org/)
suggests there is a 99% likelihood of a coiled coil domain within the N-terminal region of
KIAA1509. It is likely that the coiled coil domain of KIAA1509 mediates
homodimerization and constitutive activation of the PDGFRβ tyrosine kinase, as has
been demonstrated for ETV6-PDGFRβ and other PDGFRβ fusions.11
In summary, we have identified KIAA1509 as a novel fusion partner for PDGFRB
in a patient with t(5;14)(q33;q32) and a MPD. Treatment with imatinib resulted in a
rapid, complete, and sustained hematologic and cytogenetic response. Like other
PDGFRβ fusion proteins associated with a CMML phenotype, it is most likely that the
KIAA1509-PDGFRβ fusion is a constitutively activated tyrosine kinase that is imatinib-
sensitive. In support of this hypothesis, imatinib resulted in complete remission the
patient with the t(5;12)(q33;q32). These data provide further evidence that patients with
a CMML phenotype and translocations involving the PDGFRß locus are good candidates
for therapy with imatinib. However, cloning of these chromosomal translocations may be
difficult due to lack of RNA and limiting amounts of genomic DNA. Strategies such as
LDI-PCR, in conjunction with new methods for whole genome amplification to expand
DNA template,25 should allow for reliable identification of patients with CMML with
PDGFRß rearrangements that may be imatinib responsive.
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Titles and Legends to Figures
Figure 1: White blood cell count of patient with t(5;14)(q33;q32) before and after
initiation of imatinib therapy. The graph shows the patient’s total peripheral white
blood cell count, measured at the time of diagnosis and then subsequently while enrolled
in a clinical trial of imatinib therapy in chronic myelomonocytic leukemia.
Figure 2: Fluorescence in situ hybridization demonstrates a breakpoint within the
PDGFRB locus in a patient with t(5;14)(q33;q32)
Three color FISH analysis with three cosmid probes (c4-6: yellow; c4-1: green; c12-a:
red) spanning the PDGFRB gene were used to document a break within PDGFRB.
Figure 3: Cloning of KIAA1509 as a fusion partner to PDGFRB in a patient with
A) Shows the KIAA1509, PDGFRB, and KIAA1509-PDGFRB proteins. The position of
the breakpoint is indicated by arrowheads.
B) Shows the RNA and protein sequence of the KIAA-PDGFRB breakpoint.
C) RT-PCR of patient and normal granulocyte RNA shows expression of KIAA1509-
PDGFRB fusion product in the patient (Pt) with t(5;14)(q33;q32) and shows expression
of KIAA1509 in patient (Pt) and control (Cn) granulocyte RNA.
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