Comprehensive genomic profiling identifies a novel TNKS2–PDGFRA fusion that defines a myeloid neoplasm with eosinophilia that responded dramatically to imatinib therapy

Myeloid and lymphoid neoplasms with PDGFRA gene rearrangements are a category of rare diseases that typically manifest with peripheral blood eosinophilia accompanied by eosinophilic tissue infiltrates, and may be associated with typical or atypical mast cell proliferations. These tumors can present as myeloproliferative neoplasms, acute myeloid leukemias or lymphoblastic leukemias/ lymphomas and are, consequently, classified within the larger category of ‘Myeloid and lymphoid neoplasms with eosinophilia and abnormalities of PDGFRA, PDGFRB or FGFR1’ in the 2008 World Health Organization (WHO) classification. For neoplasms harboring PDGFRA rearrangements, FIP1L1–PDGFRA is by far the most common fusion detected, reflecting an 800-kb intrachromosomal deletion [del(4)(q12q12)]. Identification of PDGFRA rearrangement is both an important diagnostic and predictive marker, as these neoplasms are typically responsive to treatment with imatinib. The atypical mast cell proliferations that accompany these tumors may result in a mistaken diagnosis of systemic mastocytosis (SM), which is associated with an activating D816V alteration in KIT. The discrimination of these entities is important, as PDGFRA-rearranged tumors with eosinophilia, unlike SM harboring KIT D816V, are typically imatinib responsive. We describe a novel TNKS2–PDGFRA fusion in a myeloid neoplasm with eosinophilia, detected via comprehensive genomic profiling with a next-generation sequencing-based assay (FoundationOne), the presence of which correlated with the results from multiprobe fluorescent in situ hybridization (FISH) testing. Initially this patient was diagnosed with an aggressive SM (aSM); however, detection of this novel fusion, a translocation between chromosomes 4(q12) and 10(q23.3), resulted in diagnostic reclassification and led to targeted drug therapy with a resulting dramatic clinical response. A 58-year-old Caucasian woman presented with left upper quadrant pain and hepatosplenomegaly with the splenic tip palpable to 15 cm below the left costal margin and liver palpable 5 cm below the right costal margin, with 6 years of chronic, untreated hepatitis C and hepatic cirrhosis diagnosed 2 years prior. An abdominal magnetic resonance imaging scan confirmed splenomegaly with the evidence of splenic infarct and a nodular liver, consistent with cirrhosis. A small amount of ascites was present. Her medical history was significant for mild thrombocytopenia of several years duration with no evidence of bleeding. A bone marrow core biopsy was performed and was hypercellular (100% cellularity) with dense infiltrates and aggregates of 415 spindled mast cells as well as increased eosinophils. Mast cells were positive for CD2 and CD25 expression by immunohistochemistry. Targeted genomic analysis for mutations in KIT was ordered, but ultimately failed due to insufficient sample material. Cytogenetic analysis was ordered but the results were not immediately available, given the inherent time needed for processing. On the basis of these findings, the patient was initially diagnosed with aSM. A peripheral blood count performed a month after initial diagnosis revealed leukoerythroblastic features with a marked absolute eosinophilia (white blood cells of 20.6 × 10/l, absolute eosinophil count of 3708/μl) and no circulating blasts. An expanded blast population was not seen either in the marrow aspirate smear or using CD34 immunohistochemistry on the core biopsy. The patient’s clinical status deteriorated rapidly with worsening thrombocytopenia and progressive anasarca, necessitating hospitalization. Diuretics were of little benefit. Subsequent FISH testing was reported positive for a PDGFRA gene rearrangement and was attributed to presence of the canonical FIP1L1–PDGFRA fusion. However, karyotyping identified a translocation involving chromosomes 4 and 10. Comprehensive genomic profiling by FoundationOne performed on a bone marrow aspirate fully characterized the presence of a t(4:10) abnormality, identified as a novel fusion of TNKS2 and PDGFRA (Figure 1). Further, a KRAS G12D point mutation was detected. These findings resulted in reclassification of this disease from aSM to a myeloid neoplasm with eosinophilia harboring a PDGFRA rearrangement. On the basis of this diagnosis, the patient was started on a course of imatinib (400 mg, daily) and the clinical benefit was dramatic with immediate onset of diuresis, resolution of the anasarca, reduction in splenomegaly and steady improvement in the platelet count. At the time of publication, the patient remains on a maintenance dose of imatinib (100 mg, daily) and a subsequent bone marrow biopsy 4 months after initiation of therapy revealed a dramatic normalization in marrow cellularity without eosinophilia or mast cell proliferation. Follow-up multiprobe FISH for PDGFRA abnormality at this time was negative. A bone marrow aspirate was collected via needle biopsy and comprehensive genomic profiling (FoundationOne) was performed in a Clinical Laboratory Improvement Amendmentscertified laboratory, College of American Pathologists and New York State accredited (Foundation Medicine, Cambridge, MA, USA). Methods of the clinical cancer gene assay used to analyze this patient have been previously published and the assay performance has been validated rigorously. Here we provide a brief summary. DNA is extracted from formalin-fixed, paraffinembedded tissue (⩾1mm) containing no less than 20% tumor nuclei by enzymatic digestion and subsequent purification. DNA is fragmented by sonication to 200 bp segments. Indexed sequencing adapters are ligated to the DNA fragments and PCR amplified to yield 500 ng of sequencing library. Hybridization selection is performed using individually synthesized baits targeting 3679 exons of 236 cancer-related genes and 47 introns of 19 genes frequently rearranged in cancer. The Illumina HiSeq 2500 (Illumina Inc, San Diego, CA, USA) platform is used in 49× 49 paired-end sequencing. Sequence data are mapped to the human genome (hg19) using BWA aligner v0.5.9. Sequence data are analyzed through a computational analysis pipeline to call variants present in the sample, including substitutions, short insertions and deletions, rearrangements and copy-number variants. Citation: Blood Cancer Journal (2015) 5, e278; doi:10.1038/bcj.2014.95