Inflammatory Myofibroblastic Tumors Harbor Multiple Potentially Actionable Kinase Fusions

Case Report

A 6-year-old boy presented with a 1-year history of cough and fatigue. Imaging demonstrated the presence of a large left-sided chest mass. Biopsy of the mass revealed IMT, negative for ALK expression by standard clinical IHC and for ALK rearrangement by break-apart FISH. The tumor was deemed unresectable due to its intimate association with the pulmonary vein, aorta, and esophagus. At the time of diagnosis, his laboratory parameters were indicative of a microcytic anemia and an inflammatory state. Several treatment regimens were administered, including anti-inflammatory agents (naproxen, corticosteroids, and indomethacin) as well as cytotoxic chemotherapy (methotrexate–vinorelbine), over the course of 24 months (Supplementary Fig. S1), with no antitumor response and minimal improvement of his anemia. While he was receiving methotrexate–vinorelbine, we performed targeted NGS-based genomic profiling of his tumor using formalin-fixed and paraffin-embedded (FFPE) tissue and surprisingly detected a TFG–ROS1 fusion (Fig. 1A). ROS1 TKIs, such as crizotinib, have proven to be an effective therapeutic strategy in lung cancers harboring ROS1 kinase fusions (8, 9). Therefore, he was treated with crizotinib (250 mg), obtained through a compassionate access program, twice daily orally. He experienced grade 1 diarrhea and visual disturbance, both of which resolved with no dose reduction. Within 3 cycles of crizotinib therapy, he symptomatically felt better, with decreased cough and significantly increased energy. Imaging studies revealed, for the first time since diagnosis, a decrease in the size of his tumor mass (Fig. 1B). Notably, his hemoglobin (Hgb) and mean corpuscular volume (MCV) rapidly increased and his erythrocyte sedimentation rate (ESR) decreased (Fig. 1C and Supplementary Table S1). He has now been on crizotinib for 4 months with excellent tolerance, improved quality of life, and continued decrease in his tumor burden.

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Figure 1.

Response to crizotinib in an 8-year-old boy with refractory IMT harboring a TFG–ROS1 fusion. A, schematic representation of the TFG–ROS1 fusion. ROS1 is located on chromosome 6q22 and TFG is located on 3q12. The breakpoint occurs in-frame between exon 4 of TFG and exon 36 of ROS1. B, CT scans before the initiation of crizotinib (left) and after 3 cycles of crizotinib (right) showing dramatic reduction in the tumor mass within the left lung. C, changes in Hgb, MCV, and ESR over the course of the patient's treatments. Arrows below the graphs, initiation of the indicated therapies. The high (H) and low (L) limits of normal for each measured parameter are indicated on the blue graphs.

Patient and Tumor Characteristics

In an effort to further characterize cases of both ALK-positive and ALK-negative IMT, we obtained 37 samples from 33 patients with this rare disease (Table 1). Patients ranged in age from infancy (less than 1 year old) to age 41. As is typical for IMT, the tumors arose at multiple anatomic locations, including thorax, mesentery, peritoneum, and bladder. The pathologic diagnosis was established based on criteria according to the WHO classification (3). ALK IHC was completed on each sample as part of the standard pathologic evaluation (Supplementary Methods). Eleven of 37 (30%) of the cases were ALK IHC negative and 26 of 37 (70%) of the cases were ALK IHC positive.

Targeted NGS Identified ALK, ROS1, and PDGFRβ Tyrosine Kinase Fusions in a Collection of IMT Samples

We hypothesized that further insight into the biology of known fusions as well as discovery of novel kinase fusions would provide new therapeutic targets to treat patients with IMT. To address this hypothesis, we analyzed genomic DNA from all 37 IMT samples using a targeted NGS-based assay (FoundationOne), which assesses 3,769 exons of 287 cancer genes and 47 introns of 19 commonly rearranged genes, including 8 tyrosine kinases (Supplementary Table S2). This platform has been previously described and successfully used in several large genomic studies of various tumor types (10–12). In each case, tumor DNA was isolated from FFPE tissue. Average coverage was 543×. Targeted NGS was successfully performed in 22 of 26 ALK-positive and 11 of 11 ALK-negative specimens (Table 1 and Supplementary Fig. S2). In cases in which there was sufficient tumor material available, the kinase fusions were verified with RNA sequencing.

Among the 11 ALK IHC–negative cases, kinase fusions were identified in 8 of 11 (73%) of the cases (Table 1, Fig. 2A and B). Two cases harbored ALK fusions (sample L5, EML4–ALK; sample L9, TPM3–ALK), which were missed by ALK IHC testing alone. Among the other 9 ALK-negative samples, 4 contained distinct ROS1 fusions (sample L3/L4, YWHAE–ROS1; sample L6, TFG–ROS1), including the index patient (sample L37), and 2 contained a PDGFRβ fusion (samples L7/L10, NAB2–PDGFRβ). Notably, neither ROS1 nor PDGFRβ fusions have been described in IMT to date. The genomic coordinates for each fusion identified are summarized in Supplementary Table S3. Importantly, all kinase fusions identified in this study (ALK, ROS1, PDGFRβ) are therapeutically targetable with existing FDA-approved TKIs (8, 13–15). No other recurrent alterations were identified (Supplementary Table S3). Further analysis of the 3 of 11 samples for which a kinase fusion was not detected in this targeted NGS assay is ongoing.

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Figure 2.

Kinase fusions identified in IMT by targeted sequencing. Starting with 37 FFPE IMT samples (26 ALK IHC positive and 11 ALK IHC negative), 33 tumors were evaluable with targeted NGS. A, genomic alterations identified in the 37 IMT tumor samples. Columns, samples; rows, genes. Red bars, ALK fusions; green bars, PDGFRβ fusions; blue bars, ROS1 fusions. The identified gene fusions were mutually exclusive. No other recurrent genomic alterations were identified by targeted NGS in these samples. B, schematic representation of the distinct ALK, PDGFRβ, and ROS1 fusions identified. In each case, the exons encompassed within each gene fusion partner are indicated.

Among the 22 ALK-positive cases analyzed, 20 harbored ALK gene fusions with various previously described 5′ gene fusion partners, including TPM3, TPM4, SEC31A, TFG, RANBP2, CLTC, and FN1 (Table 1; Fig. 2A and B). Of note, the FN1–ALK fusion detected in samples L26 and L29 harbors an atypical breakpoint within intron 18 of ALK. This fusion was initially missed by genomic DNA analysis (which targeted only intron 19 of ALK), but later identified with RNA sequencing. Novel ALK gene fusions were also detected, including LMNA–ALK (sample L12) and PRKAR1A–ALK (sample L35). The remaining 2 ALK IHC–positive cases were also negative for ALK kinase domain mutations and ALK amplification, suggesting a different mechanism of ALK expression in these tumor samples.