FGFR2::TACC2 fusion as a novel KIT-independent mechanism of targeted therapy failure in a multidrug-resistant gastrointestinal stromal tumor

Abstract

Genetic alterations in FGF/FGFR pathway are infrequent in gastrointestinal stromal tumors (GIST), with rare cases of quadruple wildtype GISTs harboring FGFR1 gene fusions and mutations. Additionally, FGF/FGFR overexpression was shown to promote drug resistance to kinase inhibitors in GISTs. However, FGFR gene fusions have not been directly implicated as a mechanism of drug resistance in GISTs. Herein, we report a patient presenting with a primary small bowel spindle cell GIST and concurrent peritoneal and liver metastases displaying an imatinib-sensitive KIT exon 11 in-frame deletion. After an initial 9-month benefit to imatinib, the patient experienced intraabdominal peritoneal recurrence owing to secondary KIT exon 13 missense mutation and FGFR4 amplification. Despite several additional rounds of tyrosine kinase inhibitors (TKI), the patient's disease progressed after 2 years and presented with multiple peritoneal and liver metastases, including one pericolonic mass harboring secondary KIT exon 18 missense mutation, and a concurrent transverse colonic mass with a FGFR2::TACC2 fusion and AKT2 amplification. All tumors, including primary and recurrent masses, harbored an MGA c.7272 T > G (p.Y2424*) nonsense mutation and CDKN2A/CDKN2B/MTAP deletions. The transcolonic mass showed elevated mitotic count (18/10 HPF), as well as significant decrease in CD117 and DOG1 expression, in contrast to all the other resistant nodules that displayed diffuse and strong CD117 and DOG1 immunostaining. The FGFR2::TACC2 fusion resulted from a 742 kb intrachromosomal inversion at the chr10q26.3 locus, leading to a fusion between exons 1-17 of FGFR2 and exons 7-17 TACC2, which preserves the extracellular and protein tyrosine kinase domains of FGFR2. We present the first report of a multidrug-resistant GIST patient who developed an FGFR2 gene fusion as a secondary genetic event to the selective pressure of various TKIs. This case also highlights the heterogeneous escape mechanisms to targeted therapy across various tumor nodules, spanning from both KIT-dependent and KIT-independent off-target activation pathways.

Keywords: FGFR2; KIT; TKI; drug resistance; gastrointestinal stromal tumor; gene fusion.

Figure 1.. Clinical course.

Schematic diagram illustrating disease course, targeted therapeutic regimens, and disease progression. Numbers on horizontal arrow indicate number of months since initial presentation (month 0). Shaded colored rectangular boxes indicate groups of one or more tumors biopsied/resected concurrently that shared the same KIT driver mutation and secondary KIT mutations or secondary translocation.

Figure 2.. Morphologic and immunohistochemical findings (T1-T7).

A-E. The GISTs (T1-T5) were spindle cell type and composed of fascicles of uniform spindle cells with ovoid to fusiform nuclei, open chromatin, small nucleoli, and moderate amount of eosinophilic to amphophilic cytoplasm (200X). F-G. The pericolonic (T6) tumor showed more prominent epithelioid cytomorphology (F, 400X). The transverse colonic mass (T7) displayed prominent epithelioid cytomorphology with increased mitotic activity (G, 400X). A-G: Hematoxylin and eosin stain, 200X. There was extensive loss of CD117 immunoreactivity in T7 in comparison to the other tumors, including T6 (H, 200X).

Figure 3.. Primary and secondary genomic alterations identified by MSK-IMPACT.

Heatmap and Oncoprint showing primary and secondary KIT mutations, co-occurring mutations, copy number alterations, and fusion in tumors T1-T7. Only OncoKB mutations and copy number alterations are included.

Figure 4.. Schematic of predicted fusion proteins encoded by gene fusions.

The fusion is a result of an inversion of the DNA fragment between intron 17 of FGFR2 [NM_000141.4] at chr10:123243187 and intron 6 of TACC2 [NM_006997.3] at chr10:123985260, as detected by DNA-seq. This results in an RNA chimeric transcript fusing exons 1–17 of FGFR2 to exons 7–17 of TACC2 with the chromosomal breakpoint chr10:123243212(−)::chr10:123985881(+), as detected by RNA-seq. The chimeric protein products are predicted to be in-frame. Vertical dotted lines represent exon boundaries. Abbreviations: aa, amino acids.