FGFR1 fusions as a novel molecular driver in rhabdomyosarcoma

Abstract

The wide application of RNA sequencing in clinical practice has allowed the discovery of novel fusion genes, which have contributed to a refined molecular classification of rhabdomyosarcoma (RMS). Most fusions in RMS result in aberrant transcription factors, such as PAX3/7::FOXO1 in alveolar RMS (ARMS) and fusions involving VGLL2 or NCOA2 in infantile spindle cell RMS. However, recurrent fusions driving oncogenic kinase activation have not been reported in RMS. Triggered by an index case of an unclassified RMS (overlapping features between ARMS and sclerosing RMS) with a novel FGFR1::ANK1 fusion, we reviewed our molecular files for cases harboring FGFR1-related fusions. One additional case with an FGFR1::TACC1 fusion was identified in a tumor resembling embryonal RMS (ERMS) with anaplasia, but with no pathogenic variants in TP53 or DICER1 on germline testing. Both cases occurred in males, aged 7 and 24, and in the pelvis. The 2nd case also harbored additional alterations, including somatic TP53 and TET2 mutations. Two additional RMS cases (one unclassified, one ERMS) with FGFR1 overexpression but lacking FGFR1 fusions were identified by RNA sequencing. These two cases and the FGFR1::TACC1-positive case clustered together with the ERMS group by RNAseq. This is the first report of RMS harboring recurrent FGFR1 fusions. However, it remains unclear if FGFR1 fusions define a novel subset of RMS or alternatively, whether this alteration can sporadically drive the pathogenesis of known RMS subtypes, such as ERMS. Additional larger series with integrated genomic and epigenetic datasets are needed for better subclassification, as the resulting oncogenic kinase activation underscores the potential for targeted therapy.

Keywords: ANK1; FGFR1; TACC1; fusion; rhabdomyosarcoma.

Figure 1:. Morphologic and immunohistochemical findings for case #1.

a. Low power view showing nested growth pattern separated by fibrous septa; b. intermediate power showing both solid nests and alveolar growth; c. higher magnification of the alveolar pattern showing picket-fence arrangement at the periphery and centrally discohesive cells; d. solid growth with high mitotic activity, ‘starry sky’ appearance, apoptotic bodies and karyorrhexis. IHC showing in e. diffuse staining for MyoD1 and multifocal staining for myogenin in f.

Figure 2:. Morphologic and immunohistochemical findings for case #2.

a. Morphologic appearance with short spindle cells in a background of myxoid stroma; b. evidence of nuclear pleomorphism, in keeping with anaplasia. Immunohistochemistry (IHC) for: c. desmin, showing diffuse expression; d. myogenin, heterogeneous expression and highlighting some pleomorphic nuclei; and e. MyoD1, heterogeneous expression; and f. P53, showing heterogeneous, strong nuclear staining. Scale bars: 50 um.

Figure 3:. Fusion transcripts and molecular expression data.

a. upper panel. Schematic representation of the t(8;8)(p11.21;p11.23) translocation between the FGFR1 (ENST00000425967) (red) and ANK1 (ENST00000265709) (blue) genes resulting in an in-frame fusion transcript between exon 18 of FGFR1 with exon 18 of ANK1. a. lower panel. Schematic representation of the t(8;8) (p11.22;p11.23) translocation between the FGFR1 (ENST00000447712) (red) and TACC1 (ENST00000317827) (blue) genes resulting in an in-frame fusion transcript between exon 17 of FGFR1 with exon 7 of TACC1. The predicted individual chimeric proteins are also depicted demonstrating the conserved protein domains within the fusion. b. By unsupervised UMAP clustering plots of RNA expression data, cases #2, 3, 4 grouped together in a tight cluster with the ERMS control group, separate from the ARMS group.