P05.03.B METHYLOME PROFILING OF GLIOBLASTOMAS WITH FGFR3/TACC3 FUSION

Abstract

Abstract BACKGROUND Glioblastomas (GBMs) with the FGFR3-TACC3 (F3T3) gene fusion have histological, molecular, metabolic, and clinicoradiological characteristics. They have a better prognosis compared to other GBMs. Recent findings suggest that methylome profiling could further stratify these patients identifying a subgroup (defined as “outlier” F3T3+ GBMs, or GBM-F3T3-O) with a methylation profile resembling gangliogliomas (GGs), low-grade histological appearance, and a better outcome. MATERIAL AND METHODS We performed DNA methylation profiling (Infinium MethylationEPIC Array v1.0) of 32 adult diffuse gliomas with FGFR3 gene fusions (30 FGFR3-TACC3, one FGFR3-ACLY, and one FGFR3-MYO18A), plus two paired samples of a diffuse glioma with two distinct contingents (one with positive FGFR3 staining and FGFR3-TACC3 gene fusion, the other with intense EGFR staining and EGFR gene amplification). All cases corresponded to “glioblastoma, IDH-wildtype” according to the WHO CNS5. Methylation data were submitted to the DFKZ brain tumor classifier (molecularneuropathology.org), versions 11b4 and 12.5 and to dimensionality reduction with t-distributed stochastic neighbor embedding (tSNE). Copy-number variation (CNV) estimation based on conumee package was obtained from DFKZ website. RESULTS With the brain tumor classifier v11b4, most cases (26/34, 76%) were classified as methylation class (MC) GBM (17/26 with a significant score ≥0.9). Out of them, 23/26 (88%) were significantly (score ≥0.5) classified in the “GBM, mesenchymal” (16/26, 62%) or in the “GBM, RTK II” methylation families (7/26, 27%). With the classifier v12.5, again most tumors were classified as “GBM, mesenchymal” (18/34, 53%) or “GBM, RTK II” (9/34, 26%), of which twelve (12/34, 35%) with a score ≥0.9. Two were classifed as GG (score 0.69 and 0.39), both having “GBM, mesenchymal” as a second hit (score 0.19 and 0.33, respectively). Five had GG as a second hit, although with low scores (range <0.01-0.25). After tSNE dimensionality reduction of our and literature cases, most tumors clustered together with other GBM, mesenchymal and GBM, RTK II cases. Only two cases fell within a distinct cluster corresponding to GBM-F3T3-O tumors from the literature. These included two histologically defined GBMs with a survival of 26 and 100 months. Recurrent inferred CNV included chromosome (chr) 7 gain (96%) and chr10 loss (85%), followed by chr20 gain (46%), chr22q loss (46%), and chr19 gain (33%). The presence of chr19 gain (alone or associated with chr20 gain) was associated with increased survival (p=0.01). CONCLUSION Glioblastomas with FGFR3 fusions (mostly F3T3) have an epigenomic profile close to other mesenchymal and RTK II GBMs. Methylation analysis identifies methylation (GBM-F3T3-O) and CNV (chr19 gain) profiles associated with better survival.