Mutational Landscape of Ovarian Adult Granulosa Cell Tumors from Whole Exome and Targeted TERT Promoter Sequencing

Abstract

Adult granulosa cell tumor (aGCT), the most common malignant ovarian sex cord-stromal tumor, is characterized by the forkhead transcription factor FOXL2 p.C134W somatic mutation. Late recurrences are relatively common but the molecular mechanisms of relapse or aggressive behavior are not known. The mutational landscape of FOXL2 p.C134W mutation-positive tumors ( = 22) was determined using whole-exome sequencing (WES). An average of 64 coding and essential splice-site variants were identified per tumor. As the TERT promoter region is poorly covered by the WES, targeted sequencing identified the TERT -124C>T promoter mutation as the only recurrent mutation (∼40% of cases). Pathway analysis suggested an association with DNA replication/repair and the EGFR family canonical pathways. Copy number analysis confirmed that gains of chromosomes 12 and 14 occur in approximately 30% of aGCT and loss of chromosome 22 occurs in approximately 40% of cases. In summary, exome-wide analysis of the mutational landscape of aGCT revealed that, except for the TERT promoter mutation, recurrence and/or aggressive behavior is not defined by activation or loss of specific genes. This study found that although aGCTs are defined by the presence of a common gene mutation, recurrence and/or aggressive behavior cannot be attributed to subsequent mutation of specific gene(s) or pathways; however, there is a high frequency of the TERT -124C>T promoter mutation, which is associated with more aggressive disease.

FOXL2 homozygous genotype and chromosome instability are associated with recurrence in adult granulosa cell tumors of the ovary

“…An array CGH analysis of FFPE samples of 40 surgically resected aGCTs confirmed that the most frequent CNV was loss of chromosome 22q; this had occurred in 52% of the primary tumors and 82% of the recurrent tumors. Similar values (ranging from 30 to 53%) have been reported in the literature [10,11,14,15].…”

“…There are also literature reports of trisomy 12, trisomy 14, and loss of chromosome 16, although these CNVs were less frequent in our study. This discrepancy might be due (at least in part) to the number of samples used in the literature studies (10, 15, and 21 samples in references [10,11,14], respectively) or by the high proportion of recurrent tumors in our series [15]. When calculating the GI for each sample, we could not determine a predictive cut-off.…”

Genomic analysis of recurrences and high‐grade forms of polymorphous adenocarcinoma

“…Our analyses revealed that, consistent with primary PACs, recurrent PACs showed the canonical alterations affecting PRKD genes, including PRKD1 hotspot E710D mutations or a PRKD2 rearrangement. The maintenance of the highly recurrent/pathognomonic genetic alteration that characterises these tumours in the recurrences and after the acquisition of high-grade histological features is consistent with the observations made in other tumour types driven by pathognomonic genetic alterations, [41][42][43][44] and is consistent with the notion that these alterations constitute drivers of the disease. For instance, in the progression of adenoid cystic carcinomas to high-grade tumours, the MYB-NFIB fusion gene is maintained 41 ; likewise, in the progression of granulosa cell tumours, the FOXL2 C134W mutation is conserved.…”

“…The maintenance of the highly recurrent/pathognomonic genetic alteration that characterises these tumours in the recurrences and after the acquisition of high‐grade histological features is consistent with the observations made in other tumour types driven by pathognomonic genetic alterations, and is consistent with the notion that these alterations constitute drivers of the disease. For instance, in the progression of adenoid cystic carcinomas to high‐grade tumours, the MYB–NFIB fusion gene is maintained; likewise, in the progression of granulosa cell tumours, the FOXL2 C134W mutation is conserved . Consistent with the notion that, in the progression of tumours driven by pathognomonic mutations, additional genetic alterations are acquired or subclonal genetic alterations present in minor subclones of the primary tumour are selected, we observed that the recurrent tumour RS1‐T2 acquired additional subclonal ERBB2 (V839M) and ZFHX3 (G3527dup) mutations.…”

“…For instance, in the progression of adenoid cystic carcinomas to high-grade tumours, the MYB-NFIB fusion gene is maintained 41 ; likewise, in the progression of granulosa cell tumours, the FOXL2 C134W mutation is conserved. [42][43][44] Consistent with the notion that, in the progression of tumours driven by pathognomonic mutations, additional genetic alterations are acquired or subclonal genetic alterations present in minor subclones of the primary tumour are selected, [41][42][43][44] we observed that the recurrent tumour RS1-T2 acquired additional subclonal ERBB2 (V839M) and ZFHX3 (G3527dup) mutations. Moreover, our analyses revealed that a minor subclone of the primary tumour (RS1-T1), which harboured the PIK3CA D350G hotspot mutation, became dominant in the recurrent tumour (RS1-T2; Figure 4), suggesting that recurrence of PACs may be driven by selection of pre-existing subclones.…”