Whole-exome sequencing reveals rare genetic variations in ovarian granulosa cell tumor

Abstract

Ovarian granulosa cell tumor (OGCT) is a rare ovarian tumor that accounts for about 2-5% of all ovarian tumors. Despite the low grade of ovarian tumors, high and late recurrences are common in OGCT patients. Even though this tumor usually occurs in adult women with high estrogen levels, the cause of OGCT is still unknown. To screen genetic variants associated with OGCT, we collected normal and matched-tumor formalin-fixed paraffin-embedded (FFPE) from 11 OGCT patients and performed whole-exome sequencing (WES) using Illumina NovaSeq 6000. A total of 1,067,219 single nucleotide polymorphisms (SNPs) and 162,155 insertions/deletions (indels) were identified from 11 pairs of samples. Of these, we identified 44 tumor-specific SNPs in 22 genes and four tumor-specific indels in one gene that were common to 11 patients. We used three cancer databases (TCGA, COSMIC, and ICGC) to investigate genes associated with ovarian cancers. Nine genes (SEC22B, FEZ2, ANKRD36B, GYPA, MUC3A, PRSS3, NUTM2A, OR8U1, and KRTAP10-6) associated with ovarian cancers were found in all three databases. In addition, we identified seven rare variants with MAF ≤ 0.05 in two genes (PRSS3 and MUC3A). Of seven rare variants, five variants in MUC3A are potentially pathogenic. Furthermore, we conducted gene enrichment analysis of tumor-specific 417 genes in SNPs and 106 genes in indels using cytoscape and metascape. In GO analysis, these genes were highly enriched in "selective autophagy", and "regulation of anoikis". Taken together, we suggest that MUC3A is implicated in OGCT development, and MUC3A could be used as a potential biomarker for OGCT diagnosis.

FIGURE 1

Comparison criteria for OGCT rare variant with 11 patients. The normal and cancer tissue isolated from 11 OGCT patients were involved in identification of rare mutation using whole-exome sequencing. Green and red boxes indicate normal and matched-tumor samples, respectively. The scope was narrowed step by step, and the critical nonsynonymous variants closely related to OGCT were finally identified by evaluating the influence of phenotype. OGCT: Ovarian granulosa cell tumor.

FIGURE 2

Venn diagram of the three cancer-related databases (ICGC, TCGA, and COSMIC). The Venn diagram shows the genes harboring tumor-specific nonsynonymous variants matched with each database, including TCGA (yellow), ICGC (pink), and COSMIC (blue) cancer genome projects. Nine were included in the common set as commonly identified genes in all databases. COSMIC: The Catalogue Of Somatic Mutations In Cancer, ICGC: International Cancer Genome Consortium, TCGA: The Cancer Genome Atlas.

FIGURE 3

GO function enrichment analysis of candidate genes in OGCT patients. GO enrichment analysis of tumor-specific genes common to 11 patients was retrieved using Metascape software. Significantly (P<0.05) enriched GO terms in cellular components (A), molecular functions (B), and biological processes (C) branches are presented. Bar chart of enriched GO term clusters; color intensity statistical significance. OGCT: Ovarian granulosa cell tumor.

FIGURE 4

Gene ontology (GO) functional network analysis. Statistically significant enriched GO terms visualized by Cytoscape software add-on ClueGO plugin. p-value was adjusted by Benjamini-Hochberg false discovery rate. Node represents each statistically significant enriched GO term. The different size of nodes indicates the number of mapped genes in each GO term. In GO functional network analysis, the most significant and representative GO term is highlighy in bold and the offspring categories are connected with gray title.