Next-Generation Sequencing Reveals a Very Low Prevalence of Deleterious Mutations of Homologous Recombination Repair Genes and Homologous Recombination Deficiency in Ovarian Clear Cell Carcinoma

Abstract

Ovarian clear cell carcinoma (OCCC) is aggressive and drug-resistant. The prevalence of homologous recombination repair (HRR) gene mutations and homologous recombination deficiency (HRD) remains largely unknown. It is also not clear whether the commonly used molecular-based classification for endometrial carcinoma (EC) is potentially applicable in OCCC. In this study, surgically resected samples were collected from 44 patients with OCCC. Genomic alterations were determined using next-generation sequencing. HRD was estimated by genomic instability. Of 44 patients with OCCC, two (4.5%) harbored likely pathogenic mutations in HRR genes. Notably, no pathogenic or likely pathogenic mutations were found in BRCA1/2. A total of 24 variants of uncertain significance (VUS) in HRR-related genes occurred in 18 (40.9%) patients. HRD was observed in only one case (2.3%). In addition, TP53 mutation and microsatellite instability-high (MSI-H) were identified in three patients (6.8%) and in one patient (2.3%), respectively. TP53 mutation was significantly associated with disease-free survival and overall survival. No POLE mutations were found. In conclusion, our results revealed a very low prevalence of HRR gene mutations and HRD in OCCC. Moreover, TP53 mutations and MSI-H are uncommon, while POLE mutations are extremely rare in OCCC. Our findings indicate that the evaluation of HRR gene mutations, HRD status, POLE mutations, and MSI-H may have limited clinical significance for OCCC treatment and prognostic stratification.

Keywords: homologous recombination deficiency; homologous recombination repair gene; molecular classification; next-generation sequencing; ovarian clear cell carcinoma.

Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Copyright © 2022 Liu, Zhang, Chen, Pang, Wu and Liang.

Figures

Figure 1

Variants of HRR-related genes and other genes in patients with OCCC. Mutational profile of both pathogenic/likely pathogenic variants and VUS (A) and pathogenic/likely pathogenic variants (B). Each column represents one case, and rows represent an individual gene. The patients are presented in decreasing order based on the number of patients in whom a gene is mutated. The right panel indicates the frequency of gene mutations. Mutation types are indicated by different colors. Gray denotes an absence of mutations. Only variants with a VAF of >3% are shown. Clinicopathological features including age at diagnosis, FIGO stage, tumor size, neoadjuvant therapy, and tumor recurrence are annotated below the oncoprint.

Figure 2

Relationship between TP53 mutation status and patients’ prognosis and HRD status in OCCC patients. (A–C) Immunohistochemistry was performed on tumors with TP53 mutation, showing intense and diffuse p53 immunostaining for likely pathogenic missense mutation (A), completely absent p53 immunostaining for splicing mutation (B), and rare p53-positive cells with VUS (C). (D, E) Kaplan–Meier survival curves based on TP53 immunohistochemistry results. Patients with TP53 mutations had poor DFS (p = 0.0101) (D) and OS (p = 0.0074) (E). p-values are calculated using the log-rank test. (F) HRD score in patients with OCCC. The columns and rows represent individual patient and HRD scores, respectively.

Figure 3

TP53 mutation, POLE mutation, and MSI status in patients with OCCC. (A) Tumors were stratified into three groups: TP53-wild-type subgroup, TP53-mutant subgroup and microsatellite instability-high (MSI)-H subgroup. The MSI-H case showed intact expression of MLH1 (B) and PMS2 (C), but loss of MSH2 (D) or MSH6 (E) expression. Positively staining stromal cells were seen in the background as an internal control. (F) Lynch syndrome was confirmed by the presence of MSH2 pathogenic germline variant in the MSI-H patient.