Molecular profiling reveals novel therapeutic targets and clonal evolution in ovarian clear cell carcinoma

BMC Cancer. 2024 Nov 14;24(1):1403. doi: 10.1186/s12885-024-13125-5.

Abstract

Background: Ovarian clear cell carcinoma (OCCC) has a disproportionately high incidence among women in East Asia. Patients diagnosed with OCCC tend to experience worse clinical outcomes than those with high-grade serous carcinoma (HGSC) at advanced stages. The unfavorable prognosis of OCCC can be partly attributed to its frequent resistance to conventional chemotherapy. Within a precision medicine framework, we sought to provide a comprehensive molecular characterization of OCCC using whole-exome sequencing to uncover potential molecular targets that may inform novel therapeutic strategies.

Methods: We performed whole-exome sequencing analysis on tumor-normal paired samples from 102 OCCC patients. This comprehensive genomic characterization of a substantial cohort of OCCC specimens was coupled with an analysis of clonal progression.

Results: On analyzing 102 OCCC samples, ARID1A (67%) and PIK3CA (49%) emerged as the most frequently mutated driver genes. We identified tier 1 or 2 clinically actionable molecular targets in 40% of cases. This included DNA mismatch repair deficiency (n = 1), as well as BRCA2 (n = 1), PIK3CA (n = 36), KRASG12C (n = 1), and ATM (n = 4) mutations. Furthermore, 45% of OCCC samples displayed ARID1A biallelic loss. Interestingly, we identified previously unreported mutations in the 5' untranslated region of the TERT gene that harbored an adverse prognostic significance. Clock-like mutational processes and activated APOBECs were major drivers of somatic point mutations. Mutations arising from DNA mismatch repair deficiency were uncommon. Reconstruction of clonal evolution revealed that early genetic events likely driving tumorigenesis included mutations in the ARID1A, PIK3CA, TERT, KRAS, and TP53 genes.

Conclusions: Our study provides a comprehensive characterization of the genomic landscape and clonal evolution in OCCC within a substantial cohort. These findings unveil potentially actionable molecular alterations that could be leveraged to develop targeted therapies.

Keywords: TERT mutation; Clinical actionability; Clonal evolution; Mutational signature; Ovarian clear cell carcinoma; Whole-exome sequencing.

MeSH terms

  • Adenocarcinoma, Clear Cell* / genetics
  • Adenocarcinoma, Clear Cell* / pathology
  • Adult
  • Aged
  • Aged, 80 and over
  • Biomarkers, Tumor / genetics
  • Class I Phosphatidylinositol 3-Kinases / genetics
  • Clonal Evolution* / genetics
  • DNA-Binding Proteins / genetics
  • Exome Sequencing*
  • Female
  • Humans
  • Middle Aged
  • Molecular Targeted Therapy / methods
  • Mutation*
  • Ovarian Neoplasms* / genetics
  • Ovarian Neoplasms* / pathology
  • Prognosis
  • Transcription Factors / genetics

Substances

  • ARID1A protein, human
  • Class I Phosphatidylinositol 3-Kinases
  • Transcription Factors
  • DNA-Binding Proteins
  • PIK3CA protein, human
  • Biomarkers, Tumor