Homologous Recombination Deficiency Assays in Epithelial Ovarian Cancer: Current Status and Future Direction

Abstract

Epithelial ovarian cancer (EOC) patients are generally diagnosed at an advanced stage, usually relapse after initial treatments, which include debulking surgery and adjuvant platinum-based chemotherapy, and eventually have poor 5-year survival of less than 50%. In recent years, promising survival benefits from maintenance therapy with poly(ADP-ribose) polymerase (PARP) inhibitor (PARPi) has changed the management of EOC in newly diagnosed and recurrent disease. Identification of BRCA mutations and/or homologous recombination deficiency (HRD) is critical for selecting patients for PARPi treatment. However, the currently available HRD assays are not perfect predictors of the clinical response to PARPis in EOC patients. In this review, we introduce the concept of synthetic lethality, the rationale of using PARPi when HRD is present in tumor cells, the clinical trials of PARPi incorporating the HRD assays for EOC, the current HRD assays, and other HRD assays in development.

Keywords: PARP inhibitor; RAD51 foci formation; epithelial ovarian cancer; genomic scar; homologous recombination deficiency; mutational signatures.

Figure 1

Homologous recombination deficiency assays in epithelial ovarian cancer. Homologous recombination repair (HRR) is an important pathway for repairing DNA double-strand breaks (DSBs). In HRR, DSBs are detected and bound by BRCA1/2 and other HRR protein complexes to localize RAD51 to the exposed single-strand DNA, which then invades the DNA sequence on a homologous sister chromatid to synthesize the new DNA strand. Homologous recombination deficiency (HRD) occurs when HRR is impaired, especially by BRCA mutation. DSBs are repaired by other error-prone repair pathways, including nonhomologous end joining (NHEJ), which may cause point mutations, small insertions or deletions, and even large-scale chromosomal rearrangements in the repaired DNA strands. In the S phase of the cell cycle, the replication forks stop when encountering DNA damage to allow DNA repair before replication continues. After the damage is repaired, the stalled fork resumes replication. If the damage cannot be repaired, the stalled replication fork undergoes fork collapse, comprising fork degradation to cell apoptosis. In general, HRD assays have three main categories: germline or somatic mutations of genes in the HRR pathway, genomic scars or mutational signatures representing the patterns of genomic instability, and checking the functional status of HRR. Germline and somatic BRCA tests should be performed in all patients with newly diagnosed epithelial ovarian cancer (EOC). The current HRD assays based on SNP-based microarray technologies measure loss of heterozygosity (LOH), telomeric allelic imbalance (TAI), and large-scale state transitions (LSTs). The genomic instability score (GIS) combines the information derived from the LOH, TAI, and LST to represent the degree of genomic instability. Functional assays of HRR status include RAD51 foci assays and DNA fiber assays. The RAD51 subnuclear foci is generally present after DNA damage in normal cells, but HRD cells cannot form RAD51 foci. The DNA fiber assay was developed to evaluate the dynamics of the replication fork. Mutational signatures describe distinct patterns of nucleotide transitions with the surrounding nucleotide context from next-generation sequencing (NGS) data for human tumors. The developing comprehensive genomic scar assays include whole genome sequencing (WGS), whole exome sequencing (WES), and target gene panels consisting of variable sizes of selected cancer-susceptible genes. PARPi maintenance therapy benefits newly diagnosed advanced stage and platinum-sensitive recurrent EOC patients. The current genomic scar-based HRD assays can identify additional wild-type BRCA patients who may benefit from PARPi therapy. However, some issues need to be resolved. For tissue retrieval, multistep sampling to obtain archival and pretreatment tumor tissues over the clinical course has the potential to guide the therapy. For precision medicine, it is ideal to develop a comprehensive model to integrate clinical platinum sensitivity, genomic scar/mutational signatures, and functional tests to provide both past evidence of HRD and the current functional ability of HRR.