Homologous Recombination Deficiency: Exploiting the Fundamental Vulnerability of Ovarian Cancer

Abstract

Approximately 50% of epithelial ovarian cancers (EOC) exhibit defective DNA repair via homologous recombination (HR) due to genetic and epigenetic alterations of HR pathway genes. Defective HR is an important therapeutic target in EOC as exemplified by the efficacy of platinum analogues in this disease, as well as the advent of PARP inhibitors, which exhibit synthetic lethality when applied to HR-deficient cells. Here, we describe the genotypic and phenotypic characteristics of HR-deficient EOCs, discuss current and emerging approaches for targeting these tumors, and present challenges associated with these approaches, focusing on development and overcoming resistance.

Significance: Defective DNA repair via HR is a pivotal vulnerability of EOC, particularly of the high-grade serous histologic subtype. Targeting defective HR offers the unique opportunity of exploiting molecular differences between tumor and normal cells, thereby inducing cancer-specific synthetic lethality; the promise and challenges of these approaches in ovarian cancer are discussed in this review.

Figure 1. Cooperation of the Fanconi Anemia (FA) and BRCA1/2 proteins in a common ICL repair pathway

Stalling of replication forks on DNA ICLs induces lesion recognition by the FANCM–FAAP24–MHF1/2 complex and subsequent recruitment of the FA core complex, which in turn recruits the mono-ubiquitinated FANCD2-FANCI to the ICL region. FANCM also initiates checkpoint response, which phosphorylates multiple FA proteins. Ubiquitinated FANCD2 acts as a landing pad for recruiting several nucleases to coordinate nucleolytic incisions. Unhooking the DNA leaves the cross-linked nucleotides tethered to the complementary strand, which are bypassed by TLS polymerases. DNA incisions create a DSB, which is then repaired by HR. Downstream FA proteins such as BRCA1, BRCA2, and PALB2 promote RAD51-dependent strand invasion and resolution of recombinant intermediates.

Figure 2. Approximately 50% of high grade serous EOC have alterations in HR repair genes

Frequency of genetic and epigenetic changes involving HR pathway genes or non-HR pathway genes that modulate HR pathway. FA/BRCA pathway alterations have been experimentally found to be associated with HR deficiency (HR deficient tumors on the right). PTEN deletion and EMSY amplification have been reported to confer HR deficiency but data are evolving (Possibly HR deficient tumors on the bottom). Tumors with cyclin E1 (CCNE1) amplification are enriched for HR proficiency (HR proficient tumors on the left) and are associated with inferior outcome and response to platinum based chemotherapy. Among the remaining tumors, some may be HR deficient via miRNA upregulation or other unknown mechanisms.

Figure 3. Mechanisms of synthetic lethality between PARP1 or POLQ inhibition and HR deficiency

Inhibition of PARP1 activity in BER (I) and C-NHEJ (II) is toxic in HR-deficient cells and explains the observed PARPi-HR synthetic lethality. (III) PARPi’s induce PARP1 trapping on DNA lesions which is highly toxic in HR-deficient cells. (IV) PAR-mediated recruitment of the BARD1-BRCA1 complex is impaired by PARPi, resulting in the persistence of DNA lesions that are toxic to HR-deficient cells. (V) Inhibition of PARP1/Polθ-mediated Alt-EJ is toxic in HR-deficient cells. (VI.1) Under physiological conditions, Polθ expression is low and its impact on the repair of DNA double-strand breaks (DSB) is limited. Polθ limits RAD51-ssDNA filament assembly and subsequent HR activity; at the same time, it promotes alt-EJ through its polymerase domain.. (VI.2) Upon an HR defect, Polθ expression increases substantially and channels DSB repair into alt-EJ. (VI.3) In the case of an HR defect, inhibition of Polθ causes cell death through the persistence of toxic RAD51 intermediates and inhibition of alt-EJ.

Figure 4. Mechanisms of PARPi resistance in HR deficient cells

Known mechanisms conferring PARPi resistance in tumors cells and cross-resistance to cisplatin are indicated. An acquired genetic reversion of the original truncating mutations restores functional protein expression inducing PARPi resistance. Alternatively, acquired epigenetic reversion of BRCA1 promoter hypermethylation can restore normal BRCA1 protein expression levels conferring PARPi resistance. Hypomorphic alleles, such as BRCA1-C61G or BRCA1-Δ11, are unable to prevent tumor development but confer resistance to PARPi. Tumor cells may also become PARPi resistant through loss of PARP1 expression. Rescue of DNA end-resection in BRCA1-deficient tumors through loss of 53BP1 or REV7, increases HR capacity and confers resistance to PARPi. Loss of CHD4, a negative regulator of translesion synthesis (TLS), enhances DNA damage tolerance and induces PARPi resistance. Increased in P-glycoprotein (PGP)–mediated efflux, notably through ABCB1 upregulation (via fusion with SLC25A40) reduces intracellular PARPi concentrations inducing resistance. Desmoplastic stromal reaction is associated with reduced drug uptake conferring chemoresistance. (*: Although this mechanism has been described for cisplatin it might also apply for PARPi).

Figure 5. PARPi combinations against HR proficient tumors

Rationale behind use of specific PARPi combinations as a strategy against HR proficient tumors. Specifically, use of agents that inhibit HR such as CDK1- or HSP90 inhibitors may render HR proficient tumors into HR deficient and thus sensitize them to platinum or PARPis. The proposed mechanism of HR suppression and the clinical status of these PARPi combinations are presented in the right panel.