Differences in Expression of Key DNA Damage Repair Genes after Epigenetic-Induced BRCAness Dictate Synthetic Lethality with PARP1 Inhibition

Abstract

The triple-negative breast cancer (TNBC) subtype represents a cancer that is highly aggressive with poor patient outcome. Current preclinical success has been gained through synthetic lethality, targeting genome instability with PARP inhibition in breast cancer cells that harbor silencing of the homologous recombination (HR) pathway. Histone deacetylase inhibitors (HDACi) are a class of drugs that mediate epigenetic changes in expression of HR pathway genes. Here, we compare the activity of the pan-HDAC inhibitor suberoylanilide hydroxamic acid (SAHA), the class I/IIa HDAC inhibitor valproic acid (VPA), and the HDAC1/2-specific inhibitor romidepsin (ROMI) for their capability to regulate DNA damage repair gene expression and in sensitizing TNBC to PARPi. We found that two of the HDACis tested, SAHA and ROMI, but not VPA, indeed inhibit HR repair and that RAD51, BARD1, and FANCD2 represent key proteins whose inhibition is required for HDACi-mediated therapy with PARP inhibition in TNBC. We also observed that restoration of BRCA1 function stabilizes the genome compared with mutant BRCA1 that results in enhanced polyploid population after combination treatment with HDACi and PARPi. Furthermore, we found that overexpression of the key HR protein RAD51 represents a mechanism for this resistance, promoting aberrant repair and the enhanced polyploidy observed. These findings highlight the key components of HR in guiding synthetic lethality with PARP inhibition and support the rationale for utilizing the novel combination of HDACi and PARPi against TNBC in the clinical setting.

Candidate synthetic lethality partners to PARP inhibitors in the treatment of ovarian clear cell cancer

“…Notch signaling controls cell processes, including cancer cell and cancer stem cell fate determination. NOTCH2 expression is specifically downregulated in CCC (66). Notch signaling and ERBB2 appear to be mutually exclusive, demonstrating that Notch signaling is also a potential synthetic lethal partner of ERBB2 (67).…”

Quinazolinone derivatives as inhibitors of homologous recombinase RAD51

“…We showed correlation of RAD51 expression and IC 50 in these cell lines. In contrast, high RAD51 expressing HCC1937 increases NHEJ activity when RAD51 is inhibited 19 . We observed a slightly higher IC 50 in this cell line.…”

“…Varying spacer length in compound 17, with one methylene unit shorter (15) or longer (16), did not improve activity and indicated optimal positioning of the aromatic ring in 17. Of the substituted benzyl series, fluoro (18)(19)(20), nitro (21-22) and p-hydroxy (23) analogues showed comparable activity. A polar substrate, such as pacetamidomethyl (24) and carboxylic acid (25-26), were detrimental, while 3,4-dichloro (27) conferred a slight improvement.…”

“…Compared with B02 for growth inhibition in a panel of six TNBC cell lines with varying levels of RAD51 expression ( Figure 5), compound 17 was more potent than B02 (IC 50 ≤ 13.7 µM vs ≤ 89.1 µM) across all TNBC cell lines assessed. The differing sensitivity of TNBC cell lines to RAD51 inhibition is likely influenced by specific mutations contained by each cell line and compensatory activity of alternate DNA repair pathways in response to RAD51 inhibition 19 . We have previously shown that high RAD51 expressing MDA-MB-231 and MDA-MB-436 cells are almost entirely reliant on the HR pathway and show minimal non-homologous end joining (NHEJ) activity when HR is disrupted by RAD51 inhibition.…”

Conceptual frameworks of synthetic lethality in clear cell carcinoma of the ovary (Review)

“…In a similar manner to PARP1 inhibitors, the suppression of RAD52 reduces homologous recombination and results in synthetic lethality in cells deficient in BRCA1/2 or associated proteins (including partner and localizer of BRCA2, RAD51B/C/D and XRCC2/3), whilst sparing normal cells (44). RAD51/RAD54B and PARP1 have been reported to function as synthetic lethal interactors, where it was thus revealed that PARP1 may be a novel candidate drug target in RAD51/RAD54B-deficient cells (45). Chromatin remodeling proteins are often contained within multiprotein complexes (43).…”