Suppression of BRCA1 sensitizes cells to proteasome inhibitors

BRCA1 is a multifunctional protein best known for its role in DNA repair and association with breast and ovarian cancers. To uncover novel biologically significant molecular functions of BRCA1, we tested a panel of 198 approved and experimental drugs to inhibit growth of MDA-MB-231 breast cancer cells depleted for BRCA1 by siRNA. 26S proteasome inhibitors bortezomib and carfilzomib emerged as a new class of selective BRCA1-targeting agents. The effect was confirmed in HeLa and U2OS cancer cell lines using two independent siRNAs, and in mouse embryonic stem (ES) cells with inducible deletion of Brca1. Bortezomib treatment did not cause any increase in nuclear foci containing phosphorylated histone H2AX, and knockdown of BRCA2 did not entail sensitivity to bortezomib, suggesting that the DNA repair function of BRCA1 may not be directly involved. We found that a toxic effect of bortezomib on BRCA1-depleted cells is mostly due to deregulated cell cycle checkpoints mediated by RB1-E2F pathway and 53BP1. Similar to BRCA1, depletion of RB1 also conferred sensitivity to bortezomib, whereas suppression of E2F1 or 53BP1 together with BRCA1 reduced induction of apoptosis after bortezomib treatment. A gene expression microarray study identified additional genes activated by bortezomib treatment only in the context of inactivation of BRCA1 including a critical involvement of the ERN1-mediated unfolded protein response. Our data indicate that BRCA1 has a novel molecular function affecting cell cycle checkpoints in a manner dependent on the 26S proteasome activity.BRCA1 is an important tumor suppressor gene whose germ-line or somatic inactivation is implicated in a significant number of breast and ovarian cancers.¹ Human BRCA1 encodes an 1863 amino-acid-long protein with a RING-finger domain at the N terminus and two BRCT domains located at the C terminus.^{2, 3} BRCT domains mediate interaction with phosphorylated proteins such as Abraxas, BACH1, CtIP and others involved in sensing DNA damage and assembly of the BRCA1-associated genome surveillance complex at sites of DNA breaks.⁴ The RING domain constitutively interacts with the BRCA1-associated RING domain protein (BARD1), forming a heterodimer having an E3 ubiquitin ligase activity.⁵ Ubiquitination of target proteins, including cell cycle or DNA repair-regulating proteins (e.g. CtIP (RBBP8), nucleophosmin (NPM1, B23), claspin (CLSPN) and others), occurs either at Lys48 residue of the ubiquitin leading to the 26S proteasome-mediated degradation of target proteins or at Lys6 or Lys63 having a trafficking and signaling role.⁶ A serine cluster coiled-coil domain spanning amino acids 1280–1524 contains multiple phosphorylation sites for ATM and ATR kinases activated by DNA damage.⁷ The same region also binds PALB2 protein linking BRCA1 to another major breast cancer predisposition gene BRCA2.⁸The most prominent function of BRCA1 is associated with its role in repair of DNA damage, particularly of double-stranded DNA breaks (DSBs), one of the most severe types of DNA lesions.⁹ BRCA1 is recruited to sites of DNA damage via a series of phosphorylation and ubiquitination events, where it serves as a binding scaffold for other DNA repair proteins,^{10, 11} ubiquitinates claspin, cyclin B and CDC25C, triggering cell cycle arrest to allow time for repair,¹² and facilitates BRCA2-mediated loading of RAD51 recombinase to enable the homologous recombination (HR) mechanism of DNA repair.⁹ In addition, BRCA1 may contribute to maintaining genome integrity by stabilizing the heterochromatin structure via ubiquitination of histone H2A.¹³ BRCA1 is also required for centrosome-dependent and -independent mitotic spindle formation, providing another route, by which loss of BRCA1 could promote chromosome instability and tumor formation.^{14, 15}Such a critical role of BRCA1 in DNA repair is exploited therapeutically. DNA-damaging agents, particularly DNA-crosslinking agents such as platinum-containing drugs, or ionizing radiation lead to the accumulation of DNA breaks requiring HR for repair and, therefore, are particularly toxic to BRCA1-deficient tumor cells.¹⁶ Pharmacological inhibitors of poly-(ADP-ribose) polymerases (PARPs) selectively kill BRCA1-deficient cells owing to defective HR, functioning as a back-up repair mechanism in the absence of the PARP-mediated repair of single-stranded DNA breaks.¹⁷ However, multiple mechanisms allow BRCA1-deficient cells to develop resistance to these drugs including elevated expression of the efflux transporters pumping the drugs out of the cell, secondary mutations restoring a functional BRCA1 protein and loss of 53BP1 protein, which counteracts BRCA1 and HR by blocking resection of DNA ends around the breaks (see Lord and Ashworth¹⁸ for the latest review). Therefore, additional efforts to identify small-molecule agents especially targeting BRCA1 functions unrelated to its DNA repair function are warranted.Here we performed a high-throughput chemical screen of BRCA1-depleted MDA-MB-231 cells using a collection of 198 US Food and Drug Administration (FDA)-approved and experimental drugs. We found that 26S proteasome inhibitors were more toxic to BRCA1 knockdown than control cells. Response of BRCA1-deficient cells to bortezomib involved deregulation of the RB1-mediated cell cycle checkpoint, activation of a noncanonical ERN1-mediated unfolded protein response and 53BP1-related G2/M cell cycle arrest. Our results reveal novel aspects of BRCA1 function unrelated to DNA repair.