BRCA1 Depletion Research Articles

Quantitation of DNA double-strand break resection intermediates in human cells

5′ strand resection at DNA double strand breaks (DSBs) is critical for homologous recombination (HR) and genomic stability. Here we develop a novel method to quantitatively measure single-stranded DNA intermediates in human cells and find that the 5′ strand at endonuclease-generated break sites is resected up to 3.5 kb in a cell cycle–dependent manner. Depletion of CtIP, Mre11, Exo1 or SOSS1 blocks resection, while depletion of 53BP1, Ku or DNA-dependent protein kinase catalytic subunit leads to increased resection as measured by this method. While 53BP1 negatively regulates DNA end processing, depletion of Brca1 does not, suggesting that the role of Brca1 in HR is primarily to promote Rad51 filament formation, not to regulate end resection.

Abstract 1011: Induction of ‘BRCAness’ by treatment with histone deacetylase inhibitors sensitizes human triple negative breast cancer cells to PARP inhibitor and cisplatinum.

Abstract During DNA damage response (DDR), stability and activity of ATR and CHK1 is essential for the cell cycle arrest and subsequent DNA repair through BRCA1-regulated homologous recombination (HR). We have previously reported that ATR and CHK1 are hsp90 client proteins and treatment with hsp90 inhibitor sensitizes cancer cells to DNA damage. In the present studies, we determined that treatment with pan-HDAC inhibitors vorinostat (VS) and panobinostat (PS) induced hyper-acetylation and inhibition of chaperone function of nuclear hsp90, leading to proteasomal degradation and depletion of ATR, CHK1 and BRCA1. This led to inhibition of DDR and DNA repair following ionizing radiation (IR) through destabilization of ATR-CHK1 and BRCA1 proteins. Specific siRNA-mediated knockdown of HDAC3 but not of HDAC1 or HDAC2 also induced hyper-acetylation of the nuclear hsp90 and depletion of ATR and CHK1, indicating that among the class I HDACs, HDAC3 is the deacetylase for the nuclear hsp90. We next determined whether, by depleting DDR proteins and BRCA1 and inducing ‘BRCAness’, treatment with VS would sensitize the triple negative breast cancer (TNBC) SUM159PT and MB-231 (lacking BRCA1 mutation) as well as BRCA1 mutant HCC1937 cells to the PARP inhibitor ABT888 (veliparib). Indeed, combined treatment with VS or PS and ABT888 (10 to 20 μM) for 48 hours synergistically induced apoptosis (combination indices (CI) by isobologram analysis being < 1.0) of TNBC cells with (HCC1937) or without BRCA1 mutation (MB-231 and SUM159PT cells). As compared to treatment with each agent alone, co-treatment with VS and ABT888 also induced significantly more DNA strand breaks, as demonstrated by higher γ-H2AX levels. Combined treatment also induced markedly greater tail moment, as determined by the comet assay that evaluates the SYBR® Green-stained DNA tails by fluorescent microscopy. Co-treatment with VS and ABT888 also induced more BH3 domain-only pro-death protein BIM, while knockdown of BIM by shRNA significantly reduced the apoptosis induced by co-treatment with VS and ABT888. It is noteworthy that treatment with VS also sensitized the TNBC cells to cisplatin (2.0 to 10 μM)-induced apoptosis. Moreover, co-treatment with VS and ciplatin synergistically induced apoptosis of TNBC cells (CIs < 1.0). These findings indicate that treatment with pan-HDAC inhibitors VS or PS creates ‘BRCAness’, and in combination with a PARP inhibitor or cisplatin synergistically induces apoptosis in human TNBC cells. These findings support a compelling rationale to confirm whether the combination of VS or PS with ABT888 and cisplatin would be a highly active treatment of human TNBC, irrespective of its expression of mutant BRCA1. Citation Format: Warren C. Fiskus, Rekha Rao, Soumyasri Das Gupta, Lata Chauhan, Kapil N. Bhalla. Induction of ‘BRCAness’ by treatment with histone deacetylase inhibitors sensitizes human triple negative breast cancer cells to PARP inhibitor and cisplatinum. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1011. doi:10.1158/1538-7445.AM2013-1011

Abstract S3-7: Treatment with Histone Deacetylase Inhibitors Creates ‘BRCAness’ and Sensitizes Human Triple Negative Breast Cancer Cells to PARP Inhibitors and Cisplatin

Abstract DNA damage induces DNA damage response (DDR), which regulates cell cycle transit, DNA repair and apoptosis. During DDR, stability and activity of ATR and CHK1 is essential for the cell cycle arrest and subsequent DNA repair through homologous recombination (HR) in which BRCA1 protein is involved. We have previously reported that ATR, CHK1 and BRCA1 are hsp90 client proteins and treatment with hsp90 inhibitor sensitizes cancer cells to DNA damage. We have also previously shown that treatment with pan-HDAC inhibitors, including vorinostat (VS) and panobinostat (PS), induces hyperacetylation of hsp90, thereby inhibiting its chaperone function. In the present studies we determined that treatment with VS or PS induced hyper-acetylation and inhibition of chaperone function of nuclear hsp90, leading to proteasomal degradation and depletion of ATR, CHK1 and BRCA1. This led to inhibition of DDR and DNA repair following ionizing radiation (IR) through destabilization of ATR-CHK1 and BRCA1 proteins. Based on this, we hypothesized that treatment with VS or PS would create ‘BRCAness’ in breast cancer cells. Specific siRNA-mediated knockdown of HDAC3 but not of HDAC1 or HDAC2 also induced hyper-acetylation of the nuclear hsp90 and depletion of ATR and CHK1, indicating that among the class I HDACs, HDAC3 is the deacetylase for the nuclear hsp90. We next determined whether, by depleting DDR proteins and BRCA1 and inducing ‘BRCAness’, treatment with VS would sensitize the triple negative breast cancer (TNBC) SUM59PT, MB-231 and HCC1937 cells to the PARP inhibitor ABT888 (veliparib). Indeed, combined treatment with VS or PS with ABT888 (10 to 20 μM) for 48 hours synergistically induced apoptosis (Combination indices by isobologram analysis being < 1.0) of TNBC cells with (HCC1937) or without BRCA1 mutation (MB-231 and SUM159PT cells). As compared to treatment with each agent alone, co-treatment with VS and ABT888 also induced significantly more DNA strand breaks, as demonstrated by higher γ-H2AX levels. Combined treatment also induced markedly greater tail moment, as determined by the Comet assay that evaluates the SYBR green-stained DNA tails by fluorescent microscopy. Co-treatment with VS and ABT888 also induced more BH3 domain-only pro-death protein BIM, while knock-down of BIM by shRNA significantly reduced the apoptosis induced by co-treatment with VS and ABT888. It is noteworthy that treatment with VS also sensitized the TNBC cells to cisplatin (2.0 to 10 μM)-induced apoptosis. Moreover, co-treatment with VS and ciplatin synergistically induced apoptosis of TNBC cells (CIs < 1.0). These findings indicate that treatment with pan-HDAC inhibitors VS or PS creates BRCAness, and in combination with a PARP inhibitor or cisplatin synergistically induces apoptosis in human TNBC cells. These findings support a compelling rationale to confirm whether the combination of VS or PS with ABT888 and cisplatin would be a highly active treatment in the in vivo models of human TNBC cells, irrespective of their expression of mutant BRCA1. Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr S3-7.

Targeting BRCA1 localization to augment breast tumor sensitivity to poly(ADP-Ribose) polymerase inhibition.

PARP inhibitors have gained recent attention due to their highly selective killing of BRCA1/2-mutated and DNA double-strand break (DSB) repair-deficient tumors. Unfortunately, the majority of sporadic breast cancers carry wild-type BRCA1/2 and are proficient in DSB repair. We and others have shown that BRCA1 is a nuclear/cytoplasm shuttling protein that is transiently exported from the nucleus to the cytosol upon various stimuli. Thus, we hypothesized that depletion of nuclear BRCA1 would compromise DSB repair and subsequently render sporadic tumors susceptible to PARP inhibition. Indeed, in human sporadic breast cancer cells with functional BRCA1 and proficient DSB repair, a transient nuclear depletion of BRCA1 and subsequent homologous recombination repair deficit was induced with either truncated BRCA1 or irradiation. This rendered these human sporadic breast cancer cells susceptible to PARP inhibition. These observations were confirmed genetically using mislocated BRCA1 mutants as well as in vivo in mice bearing breast tumor xenografts. These data support the potential strategy of targeting BRCA1 location to convert BRCA1-proficient sporadic tumors to be susceptible to the synthetic lethal combination with PARP inhibitors.

Nucleolar exit of RNF8 and BRCA1 in response to DNA damage

The induction of DNA double-strand breaks (DSBs) elicits a plethora of responses that redirect many cellular functions to the vital task of repairing the injury, collectively known as the DNA damage response (DDR). We have found that, in the absence of DNA damage, the DSB repair factors RNF8 and BRCA1 are associated with the nucleolus. Shortly after exposure of cells to γ-radiation, RNF8 and BRCA1 translocated from the nucleolus to damage foci, a traffic that was reverted several hours after the damage. RNF8 interacted through its FHA domain with the ribosomal protein RPSA, and knockdown of RPSA caused a depletion of nucleolar RNF8 and BRCA1, suggesting that the interaction of RNF8 with RPSA is critical for the nucleolar localization of these DDR factors. Knockdown of RPSA or RNF8 impaired bulk protein translation, as did γ-irradiation, the latter being partially countered by overexpression of exogenous RNF8. Our results suggest that RNF8 and BRCA1 are anchored to the nucleolus through reversible interactions with RPSA and that, in addition to its known functions in DDR, RNF8 may play a role in protein synthesis, possibly linking the nucleolar exit of this factor to the attenuation of protein synthesis in response to DNA damage.

Abstract 1312: ATM transcriptional regulation mediated by BRCA1/E2F1 axis controls DNA damage response in prostate cancer

Abstract Prostate cancer (PCa) is the second leading cause of cancer-related death affecting men worldwide. Chromosomal instability is a key feature in PCa progression. Using genome-wide screen for factor binding in combination with expression profiles, we previously reported BRCA1 binding to several promoters involved in cell cycle regulation and DNA damage response. We also generated a BRCA1 depleted xenograft model in order to study the role of BRCA1 role in DNA damage response in vivo. We demonstrated that BRCA1 expression status plays a central role in doxorubicin resistance in PCa. One of the BRCA1 targets that emerged from these analyses was ATM (ataxia telangiectasia mutated).Although it is well accepted that the kinase protein ATM is a pivotal mediator in genotoxic stress, it is unknown if its transcriptional regulation plays a role in the DNA damage response. Our goal was to investigate ATM transcription regulation in PCa under different genotoxic insults. Here we exposed PC3 cells to different genotoxic agents and the ATM promoter activity was determined by a luciferase reporter assay. We found that the topoisomerase II inhibitors doxorubicin and mitoxantrone repressed ATM transcription; however etoposide and methotrexate did not show significant changes. Using BRCA1-overexpressing PC3 cell lines, we found that BRCA1 increases ATM mRNA and promoter activity. Accordingly, BRCA1 depletion by shRNA abolished ATM transcription induction. Furthermore, BRCT domain loss (BRCA1ΔBRCT) impaired the ability of BRCA1 to regulate ATM promoter activity, strongly suggesting that BRCT domain is essential for ATM regulation. Xenograft tumors generated by BRCA1 depleted PC3 cells injected in nu/nu mice demonstrated that BRCA1 knock-down abolished ATM transcriptional induction. Considering ATM phosphorylates BRCA1, we investigated BRCA's ability to activate ATM promoter after inhibition of the ATM kinase activity by KU55933. BRCA1 overexpressing PC3 cells exposed to KU55933 showed significant decreased ATM promoter activity compared to control cells suggesting ATM regulation by BRCA1 is not mediated by ATM kinase activity. In addition, we performed BRCA1-ChIP-qPCR using primers spanning every 500bp along ATM promoter; we found that BRCA1 binds at 500bp upstream of the ATM transcription start site which was disrupted by doxorubicin. We identified one E2F1 putative DNA binding site at this region suggesting that BRCA1 association to ATM promoter could be E2F1 mediated. Finally, E2F1 transfection in PC3 cells significant decreased ATM transcription which was impaired by E2F1 dominant negative (E1-363). In summary, BRCA1/E2F1 complex binds and induces ATM transcription. After genotoxic stress BRCA1 protein is displaced from the ATM promoter and E2F1 downregulates ATM transcription. Thus, BRCA1/E2F1 axis controls DNA damage response in PCa through ATM transcriptional regulation. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1312. doi:1538-7445.AM2012-1312

Dynamic Coregulatory Complex Containing BRCA1, E2F1 and CtIP Controls ATM Transcription

Chromosomal instability is a key feature in cancer progression. Recently we have reported that BRCA1 regulates the transcription of several genes in prostate cancer, including ATM (ataxia telangiectasia mutated). Although it is well accepted that ATM is a pivotal mediator in genotoxic stress, it is unknown whether ATM transcription is regulated during the molecular response to DNA damage. Here we investigate ATM transcription regulation in human prostate tumor PC3 cell line. We have found that doxorubicin and mitoxantrone repress ATM transcription in PC3 cells but etoposide and methotrexate do not affect ATM expression. We have demonstrated that BRCA1 binds to ATM promoter and after doxorubicin exposure, it is released. BRCA1 overexpression increases ATM transcription and this enhancement is abolished by BRCA1 depletion. Moreover, BRCA1-BRCT domain loss impairs the ability of BRCA1 to regulate ATM promoter activity, strongly suggesting that BRCT domain is essential for ATM regulation by BRCA1. BRCA1-overexpressing PC3 cells exposed to KU55933 ATM kinase inhibitor showed significant decreased ATM promoter activity compared to untreated cells, suggesting that ATM transcriptional regulation by BRCA1 is partially mediated by the ATM kinase activity. In addition, we have demonstrated E2F1 binding to ATM promoter before and after doxorubicin exposure. E2F1 overexpression diminishes ATM transcription after doxorubicin exposure which is impaired by E2F1 dominant negative mutants. Finally, the co-regulator of transcription CtIP increases ATM transcription. CtIP increases ATM transcription. Altogether, BRCA1/E2F1/CtIP binding to ATM promoter activates ATM transcription. Doxorubicin exposure releases BRCA1 and CtIP from ATM promoter still keeping E2F1 recruited and, in turn, represses ATM expression.

A dual role of BRCA1 in two distinct homologous recombination mediated repair in response to replication arrest

Homologous recombination (HR) is a major mechanism utilized to repair blockage of DNA replication forks. Here, we report that a sister chromatid exchange (SCE) generated by crossover-associated HR efficiently occurs in response to replication fork stalling before any measurable DNA double-strand breaks (DSBs). Interestingly, SCE produced by replication fork collapse following DNA DSBs creation is specifically suppressed by ATR, a central regulator of the replication checkpoint. BRCA1 depletion leads to decreased RPA2 phosphorylation (RPA2-P) following replication fork stalling but has no obvious effect on RPA2-P following replication fork collapse. Importantly, we found that BRCA1 promotes RAD51 recruitment and SCE induced by replication fork stalling independent of ATR. In contrast, BRCA1 depletion leads to a more profound defect in RAD51 recruitment and SCE induced by replication fork collapse when ATR is depleted. We concluded that BRCA1 plays a dual role in two distinct HR-mediated repair upon replication fork stalling and collapse. Our data established a molecular basis for the observation that defective BRCA1 leads to a high sensitivity to agents that cause replication blocks without being associated with DSBs, and also implicate a novel mechanism by which loss of cell cycle checkpoints promotes BRCA1-associated tumorigenesis via enhancing HR defect resulting from BRCA1 deficiency.

Profiling of the BRCA1 transcriptome through microarray and ChIP-chip analysis.

A role for BRCA1 in the direct and indirect regulation of transcription is well established. However, a comprehensive view of the degree to which BRCA1 impacts transcriptional regulation on a genome-wide level has not been defined. We performed genome-wide expression profiling and ChIP-chip analysis, comparison of which revealed that although BRCA1 depletion results in transcriptional changes in 1294 genes, only 44 of these are promoter bound by BRCA1. However, 27% of these transcripts were linked to transcriptional regulation possibly explaining the large number of indirect transcriptional changes observed by microarray analysis. We show that no specific consensus sequence exists for BRCA1 DNA binding but rather demonstrate the presence of a number of known and novel transcription factor (TF)- binding sites commonly found on BRCA1 bound promoters. Co-immunoprecipitations confirmed that BRCA1 interacts with a number of these TFs including AP2-α, PAX2 and ZF5. Finally, we show that BRCA1 is bound to a subset of promoters of genes that are not altered by BRCA1 loss, but are transcriptionally regulated in a BRCA1-dependent manner upon DNA damage. These data suggest a model, whereby BRCA1 is present on defined promoters as part of an inactive complex poised to respond to various genotoxic stimuli.

Reduced Level of Ribonucleotide Reductase R2 Subunits Increases Dependence on Homologous Recombination Repair of Cisplatin-Induced DNA Damage

Ribonucleotide reductase (RNR) catalyzes the rate-limiting step in the production of deoxyribonucleoside triphosphates (dNTPs) required for replicative and repair DNA synthesis. Mammalian RNR is a heteromeric enzyme consisting primarily of R1 and R2 subunits during the S phase of the cell cycle. We have shown previously that the presence of excess R2 subunits protects p53-deficient human colon cancer cells from cisplatin-induced DNA damage and replication stress. However, the mode of DNA repair influenced by changes in the level of the R2 subunit remained to be defined. In the present study, we demonstrated that depletion of BRCA1, an important factor of homologous recombination repair (HRR), preferentially sensitized stable R2-knockdown p53(-/-) HCT116 cells to the cytotoxicity of cisplatin and γ-H2AX induction. In accord with this finding, these R2-knockdown cells exhibited increased dependence on HRR, as evidenced by elevated levels of cisplatin-induced Rad51 foci and sister chromatid exchange frequency. Furthermore, stable knockdown of the R2 subunit also led to decreased cisplatin-induced gap-filling synthesis in nucleotide excision repair (NER) and a reduced dATP level in the G(2)/M phase of the cell cycle. These results suggest that an increased level of the R2 subunit extends the availability of dATP in the G(2)/M phase to promote the repair of NER-mediated single-strand gaps that are otherwise converted into double-strand breaks in the subsequent S phase. We propose that HRR becomes important for recovery from cisplatin-DNA lesions when the postexcision process of NER is restrained by reduced levels of the R2 subunit and dATP in p53-deficient cancer cells.

BRCA1 Loss Induces GADD153-Mediated Doxorubicin Resistance in Prostate Cancer

BRCA1 plays numerous roles in the regulation of genome integrity and chemoresistance. Although BRCA1 interaction with key proteins involved in DNA repair is well known, its role as a coregulator in the transcriptional response to DNA damage remains poorly understood. In this study, we show that BRCA1 plays a central role in the transcriptional response to genotoxic stress in prostate cancer. BRCA1 expression mediates apoptosis, cell-cycle arrest, and decreased viability in response to doxorubicin treatment. Xenograft studies using human prostate carcinoma PC3 cells show that BRCA1 depletion results in increased tumor growth. A focused survey of BRCA1-regulated genes in prostate carcinoma reveals that multiple regulators of genome stability and cell-cycle control, including BLM, FEN1, DDB2, H3F3B, BRCA2, CCNB2, MAD2L1, and GADD153, are direct transcriptional targets of BRCA1. Furthermore, we show that BRCA1 targets GADD153 promoter to increase its transcription in response to DNA damage. Finally, GADD153 depletion significantly abrogates BRCA1 influence on cell-cycle progression and cell death in response to doxorubicin treatment. These findings define a novel transcriptional pathway through which BRCA1 orchestrates cell fate decisions in response to genotoxic insults, and suggest that BRCA1 status should be considered for new chemotherapeutic treatment strategies in prostate cancer.

A genetic screen identifies BRCA2 and PALB2 as key regulators of G2 checkpoint maintenance

To identify key connections between DNA-damage repair and checkpoint pathways, we performed RNA interference screens for regulators of the ionizing radiation-induced G2 checkpoint, and we identified the breast cancer gene BRCA2. The checkpoint was also abrogated following depletion of PALB2, an interaction partner of BRCA2. BRCA2 and PALB2 depletion led to premature checkpoint abrogation and earlier activation of the AURORA A-PLK1 checkpoint-recovery pathway. These results indicate that the breast cancer tumour suppressors and homologous recombination repair proteins BRCA2 and PALB2 are main regulators of G2 checkpoint maintenance following DNA-damage.

BRCA1 A-Complex fine tunes repair functions of BRCA1

BRCA1 A-Complex fine tunes repair functions of BRCA1

Abstract 2160: Critical BRCA1 role as a transcriptional regulator in prostate cancer DNA damage response

Abstract Loss or mutation of the BRCA1 gene is associated with nearly 5% of all breast cancers. Since many cases of sporadic cancers that also show decreased BRCA1 expression are often associated with higher grade tumors, significant interest has developed in defining mechanisms of BRCA1 regulation at the level of transcription. BRCA1 plays numerous roles in regulating genome integrity. It interacts with crucial proteins and is considered a gene-specific transcriptional co-regulator; however, BRCA1's role in the transcriptional response to DNA damage is poorly understood. In this study we show that BRCA1 plays a central role in the transcriptional response to genotoxic stress in prostate cancer. Using BRCA1-depleted or BRCA1-overexpressing human prostate cancer cell lines, we found that BRCA1 mediates apoptosis, cell cycle arrest and decreased viability in response to doxorubicin treatment. Furthermore, xenograft studies using human prostate carcinoma PC3 cells demonstrate that BRCA1 depletion results in increased tumor growth. In addition, genome-wide screens using the combined application of chromatin immunoprecipitation and microarray technology (ChIP-chip) reveals that BRCA1 is highly enriched at the promoters of greater than 1300 genes. Gene Ontology (GO) analysis of this “BRCA1 ChIP signature” reveals a significant enrichment in genes that function in cell cycle regulation and the response to DNA damage including “M phase”’ and “Mitotic checkpoint” terms, suggesting a specific role for BRCA1 in controlling mitotic events following genotoxic stress. We have validated multiple members of this BRCA1 ChIP signature including: BLM, FEN1, DDB2, H3F3B, BRCA2, CCNB2, MAD2L1, GADD153 and ATM. Further focused analysis reveals that BRCA1 occupancy at the ATM promoter increases its transcription and H2AX phosphorylation. Notably, following doxorubicin exposure, BRCA1 is released from the ATM promoter and redistributed to other genes like GADD153 where it induces expression, apoptosis and cell cycle arrest. RNAi depletion of GADD153 blocks BRCA1-dependent apoptosis and cell cycle arrest in response to doxorubicin, suggesting that GADD153 is required for BRCA1 mediated drug sensitivity. These findings define a novel mechanism through which BRCA1 influences cell fate decisions in response to genotoxic insult through direct transcriptional control of genes, including GADD153 and ATM. Thus, tumors with absent or reduced expression of BRCA1 are likely to show a marked resistance to chemotherapy for prostate cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2160. doi:10.1158/1538-7445.AM2011-2160

Cell Cycle-Dependent Induction of Homologous Recombination by a Tightly Regulated I-SceI Fusion Protein

Double-strand break repair is executed by two major repair pathways: non-homologous end joining (NHEJ) and homologous recombination (HR). Whereas NHEJ contributes to the repair of ionizing radiation (IR)-induced double strand breaks (DSBs) throughout the cell cycle, HR acts predominantly during the S and G2 phases of the cell cycle. The rare-cutting restriction endonuclease, I-SceI, is in common use to study the repair of site-specific chromosomal DSBs in vertebrate cells. To facilitate analysis of I-SceI-induced DSB repair, we have developed a stably expressed I-SceI fusion protein that enables precise temporal control of I-SceI activation, and correspondingly tight control of the timing of onset of site-specific chromosome breakage. I-SceI-induced HR showed a strong, positive linear correlation with the percentage of cells in S phase, and was negatively correlated with the G1 fraction. Acute depletion of BRCA1, a key regulator of HR, disrupted the relationship between S phase fraction and I-SceI-induced HR, consistent with the hypothesis that BRCA1 regulates HR during S phase.

Identifying the Effects of BRCA1 Mutations on Homologous Recombination using Cells that Express Endogenous Wild-type BRCA1

The functional analysis of missense mutations can be complicated by the presence in the cell of the endogenous protein. Structure-function analyses of the BRCA1 have been complicated by the lack of a robust assay for the full length BRCA1 protein and the difficulties inherent in working with cell lines that express hypomorphic BRCA1 protein1,2,3,4,5. We developed a system whereby the endogenous BRCA1 protein in a cell was acutely depleted by RNAi targeting the 3'-UTR of the BRCA1 mRNA and replaced by co-transfecting a plasmid expressing a BRCA1 variant. One advantage of this procedure is that the acute silencing of BRCA1 and simultaneous replacement allow the cells to grow without secondary mutations or adaptations that might arise over time to compensate for the loss of BRCA1 function. This depletion and add-back procedure was done in a HeLa-derived cell line that was readily assayed for homologous recombination activity. The homologous recombination assay is based on a previously published method whereby a recombination substrate is integrated into the genome (Figure 1)6,7,8,9. This recombination substrate has the rare-cutting I-SceI restriction enzyme site inside an inactive GFP allele, and downstream is a second inactive GFP allele. Transfection of the plasmid that expresses I-SceI results in a double-stranded break, which may be repaired by homologous recombination, and if homologous recombination does repair the break it creates an active GFP allele that is readily scored by flow cytometry for GFP protein expression. Depletion of endogenous BRCA1 resulted in an 8-10-fold reduction in homologous recombination activity, and add-back of wild-type plasmid fully restored homologous recombination function. When specific point mutants of full length BRCA1 were expressed from co-transfected plasmids, the effect of the specific missense mutant could be scored. As an example, the expression of the BRCA1(M18T) protein, a variant of unknown clinical significance10, was expressed in these cells, it failed to restore BRCA1-dependent homologous recombination. By contrast, expression of another variant, also of unknown significance, BRCA1(I21V) fully restored BRCA1-dependent homologous recombination function. This strategy of testing the function of BRCA1 missense mutations has been applied to another biological system assaying for centrosome function (Kais et al, unpublished observations). Overall, this approach is suitable for the analysis of missense mutants in any gene that must be analyzed recessively.

Identifying the Effects of BRCA1 Mutations on Homologous Recombination using Cells that Express Endogenous Wild-type BRCA1

The functional analysis of missense mutations can be complicated by the presence in the cell of the endogenous protein. Structure-function analyses of the BRCA1 have been complicated by the lack of a robust assay for the full length BRCA1 protein and the difficulties inherent in working with cell lines that express hypomorphic BRCA1 protein1,2,3,4,5. We developed a system whereby the endogenous BRCA1 protein in a cell was acutely depleted by RNAi targeting the 3'-UTR of the BRCA1 mRNA and replaced by co-transfecting a plasmid expressing a BRCA1 variant. One advantage of this procedure is that the acute silencing of BRCA1 and simultaneous replacement allow the cells to grow without secondary mutations or adaptations that might arise over time to compensate for the loss of BRCA1 function. This depletion and add-back procedure was done in a HeLa-derived cell line that was readily assayed for homologous recombination activity. The homologous recombination assay is based on a previously published method whereby a recombination substrate is integrated into the genome (Figure 1)6,7,8,9. This recombination substrate has the rare-cutting I-SceI restriction enzyme site inside an inactive GFP allele, and downstream is a second inactive GFP allele. Transfection of the plasmid that expresses I-SceI results in a double-stranded break, which may be repaired by homologous recombination, and if homologous recombination does repair the break it creates an active GFP allele that is readily scored by flow cytometry for GFP protein expression. Depletion of endogenous BRCA1 resulted in an 8-10-fold reduction in homologous recombination activity, and add-back of wild-type plasmid fully restored homologous recombination function. When specific point mutants of full length BRCA1 were expressed from co-transfected plasmids, the effect of the specific missense mutant could be scored. As an example, the expression of the BRCA1(M18T) protein, a variant of unknown clinical significance10, was expressed in these cells, it failed to restore BRCA1-dependent homologous recombination. By contrast, expression of another variant, also of unknown significance, BRCA1(I21V) fully restored BRCA1-dependent homologous recombination function. This strategy of testing the function of BRCA1 missense mutations has been applied to another biological system assaying for centrosome function (Kais et al, unpublished observations). Overall, this approach is suitable for the analysis of missense mutants in any gene that must be analyzed recessively.

Effects of BRCA2 deficiency on telomere recombination in non-ALT and ALT cells

BackgroundRecent studies suggest that BRCA2 affects telomere maintenance. Interestingly, anti cancer treatments that involve BRCA2 and telomerase individually are currently being explored. In the light of the above recent studies their combinatorial targeting may be justified in the development of future treatments. In order to investigate effects of BRCA2 that can be explored for this combinatorial targeting we focused on the analysis of recombination rates at telomeres by monitoring T-SCEs (Telomere Sister Chromatid Exchanges).ResultsWe observed a significant increase in T-SCE frequencies in four BRCA2 defective human cell lines thus suggesting that BRCA2 suppresses recombination at telomeres. To test this hypothesis further we analyzed T-SCE frequencies in a set of Chinese hamster cell lines with or without functional BRCA2. Our results indicate that introduction of functional BRCA2 normalizes frequencies of T-SCEs thus supporting the notion that BRCA2 suppresses recombination at telomeres. Given that ALT (Alternative Lengthening of Telomeres) positive cells maintain telomeres by recombination we investigated the effect of BRCA2 depletion in these cells. Our results show that this depletion causes a dramatic reduction in T-SCE frequencies in ALT positive cells, but not in non-ALT cells.ConclusionBRCA2 suppresses recombination at telomeres in cells that maintain them by conventional mechanisms. Furthermore, BRCA2 depletion in ALT positive cells reduces high levels of T-SCEs normally found in these cells. Our results could be potentially important for refining telomerase-based anti-cancer therapies.

DNA Damage–Induced Cytotoxicity Is Dissociated from BRCA1's DNA Repair Function but Is Dependent on Its Cytosolic Accumulation

The tumor suppressor BRCA1 is a nuclear shuttling protein. However, the role of BRCA1 localization in the control of its functions remains to be elucidated. Given the central role of BRCA1 in DNA damage repair, we hypothesized that depletion of nuclear BRCA1 would compromise its nuclear function in DNA repair and thereby result in enhanced cytotoxic response to DNA damage. In this study, we showed that repair of DNA double-strand breaks required BRCA1 in the nucleus. In addition, sequestering BRCA1 in the cytosol enhanced the cytotoxic response to ionizing radiation or cisplatin in human breast and colon cancer cells. However, further genetic dissection of the mechanism of this enhanced cytotoxicity using BRCA1 mutants deficient in double-strand break repair unexpectedly revealed a dissociation of BRCA1's function in DNA repair from its effects on cellular sensitivity to DNA damage. Interestingly, we observed a dependence of the DNA damage-induced cell killing on the translocation and accumulation of BRCA1 in the cytosol. Together, these data suggest a novel role of cytoplasmic translocation of BRCA1, not only in controlling its DNA repair functions, but also in the regulation of cell death processes following DNA damage. Further dissection of the mechanism of cytotoxicity induced by BRCA1 cytoplasmic translocation revealed the involvement of the apoptotic pathway. We propose that the status of BRCA1 nuclear/cytoplasmic shuttling might provide a molecular marker to predict tumor response and a potential novel target to sensitize cancer cells to DNA damage-based therapy.

BRD7, a Subunit of SWI/SNF Complexes, Binds Directly to BRCA1 and Regulates BRCA1-Dependent Transcription

We carried out a yeast two-hybrid screen using a BRCA1 bait composed of amino acids 1 to 1142 and identified BRD7 as a novel binding partner of BRCA1. This interaction was confirmed by coimmunoprecipitation of endogenous BRCA1 and BRD7 in T47D and HEK-293 cells. BRD7 is a bromodomain containing protein, which is a subunit of PBAF-specific Swi/Snf chromatin remodeling complexes. To determine the functional consequences of the BRCA1-BRD7 interaction, we investigated the role of BRD7 in BRCA1-dependent transcription using microarray-based expression profiling. We found that a variety of targets were coordinately regulated by BRCA1 and BRD7, such as estrogen receptor alpha (ERalpha). Depletion of BRD7 or BRCA1 in either T47D or MCF7 cells resulted in loss of expression of ERalpha at both the mRNA and protein level, and this loss of ERalpha was reflected in resistance to the antiestrogen drug fulvestrant. We show that BRD7 is present, along with BRCA1 and Oct-1, on the ESR1 promoter (the gene which encodes ERalpha). Depletion of BRD7 prevented the recruitment of BRCA1 and Oct-1 to the ESR1 promoter; however, it had no effect on the recruitment of the other Swi/Snf subunits BRG1, BAF155, and BAF57 or on RNA polymerase II recruitment. These results support a model whereby the regulation of ERalpha transcription by BRD7 is mediated by its recruitment of BRCA1 and Oct-1 to the ESR1 promoter.