RNF4-mediated polyubiquitination regulates the Fanconi anemia/BRCA pathway

The Fanconi anemia/BRCA (FA/BRCA) pathway is a DNA repair pathway that is required for excision of DNA interstrand cross-links. The 17 known FA proteins, along with several FA-associated proteins (FAAPs), cooperate in this pathway to detect, unhook, and excise DNA cross-links and to subsequently repair the double-strand breaks generated in the process. In the current study, we identified a patient with FA with a point mutation in FANCA, which encodes a mutant FANCA protein (FANCAI939S). FANCAI939S failed to bind to the FAAP20 subunit of the FA core complex, leading to decreased stability. Loss of FAAP20 binding exposed a SUMOylation site on FANCA at amino acid residue K921, resulting in E2 SUMO-conjugating enzyme UBC9-mediated SUMOylation, RING finger protein 4-mediated (RNF4-mediated) polyubiquitination, and proteasome-mediated degradation of FANCA. Mutation of the SUMOylation site of FANCA rescued the expression of the mutant protein. Wild-type FANCA was also subject to SUMOylation, RNF4-mediated polyubiquitination, and degradation, suggesting that regulated release of FAAP20 from FANCA is a critical step in the normal FA pathway. Consistent with this model, cells lacking RNF4 exhibited interstrand cross-linker hypersensitivity, and the gene encoding RNF4 was epistatic with the other genes encoding members of the FA/BRCA pathway. Together, the results from our study underscore the importance of analyzing unique patient-derived mutations for dissecting complex DNA repair processes.

Homologous-recombination-deficient tumours are dependent on Polθ-mediated repair

Large-scale genomic studies have shown that half of epithelial ovarian cancers (EOCs) have alterations in genes regulating homologous recombination (HR) repair. Loss of HR accounts for the genomic instability of EOCs and for their cellular hyper-dependence on alternative poly-ADP ribose polymerase (PARP)-mediated DNA repair mechanisms. Previous studies have implicated the DNA polymerase θ (Polθ also known as POLQ, encoded by POLQ) in a pathway required for the repair of DNA double-strand breaks, referred to as the error-prone microhomology-mediated end-joining (MMEJ) pathway. Whether Polθ interacts with canonical DNA repair pathways to prevent genomic instability remains unknown. Here we report an inverse correlation between HR activity and Polθ expression in EOCs. Knockdown of Polθ in HR-proficient cells upregulates HR activity and RAD51 nucleofilament assembly, while knockdown of Polθ in HR-deficient EOCs enhances cell death. Consistent with these results, genetic inactivation of an HR gene (Fancd2) and Polq in mice results in embryonic lethality. Moreover, Polθ contains RAD51 binding motifs and it blocks RAD51-mediated recombination. Our results reveal a synthetic lethal relationship between the HR pathway and Polθ-mediated repair in EOCs, and identify Polθ as a novel druggable target for cancer therapy.

A unique subset of epithelial ovarian cancers with platinum sensitivity and PARP inhibitor resistance

Platinum and PARP inhibitor (PARPi) sensitivity commonly coexist in epithelial ovarian cancer (EOC) due to the high prevalence of alterations in the homologous recombination (HR) DNA repair pathway that confer sensitivity to both drugs. In this report, we describe a unique subset of EOC with alterations in another DNA repair pathway, the nucleotide excision repair (NER) pathway, which may exhibit a discordance in sensitivities to these drugs. Specifically, 8% of high-grade serous EOC from The Cancer Genome Atlas dataset exhibited NER alterations, including nonsynonymous or splice site mutations and homozygous deletions of NER genes. Tumors with NER alterations were associated with improved overall survival (OS) and progression-free survival (PFS), compared with patients without NER alterations or BRCA1/2 mutations. Furthermore, patients with tumors with NER alterations had similar OS and PFS as BRCA1/2-mutated patients, suggesting that NER pathway inactivation in EOC conferred enhanced platinum sensitivity, similar to BRCA1/2-mutated tumors. Moreover, two NER mutations (ERCC6-Q524* and ERCC4-A583T), identified in the two most platinum-sensitive tumors, were functionally associated with platinum sensitivity in vitro. Importantly, neither NER alteration affected HR or conferred sensitivity to PARPi or other double-strand break-inducing agents. Overall, our findings reveal a new mechanism of platinum sensitivity in EOC that, unlike defective HR, may lead to a discordance in sensitivity to platinum and PARPi, with potential implications for previously reported and ongoing PARPi trials in this disease.

Ubiquitin recognition by FAAP20 expands the complex interface beyond the canonical UBZ domain

FAAP20 is an integral component of the Fanconi anemia core complex that mediates the repair of DNA interstrand crosslinks. The ubiquitin-binding capacity of the FAAP20 UBZ is required for recruitment of the Fanconi anemia complex to interstrand DNA crosslink sites and for interaction with the translesion synthesis machinery. Although the UBZ–ubiquitin interaction is thought to be exclusively encapsulated within the ββα module of UBZ, we show that the FAAP20–ubiquitin interaction extends beyond such a canonical zinc-finger motif. Instead, ubiquitin binding by FAAP20 is accompanied by transforming a disordered tail C-terminal to the UBZ of FAAP20 into a rigid, extended β-loop that latches onto the complex interface of the FAAP20 UBZ and ubiquitin, with the invariant C-terminal tryptophan emanating toward I44^Ub for enhanced binding specificity and affinity. Substitution of the C-terminal tryptophan with alanine in FAAP20 not only abolishes FAAP20–ubiquitin binding in vitro, but also causes profound cellular hypersensitivity to DNA interstrand crosslink lesions in vivo, highlighting the indispensable role of the C-terminal tail of FAAP20, beyond the compact zinc finger module, toward ubiquitin recognition and Fanconi anemia complex-mediated DNA interstrand crosslink repair.

Abstract IA10: Fanconi anemia and novel drug targets

The fifteen Fanconi Anemia proteins cooperate in a novel DNA repair pathway, required for DNA interstrand crosslink repair during S phase of the human cell cycle. Disruption of this pathway results in congenital abnormalities, bone marrow failure, and cancer susceptibility, most notably Acute Myeloblastic Leukemia and Squamous Cell Carcinomas. A molecular understanding of the FA pathway has emerged over the last several years, and insights from this pathway have suggested novel drug targets and therapeutic strategies for FA patients. In my talk, I will discuss three research areas that may result in new drug strategies.

First, the FA pathway plays a critical role in the regulation of Cytokinesis (i.e., the orderly condensation and separation of sister chromatids during the mitosis phase of the cell cycle). Recent studies indicate that some FA proteins, including FANCD2, FANCI, and FANCM, as well as the BLM helicase, accumulate at ultrafine bridges connecting sister chromatids in mitosis. Interestingly, defects in the FA pathway cause an increase in these bridges, thereby resulting in cytokinesis failure and an increase in binucleate cells. These FA cells appear to undergo rapid p53-mediated apoptosis, perhaps contributing to the bone marrow failure observed in FA mouse models and FA patients. Pharmacologic blockade of this apoptotic cell death may result in the rescue of bone marrow hematopoietic progenitor cells and in an enhancement of hematopoiesis.

Second, downstream FA proteins (ie, FA proteins which are not required for FANCD2 monoubiquitination), such as FANCD1/BRCA2, are directly involved in homologous recombination (HR). Loss of these proteins can result in a decrease in the assembly of RAD51-mediated nucleofilaments (i.e. structures essential for HR). We have recently identified an anti-recombinase protein, called PARI (PCNA-Associated Recombination Inhibitor). Interestingly, downregulation of PARI results in an enhancement of HR in FA pathway deficient cells and a rescue of DNA crosslinker-induced chromosome radial formation. Thus, pharmacologic blockade of PARI may provide a novel strategy for promoting HR in the bone marrow cells for some FA pathway deficient patients.

Third, recent studies indicate that the FA pathway provides an important tumor suppressor activity, which is especially critical in epithelial cells. Epithelial cells which are deficient in FANCD2-Ub undergo have increased cellular proliferation and decreased senescence. This function of FANCD2-Ub in epithelial cells may account, at least in part for the predisposition of FA patients to Squamous Cell Carcinomas (SCCs). Knockdown or inhibition of the deubiquitinating enzyme, USP1, results in increased FANCD2-Ub levels and an increase in FANCD2-Ub levels in some FA mouse models and in FA patient-derived cell lines. Accordingly, a USP1 inhibitor may provide a novel strategy for SCC chemoprevention for some FA patients. To summarize, the overall goal of our research program is to identify pathway-based treatment strategies for FA.

Citation Format: Alan D. D'Andrea. Fanconi anemia and novel drug targets. [abstract]. In: Proceedings of the AACR Special Conference on Pediatric Cancer at the Crossroads: Translating Discovery into Improved Outcomes; Nov 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;74(20 Suppl):Abstract nr IA10.

Crosstalk between the nucleotide excision repair and Fanconi anemia/BRCA pathways

Cells have evolved multiple distinct DNA repair pathways to efficiently correct a variety of genotoxic lesions, and decades of study have led to an improved understanding of the mechanisms and regulation of these individual pathways. However, there is now an increasing appreciation that extensive crosstalk exists among DNA repair pathways and that this crosstalk serves to increase the efficiency and diversity of response to damage. The Fanconi anemia (FA)/BRCA and nucleotide excision repair (NER) pathways have been shown to share common factors, and often work in concert to repair damage. Genomic studies are now revealing that many tumors harbor somatic mutations in FA/BRCA or NER genes, which may provide a growth advantage, but which could also be exploited therapeutically.

Transcriptional repressor ZBTB1 promotes chromatin remodeling and translesion DNA synthesis

Timely DNA replication across damaged DNA is critical for maintaining genomic integrity. Translesion DNA synthesis (TLS) allows bypass of DNA lesions using error-prone TLS polymerases. The E3 ligase RAD18 is necessary for proliferating cell nuclear antigen (PCNA) monoubiquitination and TLS polymerase recruitment; however, the regulatory steps upstream of RAD18 activation are less understood. Here, we show that the UBZ4 domain-containing transcriptional repressor ZBTB1 is a critical upstream regulator of TLS. The UBZ4 motif is required for PCNA monoubiquitination and survival after UV damage. ZBTB1 associates with KAP-1, a transcriptional repressor whose phosphorylation relaxes chromatin after DNA damage. ZBTB1 depletion impairs formation of phospho-KAP-1 at UV damage sites and reduces RAD18 recruitment. Furthermore, phosphorylation of KAP-1 is necessary for efficient PCNA modification. We propose that ZBTB1 is required for localizing phospho-KAP-1 to chromatin and enhancing RAD18 accessibility. Collectively, our study implicates a ubiquitin-binding protein in orchestrating chromatin remodeling during DNA repair.

The carboxyl terminus of FANCE recruits FANCD2 to the Fanconi Anemia (FA) E3 ligase complex to promote the FA DNA repair pathway

Fanconi anemia (FA) is a genome instability syndrome characterized by bone marrow failure and cellular hypersensitivity to DNA cross-linking agents. In response to DNA damage, the FA pathway is activated through the cooperation of 16 FA proteins. A central player in the pathway is a multisubunit E3 ubiquitin ligase complex or the FA core complex, which monoubiquitinates its substrates FANCD2 and FANCI. FANCE, a subunit of the FA core complex, plays an essential role by promoting the integrity of the complex and by directly recognizing FANCD2. To delineate its role in substrate ubiquitination from the core complex assembly, we analyzed a series of mutations within FANCE. We report that a phenylalanine located at the highly conserved extreme C terminus, referred to as Phe-522, is a critical residue for mediating the monoubiquitination of the FANCD2-FANCI complex. Using the FANCE mutant that specifically disrupts the FANCE-FANCD2 interaction as a tool, we found that the interaction-deficient mutant conferred cellular sensitivity in reconstituted FANCE-deficient cells to a similar degree as FANCE null cells, suggesting the significance of the FANCE-FANCD2 interaction in promoting cisplatin resistance. Intriguingly, ectopic expression of the FANCE C terminus fragment alone in FA normal cells disrupts DNA repair, consolidating the importance of the FANCE-FANCD2 interaction in the DNA cross-link repair.

Small-molecule inhibitors of USP1 target ID1 degradation in leukemic cells

Inhibitor of DNA binding 1 (ID1) transcription factor is essential for the proliferation and progression of many cancer types, including leukemia. However, the ID1 protein has not yet been therapeutically targeted in leukemia. ID1 is normally polyubiquitinated and degraded by the proteasome. Recently, it has been shown that USP1, a ubiquitin-specific protease, deubiquitinates ID1 and rescues it from proteasome degradation. Inhibition of USP1 therefore offers a new avenue to target ID1 in cancer. Here, using a ubiquitin-rhodamine-based high-throughput screening, we identified small-molecule inhibitors of USP1 and investigated their therapeutic potential for leukemia. These inhibitors blocked the deubiquitinating enzyme activity of USP1 in vitro in a dose-dependent manner with an IC50 in the high nanomolar range. USP1 inhibitors promoted the degradation of ID1 and, concurrently, inhibited the growth of leukemic cell lines in a dose-dependent manner. A known USP1 inhibitor, pimozide, also promoted ID1 degradation and inhibited growth of leukemic cells. In addition, the growth of primary acute myelogenous leukemia (AML) patient-derived leukemic cells was inhibited by a USP1 inhibitor. Collectively, these results indicate that the novel small-molecule inhibitors of USP1 promote ID1 degradation and are cytotoxic to leukemic cells. The identification of USP1 inhibitors therefore opens up a new approach for leukemia therapy.

Abstract CN05-02: Targeting the Fanconi anemia/BRCA pathway

Cancer cells have genomic instability resulting from acquired defects in DNA repair. One DNA repair pathway, the Fanconi Anemia/BRCA homologous recombination pathway (Kennedy and D'Andrea, Genes & Development 19:2925, 2005), is defective in many human cancers, including breast, ovarian, pancreatic, and lung neoplasms. Disruption of the FA/BRCA Pathway results in the characteristic chromosome instability and radiation/crosslinker hypersensitivity of these tumors. In general, loss of one DNA repair pathway often leads to hyperdependence on another pathway for tumor cell survival. This hyperdependence offers a unique opportunity for the development of anticancer therapeutics. For instance, FA/BRCA pathway deficient tumors are hyperdependent on base excision repair (BER) and, accordingly, these tumors are hypersensitive to single agent treatment with PARP1 inhibitors which block BER. Our laboratory efforts are focused on profiling the FA/BRCA pathway and the other five major DNA repair pathways in tumor cells (Kennedy and D'Andrea, JCO 24: 3799, 2006). Each DNA repair pathway has a characteristic protein biomarker and repairs a specific type of DNA lesion. By profiling these pathways in primary tumor samples with activation-specific antibodies to DNA repair proteins, we are developing methods to: 1) predict the sensitivity of tumors to conventional chemotherapy and radiation (Personalized Medicine); 2) to subset tumors for their sensitivity to novel classes of DNA repair inhibitors (i.e., PARP1, Chk1, and ATM inhibitors); and 3) to screen for new small molecule inhibitors of other DNA repair pathways. This combination of novel DNA repair inhibitors, conventional DNA damaging agents, and DNA repair biomarkers offers new opportunities for developing more effective anticancer therapy.

The FA/BRCA pathway was elucidated through the systematic study of the rare inherited chromosome breakage disorder, Fanconi Anemia (Moldovan and D'Andrea, Ann Rev Genet 43:223, 2009). FA is an autosomal recessive disease characterized by bone marrow failure, congenital malformations, and cellular sensitivity to cisplatin, mitomycin C, and other DNA interstrand crosslinking agents. Patients with FA develop hematopoietic malignancies and squamous cell carcinomas. Based on somatic cell fusion studies, there are sixteen FA complementation groups (A, B, C, D1, D2, E, F, G, I, J, L, M, N, O, P, Q), and the corresponding gene for each of these complementation groups has been identified. Interestingly, the sixteen FA proteins cooperate in a common cellular pathway in normal human cells, referred to as the Fanconi Anemia/BRCA pathway. Eight of the FA proteins (A, B, C, E, F, G, L, M) are assembled in a core complex (the FA core complex) which is an active ubiquitin E3 ligase. In response to DNA damage, the FA core complex modifies (monoubiquitinates) the downstream FANCD2 protein. Monoubiquitinated FANCD2 translocates to nuclear foci where it interacts with the FANCD1/BRCA2 protein and participates in the process of homologous recombination DNA repair. Additional FA proteins (namely, FANCJ/BRIP1 and FANCN/PALB2) function downstream of FANCD2 monoubiquitination. At least three of the FA genes (FANCD1, FANCJ, and FANCN) are inherited breast cancer susceptibility genes. Disruption of any step in the FA/BRCA pathway results in the common clinical and cellular phenotype of FA patients.

Human tumor cells, derived from cancer patients from the general (non-FA) population, often exhibit genomic instability. Genomic instability of tumors has important clinical consequences. On the one hand, genomic instability gives the tumor the ability to break and fuse chromosomes, inactivate tumor suppressor genes, form novel oncogene fusions, and amplify drug resistance genes. Thus, the tumor with genomic instability may become more malignant and drug resistant over time. On the other hand, in order to achieve a state of genomic instability, a tumor cell must inactivate one of its major DNA repair pathways. This inactivation appears to account, at least in part, for the selective hypersensitivity of cancer cells to the cytotoxic effects of conventional anticancer radiation and chemotherapy.

Recent studies indicate that some human tumors inactivate the FA/BRCA pathway. Pathway inactivation may result from somatic mutation of genes in the FA/BRCA pathway or by epigenetic silencing. For instance, methylation of one of the FA genes, FANCF, has been implicated as a mechanism for genomic instability in a wide variety of cancers, including ovarian, breast, lung, cervical, and head and neck squamous cell carcinomas. Somatic inactivation of the FA/BRCA pathway appears to account for the genomic instability and the cisplatin hypersensitivity of many of these cancers. In my presentation, I will review the features of the FA/BRCA pathway in human cells, and how knowledge of this pathway in cancers can lead to the prediction of drug response.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):CN05-02.

Citation Format: Alan D. D'Andrea. Targeting the Fanconi anemia/BRCA pathway. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr CN05-02.

BRCA1: a missing link in the Fanconi anemia/BRCA pathway

Domchek and colleagues provide a case report of a 28-year-old woman with congenital abnormalities, inherited ovarian cancer, and carboplatin hypersensitivity. Interestingly, the woman had validated germline mutations in both BRCA1 alleles. These findings further implicate BRCA1 in the Fanconi anemia/BRCA pathway and have important implications for BRCA1 genetic testing.

Stressed out: endogenous aldehydes damage hematopoietic stem cells

Despite a well-defined role for the Fanconi anemia (FA) pathway in mediating DNA repair, the mechanisms underlying the bone marrow failure in FA patients are poorly defined. Recently in Nature, Garaycoechea et al. (2012), identify aldehyde-mediated genotoxicity of hematopoietic stem cells as a cause for bone marrow failure.

Chromatin remodeling at DNA double-strand breaks

DNA double-strand breaks (DSBs) can arise from multiple sources, including exposure to ionizing radiation. The repair of DSBs involves both posttranslational modification of nucleosomes and concentration of DNA-repair proteins at the site of damage. Consequently, nucleosome packing and chromatin architecture surrounding the DSB may limit the ability of the DNA-damage response to access and repair the break. Here, we review early chromatin-based events that promote the formation of open, relaxed chromatin structures at DSBs and that allow the DNA-repair machinery to access the spatially confined region surrounding the DSB, thereby facilitating mammalian DSB repair.

Abstract 1788: The CDK inhibitor dinaciclib sensitizes triple-negative breast cancer cells to PARP inhibition

Background: Triple Negative Breast Cancer (TNBC) comprises 15% of all breast cancers, and has a poor prognosis relative to other breast cancer subtypes. Inhibition of poly (ADP-ribose) polymerase (PARP) causes the degeneration of single-strand DNA breaks to more lethal double-strand breaks (DSBs), and also traps PARP-DNA complexes, which must be repaired or bypassed by homologous recombination (HR). BRCA1 plays a critical role in HR and its activity is in part regulated by cyclin-dependent kinase 1 (CDK1)-mediated phosphorylation. PARP inhibition results in synthetic lethality in cells that have impaired HR, such as BRCA-deficient cells. Other CDK family members activate additional components of the HR pathway. Here, we show that HR-proficient TNBC cells can be sensitized to PARP inhibition through use of CDK inhibition to impair BRCA1 function and disrupt HR.

Methods: We examined the effects of dinaciclib (CDK1, 2, 5 and 9 inhibitor), γ-irradiation and veliparib (PARP inhibitor) on a panel of BRCA1 wild type TNBC cell lines (MDA-MB-231, MDA-MB-468, and BT549). Levels of phospho-S1497 BRCA1 (pBRCA1; CDK phosphorylation site), γ-H2AX, and RAD51 were measured by western blot to assess effects on HR proteins. A direct assessment of DSB repair was measured using the U2OS-DR-GFP reporter system. Cell viability was measured using Cell-Titer Glo assays. Patient-derived TNBC xenograft models were established in immunocompromised NOD-SCID-IL2γ-/- mice, and implanted orthotopically into cohorts of mice for in vivo efficacy studies.

Results: There was a significant reduction in total and pBRCA1 and RAD51 protein levels with increasing concentrations of dinaciclib in all TNBC cell lines. In response to 10 Gy γ-irradiation treatment, pretreatment with dinaciclib (20 nM) reduced the percentage of cells with greater than five BRCA1 foci from 54% to 5% (P < 0.001); and the percentage of cells with greater than 5 RAD51 foci from 26% to 4% (P = 0.001). In U2OS-DR-GFP assays, expression of GFP was detected in 3.4% of the vehicle group and in 1.9% of dinaciclib treated cells. Cell viability assays following five days of dinaciclib, veliparib or the combination revealed in vitro cytotoxic synergy in all three TNBC cell lines. In an orthotopic TNBC model derived from a primary patient sample, the relative tumor volumes over a 30-day treatment period for vehicle, dinaciclib, veliparib and combination- treated mice were 5.6-fold, 3.3-fold, 3.2-fold and 0.66-fold (P < 0.001) that of the initial tumor volume at the start of treatment. Tumor volume decreased only in the combination arm.

Conclusion: CDK inhibition effectively inhibits HR, and renders BRCA-proficient TNBC cells sensitive to PARP inhibition. This combination represents an effective strategy for the treatment of TNBC.

Citation Format: Shawn F. Johnson, Neil Johnson, David Chi, Benjamin Primack, Alan D. D'Andrea, Elgene Lim, Geoffrey I. Shapiro. The CDK inhibitor dinaciclib sensitizes triple-negative breast cancer cells to PARP inhibition. [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 1788. doi:10.1158/1538-7445.AM2013-1788

PARI overexpression promotes genomic instability and pancreatic tumorigenesis

Treatment options for patients with pancreatic ductal adenocarcinoma (PDAC) remain limited. Therapeutic targets of interest include mutated molecules that predispose to pancreatic cancer such as KRAS and TP53. Here, we show that an element of the homologous recombination pathway of DNA repair, the PARP-binding protein C12orf48/PARI (PARPBP), is overexpressed specifically in pancreatic cancer cells where it is an appealing candidate for targeted therapy. PARI upregulation in pancreatic cancer cells or avian DT40 cells conferred DNA repair deficiency and genomic instability. Significantly, PARI silencing compromised cancer cell proliferation in vitro, leading to cell-cycle alterations associated with S-phase delay, perturbed DNA replication, and activation of the DNA damage response pathway in the absence of DNA damage stimuli. Conversely, PARI overexpression produced tolerance to DNA damage by promoting replication of damaged DNA. In a mouse xenograft model of pancreatic cancer, PARI silencing was sufficient to reduce pancreatic tumor growth in vivo. Taken together, our findings offered a preclinical proof-of-concept for PARI as candidate therapeutic target to treat PDAC.

Molecular pathogenesis and clinical management of Fanconi anemia

Fanconi anemia (FA) is a rare genetic disorder associated with a high frequency of hematological abnormalities and congenital anomalies. Based on multilateral efforts from basic scientists and clinicians, significant advances in our knowledge of FA have been made in recent years. Here we review the clinical features, the diagnostic criteria, and the current and future therapies of FA and describe the current understanding of the molecular basis of the disease.

Structural basis of Rev1-mediated assembly of a quaternary vertebrate translesion polymerase complex consisting of Rev1, heterodimeric polymerase (Pol) ζ, and Pol κ

DNA synthesis across lesions during genomic replication requires concerted actions of specialized DNA polymerases in a potentially mutagenic process known as translesion synthesis. Current models suggest that translesion synthesis in mammalian cells is achieved in two sequential steps, with a Y-family DNA polymerase (κ, η, ι, or Rev1) inserting a nucleotide opposite the lesion and with the heterodimeric B-family polymerase ζ, consisting of the catalytic Rev3 subunit and the accessory Rev7 subunit, replacing the insertion polymerase to carry out primer extension past the lesion. Effective translesion synthesis in vertebrates requires the scaffolding function of the C-terminal domain (CTD) of Rev1 that interacts with the Rev1-interacting region of polymerases κ, η, and ι and with the Rev7 subunit of polymerase ζ. We report the purification and structure determination of a quaternary translesion polymerase complex consisting of the Rev1 CTD, the heterodimeric Pol ζ complex, and the Pol κ Rev1-interacting region. Yeast two-hybrid assays were employed to identify important interface residues of the translesion polymerase complex. The structural elucidation of such a quaternary translesion polymerase complex encompassing both insertion and extension polymerases bridged by the Rev1 CTD provides the first molecular explanation of the essential scaffolding function of Rev1 and highlights the Rev1 CTD as a promising target for developing novel cancer therapeutics to suppress translesion synthesis. Our studies support the notion that vertebrate insertion and extension polymerases could structurally cooperate within a megatranslesion polymerase complex (translesionsome) nucleated by Rev1 to achieve efficient lesion bypass without incurring an additional switching mechanism.

To the rescue: the Fanconi anemia genome stability pathway salvages replication forks

DNA damage can arrest replication forks during S phase. Failure to stabilize and restart arrested forks results in fork collapse and genomic instability. In this issue of Cancer Cell, Schlacher et al. show that the Fanconi anemia and BRCA2 tumor suppressor pathways cooperate to protect stalled replication forks from degradation.

Bone marrow failure in Fanconi anemia is triggered by an exacerbated p53/p21 DNA damage response that impairs hematopoietic stem and progenitor cells

Fanconi anemia (FA) is an inherited DNA repair deficiency syndrome. FA patients undergo progressive bone marrow failure (BMF) during childhood, which frequently requires allogeneic hematopoietic stem cell transplantation. The pathogenesis of this BMF has been elusive to date. Here we found that FA patients exhibit a profound defect in hematopoietic stem and progenitor cells (HSPCs) that is present before the onset of clinical BMF. In response to replicative stress and unresolved DNA damage, p53 is hyperactivated in FA cells and triggers a late p21(Cdkn1a)-dependent G0/G1 cell-cycle arrest. Knockdown of p53 rescued the HSPC defects observed in several in vitro and in vivo models, including human FA or FA-like cells. Taken together, our results identify an exacerbated p53/p21 "physiological" response to cellular stress and DNA damage accumulation as a central mechanism for progressive HSPC elimination in FA patients, and have implications for clinical care.

Non-specific chemical inhibition of the Fanconi anemia pathway sensitizes cancer cells to cisplatin

Background

Platinum compounds such as cisplatin and carboplatin are DNA crosslinking agents widely used for cancer chemotherapy. However, the effectiveness of platinum compounds is often tempered by the acquisition of cellular drug resistance. Until now, no pharmacological approach has successfully overcome cisplatin resistance in cancer treatment. Since the Fanconi anemia (FA) pathway is a DNA damage response pathway required for cellular resistance to DNA interstrand crosslinking agents, identification of small molecules that inhibit the FA pathway may reveal classes of chemicals that sensitize cancer cells to cisplatin.

Results

Through a cell-based screening assay of over 16,000 chemicals, we identified 26 small molecules that inhibit ionizing radiation and cisplatin-induced FANCD2 foci formation, a marker of FA pathway activity, in multiple human cell lines. Most of these small molecules also compromised ionizing radiation-induced RAD51 foci formation and homologous recombination repair, indicating that they are not selective toward the regulation of FANCD2. These compounds include known inhibitors of the proteasome, cathepsin B, lysosome, CHK1, HSP90, CDK and PKC, and several uncharacterized chemicals including a novel proteasome inhibitor (Chembridge compound 5929407).

Isobologram analyses demonstrated that half of the identified molecules sensitized ovarian cancer cells to cisplatin. Among them, 9 demonstrated increased efficiency toward FA pathway-proficient, cisplatin-resistant ovarian cancer cells. Six small molecules, including bortezomib (proteasome inhibitor), CA-074-Me (cathepsin B inhibitor) and 17-AAG (HSP90 inhibitor), synergized with cisplatin specifically in FA-proficient ovarian cancer cells (2008 + FANCF), but not in FA-deficient isogenic cells (2008). In addition, geldanamycin (HSP90 inhibitor) and two CHK1 inhibitors (UCN-01 and SB218078) exhibited a significantly stronger synergism with cisplatin in FA-proficient cells when compared to FA-deficient cells, suggesting a contribution of their FA pathway inhibitory activity to cisplatin sensitization.

Conclusion

Our findings suggest that, despite their lack of specificity, pharmaceutical inhibition of the FA pathway by bortezomib, CA-074-Me, CHK1 inhibitors or HSP90 inhibitors may be a promising strategy to sensitize cisplatin-resistant, FA pathway-proficient tumor cells to cisplatin. In addition, we identified four new small molecules which synergize with cisplatin. Further development of their analogs and evaluation of their combination with cisplatin may lead to the development of efficient cancer treatments.

Abstract SY11-01: Targeting the Fanconi anemia/BRCA pathway in cancer therapy

Cancer cells have genomic instability resulting from acquired defects in DNA repair. One DNA repair pathway, the Fanconi Anemia/BRCA homologous recombination pathway (Kennedy and D'Andrea, Genes&Development 19:2925, 2005), is defective in many human cancers, including breast, ovarian, pancreatic, and lung neoplasms. Disruption of the FA/BRCA Pathway results in the characteristic chromosome instability and radiation/crosslinker hypersensitivity of these tumors. In general, loss of one DNA repair pathway often leads to hyperdependence on another pathway for tumor cell survival. This hyperdependence offers a unique opportunity for the development of anticancer therapeutics. For instance, FA/BRCA pathway deficient tumors are hyperdependent on Base Excision Repair (BER) and, accordingly, these tumors are hypersensitive to single agent treatment with PARP1 inhibitors which block BER. Our laboratory efforts are focused on profiling the FA/BRCA pathway and the other five major DNA repair pathways in tumor cells (Kennedy and D'Andrea, JCO 24: 3799, 2006). Each DNA repair pathway has a characteristic protein biomarker and repairs a specific type of DNA lesion. By profiling these pathways in primary tumor samples with activation-specific antibodies to DNA repair proteins, we are developing methods (1) to predict the sensitivity of tumors to conventional chemotherapy and radiation (Personalized Medicine) (2) to subset tumors for their sensitivity to novel classes of DNA repair inhibitors, (i.e., PARP1, Chk1, and ATM inhibitors) and (3) to screen for new small molecule inhibitors of other DNA repair pathways. This combination of novel DNA repair inhibitors, conventional DNA damaging agents, and DNA repair biomarkers offers new opportunities for developing more effective anticancer therapy.

The FA/BRCA pathway was elucidated through the systematic study of the rare inherited chromosome breakage disorder, Fanconi Anemia (Moldovan and D'Andrea, Ann Rev Genet 43:223, 2009). FA is an autosomal recessive disease characterized by bone marrow failure, congenital malformations, and cellular sensitivity to Cisplatin, Mitomycin C, and other DNA interstrand crosslinking agents. Patients with FA develop hematopoietic malignancies and squamous cell carcinomas. Based on somatic cell fusion studies, there are fifteen FA complementation groups (A, B, C, D1, D2, E, F, G, I, J, L, M, N, O, P), and the corresponding gene for each of these complementation groups has been identified. Interestingly, the fifteen FA proteins cooperate in a common cellular pathway in normal human cells, referred to as the Fanconi Anemia/BRCA pathway. Eight of the FA proteins (A, B, C, E, F, G, L, M) are assembled in a core complex (the FA core complex) which is an active ubiquitin E3 ligase. In response to DNA damage, the FA core complex modifies (monoubiquitinates) the downstream FANCD2 protein. Monoubiquitinated FANCD2 translocates to nuclear foci where it interacts with the FANCD1/BRCA2 protein and participates in the process of homologous recombination DNA repair. Additional FA proteins (namely, FANCJ/BRIP1 and FANCN/PALB2) function downstream of FANCD2 monoubiquitination. At least three of the FA genes (FANCD1, FANCJ, and FANCN) are inherited breast cancer susceptibility genes. Disruption of any step in the FA/BRCA pathway results in the common clinical and cellular phenotype of FA patients.

Human tumor cells, derived from cancer patients from the general (non-FA) population, often exhibit genomic instability. Genomic instability of tumors has important clinical consequences. On the one hand, genomic instability gives the tumor the ability to break and fuse chromosomes, inactivate tumor suppressor genes, form novel oncogene fusions, and amplify drug resistance genes. Thus, the tumor with genomic instability may become more malignant and drug resistant over time. On the other hand, in order to achieve a state of genomic instability, a tumor cell must inactivate one of its major DNA repair pathways. This inactivation appears to account, at least in part, for the selective hypersensitivity of cancer cells to the cytotoxic effects of conventional anti-cancer radiation and chemotherapy.

Recent studies indicate that some human tumors inactivate the FA/BRCA pathway. Pathway inactivation may result from somatic mutation of genes in the FA/BRCA pathway or by epigenetic silencing. For instance, methylation of one of the FA genes, FANCF, has been implicated as a mechanism for genomic instability in a wide variety of cancers, including ovarian, breast, lung, cervical, and head and neck squamous cell carcinomas. Somatic inactivation of the FA/BRCA pathway appears to account for the genomic instability and the cisplatin hypersensitivity of many of these cancers.

A wide array of biomarkers are available for measuring the activity of the FA/BRCA pathway in human tumors, or for measuring the activity of the other human DNA repair pathways. Since many of the genes in the FA/BRCA pathway (i.e., the fifteen cloned FA genes) have been identified, tumors can be screened for germline or somatic mutations in these genes. Furthermore, tumors can be analyzed for function of the pathway by following various biochemical events in the pathway. For instance, the full function of the pathway requires monoubiquitination of the FANCD2 protein, ATR and CHK1 dependent phosphorylation of subunits of the pathway, and assembly of FANCD2 and FANCE nuclear foci. A tumor which has defects in any of these genetic or biochemical biomarkers has a defect in the FA/BRCA pathway and may therefore have a hypersensitivity to crosslinking drugs such as cisplatin. Thus, biochemical monitoring of DNA repair pathways may be a means for predicting drug sensitivity of individual tumors.

Loss of DNA repair pathways can lead to hyperdependence on other survival pathways. Inhibition of these alternative pathways may represent a therapeutic approach which is selectively toxic to repair pathway deficient tumor cells. For instance, breast and ovarian tumor cells which are deficient in the homologous recombination (HR) pathway are hypersensitive to drugs (PARP1 inhibitors) which selectively inactivate a compensatory DNA Repair pathway, the Base Excision Repair (BER) pathway. We recently used a high throughput siRNA screening approach to identify DNA damage response genes that were critical for the survival of FA/BRCA pathway deficient tumor cells (Kennedy et al, J. Clin Invest 117:1440, 2007). Using this approach we identified the DNA damage response kinase, ATM, as being important for the survival of cells deficient in the FA pathway. Accordingly, we found that the Atm -/- Fancg -/- mouse genotype was deleterious when Fancg +/− Atm +/− mice were interbred. We also demonstrated constitutive activation of ATM in FA pathway deficient cells, which was abrogated by reconstitution of the pathway. Furthermore, inhibition of ATM using siRNA oligonucleotides or the specific ATM inhibitor KU55933 resulted in DNA breakage and cell death specifically in cells with a non functioning FA pathway.

These data suggest that ATM and the FA pathway function in parallel and compensatory roles following endogenous DNA Damage. Moreover, pharmaceutical inhibition of ATM may be selectively toxic to cancer cells that have lost function of the FA pathway. We are currently exploring other therapeutic strategies to selectively target tumors with a defect in the FA/BRCA pathway or with a defect in one of the other human DNA repair pathways. For instance, we recently determined that tumors which are deficient in the FA/BRCA pathway are hypersensitive to CHK1 inhibitors (Chen et al, Mol Cancer 8: 24, 2009). In my presentation, I will review the features of the six major DNA repair pathways in human cells, and how knowledge of the disruption of these pathways in cancers can lead to the prediction of drug response.

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 SY11-01. doi:1538-7445.AM2012-SY11-01

Abstract 2540: Identification of factors governing sensitivity of NSCLC cell lines to inhibition of Poly (ADP-Ribose) Polymerase (PARP)

Recently, Poly (ADP Ribose) Polymerase-1 (PARP-1) has been shown to be an important target in subsets of breast and ovarian cancers. PARP inhibitors are emerging as important new anticancer agents, especially in cancers defective in homologous recombination (HR) repair, such as those lacking BRCA1 or BRCA2. To date, the potential role of PARP inhibition in NSCLC has not been extensively studied. BRCA1 or BRCA2 promoter hypermethylation and ATM mutation have been described in primary NSCLCs, alterations that may sensitize cells to PARP inhibition. We have examined a panel of 26 genotypically-defined NSCLC cell lines for sensitivity to the PARP-1 inhibitor AG014699 using colony formation assays. We have identified 5cell lines that are exquisitely sensitive (IC50 ≤ 50nM), 9 cell lines that are moderately sensitive (IC50 ≤ 60-500nM) and 12 cell lines that are resistant (IC50 > 5 µM). To determine whether sensitive cell lines have defective HR compared to resistant cell lines, we examined the formation of Rad51 foci following exposure to PARP inhibition, as well as to gamma-irradiation and cisplatin. Both sensitive and resistant cell lines demonstrated efficient formation of Rad51 foci as well as gamma-H2AX foci in response to DNA damaging treatments, suggesting correct initiation of HR. In resistant cell lines, the repair process following PARP inhibition is completed within 24 hours, with resolution of Rad51 and gamma H2AX foci. No alterations in cell cycle distribution were detected in these cell lines, suggesting that the efficiency of repair allows proliferation to continue largely unabated. However, in sensitive cell lines, these foci persist greater than 30 hours following DNA damaging treatments. These results suggest that although sensitive lines are able to initiate HR repair, they are unable to complete the process, so that Rad51 foci are not resolved. The persistence of DNA damage in these cell lines is confirmed by persistent gamma H2AX focus formation as well as S/G2 arrest, the latter representing intact checkpoint control. We are currently investigating whether PARP inhibitor-sensitive cell lines have a deficiency in one of the helicases or resolvases required for resolution of the complex Holliday junctions formed during HR repair. Our results may define a novel subset of NSCLCs with a late-step defect in HR that can be approached with PARP inhibition as a novel treatment strategy.

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 2540. doi:1538-7445.AM2012-2540

Abstract 1448: Whole genome RNAi screen identifies proteasome inhibition as a strategy for NSCLC radiosensitization

Background: Each year, approximately 60,000 patients in the US are diagnosed with locally advanced non-small cell lung carcinoma (NSCLC). The majority is treated with a combination of radiation therapy (RT), chemotherapy +/− surgery. Despite best available therapy, over a third of patients fail locoregionally. The addition of concurrent chemotherapy to RT adds only about a 5% absolute survival benefit. Novel radiosensitizers may improve the therapeutic index of RT. Materials and Methods: We performed whole genome pooled RNAi screens using the Hannon-Elledge library of 74,705 distinct shRNAs directed against over 18,000 genes, in two NSCLC cell lines A549 and NCI-H460. After stable transduction, we passaged the lines for 12 population doublings, and extracted DNA both before and after passaging to compare the representation of each shRNA at each time point. We defined top hits as those genes for which multiple shRNAs decreased in representation by at least 50% during passaging, signifying silencings that were detrimental to proliferation. Results: The top hit of our screen was PSMA1, a subunit of the 20S proteasome; out of six shRNAs, between four and six scored in the two lines in screens performed in triplicate. Bortezomib, an inhibitor of the 20S proteasome, has shown activity against NSCLC in preclinical studies and Phase I/II clinical trials. We observed that bortezomib results in synergistic cytotoxicity in cells treated with fractionated ionizing radiation (IR) in vitro. 10 nM bortezomib resulted in 46% clonogenic survival of unirradiated A549 cells, but only 29% survival of cells treated with 1 Gy x 3 daily fractions compared to cells treated with IR alone. Similar results were observed with MG-132 and with NCI-H460. In soft agar anchorage-independent growth assays, bortezomib resulted in less than 1% colony formation following 1 Gy x 3 daily fractions compared to cells treated with IR alone. In vivo experiments are underway with subcutaneous xenografts in nude mice treated with concurrent CT-guided conformal RT. A retrospective analysis of 443 patients with profiled lung adenocarcinomas showed worse overall survival among patients with tumors showing high proteasome gene expression (median OS 4.2 vs. 6.2 y, 5-year OS 47.5 vs. 61.0%, log rank p = 0.04). Conclusions: Proteasome inhibition emerged as the top drug target of an RNAi screen designed to identify targets with sustained activity over multiple cell generations. Its synergistic impact on NSCLC viability when coupled with fractionated RT should be further explored in preclinical studies and early clinical trials.

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 1448. doi:1538-7445.AM2012-1448