DNA Repair Defects Emerge as a New Category for Anticancer Therapies

A coordinated network of signaling pathways works to protect the cell from the toxic effects of DNA damage. Its vital importance to cellular integrity is underscored by the fact that hereditary mutations in DNA repair genes dramatically increase cancer risk, as exemplified by the breast cancer susceptibility (BRCA1/2) genes, which encode proteins involved in the homologous recombination (HR) repair pathway.

An increasing appreciation of the mechanisms of HR-based DNA repair and the extraordinary sensitivity of BRCA1/2-mutant cells to DNAdamaging conventional therapies have also fueled the development of targeted therapies that exploit HR deficiency.

Coping with DNA Damage

The poly(ADP-ribose) polymerase (PARP) inhibitor olaparib (Lynparza) became the first approved drug based on the concept of targeting HR deficiency in cancer in December 2014. Since then, the identification of BRCA1/2 mutations and other HR pathway mutations that confer BRCAness in a range of other tumor types suggests that this strategy could prove to be the jumping off point for a new treatment paradigm for cancer.The cells in our body come under frequent assault from a wide variety of stressors, from both the internal and external environments, that can cause several different types of structurally distinct DNA damage. In order to cope, cells have evolved a complex signaling network, known as the DNA damage response (DDR), that plays a vital role in detecting and repairing DNA damage or, if the damage is irreparable, in initiating cell death to clear the damaged cell from the body.

The most common type of DNA damage, with tens of thousands occurring in each cell every day, are single-strand breaks (SSBs), affecting just one strand of the DNA double helix. They are usually rapidly and efficiently repaired, primarily through the base excision repair (BER) pathway, and thus are not particularly toxic. In some cases, because of damaged repair pathways or errors in the repair process itself, SSBs are allowed to accumulate, resulting in the formation of a double-strand break (DSB), where the damage impacts both strands of the DNA helix. These are far more toxic to the cell and their effective repair is vital for cell survival.

A Hallmark of Cancer

One of the major pathways of DSB repair is HR, a mostly error-free process that uses a homologous DNA template to repair the damaged DNA exactly as it was. The template used is most commonly the sister chromatids; therefore, HR is mostly limited to the S and G2 phases of the cell cycle when these are more easily accessible. HR involves 3 main steps: the DNA is resected to generate single-stranded DNA ends, a step that is dependent on the activity of a complex of 3 key proteins, MRE11, NBS1, and RAD50 (known collectively as the MRN complex) and replication protein A (RPA) binds to the resulting DNA ends; RAD51 then forms filaments made up of nucleic acids and proteins on the RPA-coated strands, which seek out homologous sequences within the sister chromatids; using the homologous DNA template, RAD51 performs a recombinase reaction to repair the damaged DNA.Unrepaired damage can impact the integrity of the genome, creating the genomic instability that is a hallmark of malignant cells and leading to accumulation of further genomic aberrations that support cancer cell growth and survival. It is unsurprising, therefore, that many different types of malignancies display DNA repair defects.

The most notorious are mutations in the BRCA1 and BRCA2 genes, which are linked to a dramatic increase in the risk of hereditary breast and ovarian cancers. Overall BRCA1/2 mutations are present in 5% to 10% of breast cancers and 10% to 15% of ovarian cancers, but the prevalence is highest in the most aggressive forms of these diseases, triple- negative breast cancer (TNBC) and high-grade serous ovarian cancer, respectively.

Mutations in the BRCA1/2 genes are believed to cause cancer in several different ways, but the best understood mechanism is the role that the proteins they encode play in the HR pathway of DNA DSB repair, predominantly in regulating the recruitment and function of the RAD51 protein.

Targeting DNA Repair

The loss of the BRCA1/2 proteins results in a defective HR pathway, causing cells to become more dependent on the error-prone non-homologous end-joining pathway to repair DSBs, leading to an accumulation of DNA defects and ultimately driving the development of cancer.During the past 2 decades, DNA repair deficiencies have increasingly emerged as a potential vulnerability of cancer cells that could be therapeutically exploited. This has been reinforced by the finding that DNA repair defects seem to increase the vulnerability of cancer cells to DNA-damaging chemotherapies, most notably platinum-based agents, and ionizing radiation. Too much damage to the DNA is untenable for a cell. A defect in one DNA repair pathway drives a cancer cell to become dangerously dependent on other methods of repair for survival. Thus, when multiple repair pathways are knocked out, which might happen when DNA-damaging therapies are applied to cancer cells with a pre-existing DNA repair defect such as a BRCA1/2 mutation, cell death ensues.

In addition to increased sensitivity to conventional therapies, targeted therapies have been developed that exploit this same vulnerability by identifying repair defects that are synthetically lethal with an HR deficiency. The concept of synthetic lethality refers to a situation where 2 individual cellular defects do not affect cell viability on their own, but lead to cell death when both occur at the same time.

The idea of using synthetic lethality in this manner is exemplified by the development of PARP inhibitors for the treatment of tumors with BRCA1/2 mutations. PARPs play a role in the BER pathway of SSB repair; in the presence of a PARP inhibitor, SSBs go unrepaired, leading to the development of DSBs. When a cancerous cell also has defective HR due to mutations in the BRCA1/2 genes, those DSBs also go unrepaired, leading to cell death. Thus, BRCA1/2-mutant tumors are exquisitely sensitive to PARP inhibition.

Because BRCA1/2 mutations are best established in breast and ovarian cancers, the focus of PARP inhibitor development has been in these tumor types. Olaparib was granted accelerated approval by the FDA for the treatment of patients with advanced BRCA1/2- mutant ovarian cancer who had already received 3 or more chemotherapy treatments. The approval was based on response rates in excess of 30% in a phase II trial, and confirmatory phase III trials are ongoing.

Other PARP inhibitors are following in olaparib’s footsteps, including rucaparib, niraparib, and talazoparib. At the 2016 ASCO Annual Meeting, the results of part 1 of a 2-part study of niraparib in combination with bevacizumab in patients with recurrent platinum-sensitive ovarian cancer were presented. Among 12 patients, 1 had a complete response, 4 experienced partial responses, and 6 had stable disease, totaling a disease control rate of more than 90%.

HR Deficiency Edges Beyond BRCA

Talazoparib, which has a novel mechanism of action that blocks multiple BRCA-dependent DNA repair mechanisms, showed promise in phase I data presented at the 2016 American Association for Cancer Research Annual Meeting, with a response rate of 57% in 40 patients who received a combination of talazoparib and low-dose chemotherapy.Several studies have demonstrated that treatment with PARP inhibitors in ovarian cancer can be effective regardless of the mutation status of the BRCA1/2 genes. This may be partly explained by the fact that the BRCA1/2 genes can be changed in other ways, such as through epigenetic alterations, but it also likely reflects the fact that other HR defects exist in ovarian cancer, which may also dictate sensitivity to PARP inhibition.

A genome-wide sequencing study in ovarian cancer performed by The Cancer Genome Atlas research network revealed that up to half of all epithelial ovarian cancers have some form of HR defect. In addition to germline BRCA1/2 mutations in 14% of patients and somatic mutations in a further 6%, defects in other components of the HR pathway included PALB2, FANCA, FANCI, FANCL, FANCC, RAD50, RAD51, ATM, ATR, CHEK1, and CHEK2 mutations.

Numerous studies have now demonstrated that these and other HR defects also render tumors more sensitive to conventional DNA-damaging therapies and PARP inhibitors, in the absence of a BRCA1/2 mutation—a phenomenon that has been dubbed BRCAness. For example, a recent study used targeted sequencing of 12 key HR genes in ovarian tumors and found that these mutations conferred sensitivity to platinum- based chemotherapy; improved OS followed treatment with these drugs.

It also appears that ovarian cancer is not unique in its HR defects. Genome sequencing studies have begun to reveal BRCAness across a range of tumor types, including breast, prostate, and pancreatic cancers. Up to 20% of metastatic castration-resistant prostate cancers are believed to have at least 1 mutation in an HR-associated gene, including BRCA1, BRCA2, ATM, and CDK12.

Nearly one-quarter of pancreatic ductal adenocarcinoma tumors possessed either a germline or somatic mutation in the BRCA1, BRCA2, or PALB2 gene, with ATM gene mutations in 8%. A proportion of gastric cancers have also been shown to exhibit an HR mutational signature, similar to that of ovarian and breast cancers, including prevalent mutations in the ATM gene.

These findings suggest that exploiting HR deficiencies in cancer could become a much more far-reaching treatment paradigm in the future. Given the unique sensitivity of tumors with HR defects to DNA-damaging chemotherapy and ionizing radiation, it has been proposed that developing small-molecule inhibitors of HR pathway components to induce HR deficiency might also have a place in the anticancer therapeutic arsenal. By artificially introducing HR and potentially other DNA repair pathway defects in cancer cells that are HR proficient, it might be possible to boost the efficacy of conventional therapies.

Several such drugs are in clinical development (Tables 1 and 2). These include ATM, ATR, and CHEK1/2 inhibitors, all important kinases in the HR pathway. Results of a phase I trial of the ATR inhibitor VX-970 were reported at the 2016 ASCO Annual Meeting. The drug was well tolerated as monotherapy or in combination with carboplatin in patients with advanced cancers and showed promising signs of antitumor activity, including a complete response lasting more than 19 months.

Particularly important in this context is the complex interplay between the HR pathway and other important cellular networks, such as those controlling the cell cycle, protein stability, and growth factor receptor signaling. It is possible that this may provide alternative targets for inducing HR or for identifying other synthetic lethal partners for pre-existing HR defects in cancer cells.

Identifying BRCAness

Recent studies have found that many components of DNA repair pathways appear to be regulated by heat-shock proteins, which help to ensure correct protein folding. For example, BRCA2 has been shown to be a client protein of HSP90. This has prompted suggestions that locally inducing mild hyperthermia in the tumor could allow specific perturbation of the HR pathway within the tumor to sensitize it to concomitant radiation, chemotherapy, or even PARP inhibitor treatment.In order to optimize the clinical benefit from targeting HR deficiencies in cancer cells, several limitations must be overcome. The most significant issue is how to most effectively identify BRCAness—that is, those HR defects that predict sensitivity to DNA-damaging drugs.

One approach being developed is to identify a panel of HR mutations, a BRCAness panel that could be used as an inclusion criterion in clinical trials. Transcriptional signatures of BRCAness are also being developed; one group has created a 44-gene expression signature that permits identification of subgroups of patients who have deficiencies in DNA repair genes.

Another strategy is to develop functional biomarkers of HR deficiency. The main focus has been on the development of an immunohistochemical assay to detect nuclear localization of the RAD51 protein, since it plays such a central role in the HR pathway. Lack of RAD51 in the nucleus could imply an HR-deficient tumor. Furthest along in development, however, is a next-generation sequencing assay that generates an HR deficiency (HRD) score, the development of which is being pioneered by Myriad Genetics, which also produces the BRACAnalysis test that is used to identify patients with ovarian cancer with BRCA1/2 mutations who are eligible for PARP inhibitor therapy.

The company’s myChoiceHRD assay is based on the premise that HR deficiency results in a characteristic scarring of the genome—an accumulation of genomic damage—which can be quantified. It generates an HRD score from the sum of 3 independent DNA-based measures of genome scarring: loss of heterozygosity (LOH), telomeric allelic imbalance (TAI), and largescale state transitions (LST). The HRD score is combined with BRCA1/2 mutation status to determine whether a tumor is HR-deficient or HR-proficient.

A pooled analysis of 6 phase II trials of patients with TNBC who received a platinum-based chemotherapy regimen found that an HRD score that indicated HR deficiency was significantly associated with a greater chance of achieving pathologic complete response, irrespective of BRCA1/2 mutation status.

The HRD score has also been evaluated as a companion to niraparib therapy in ovarian cancer; patients with HR deficiency as measured by their HRD score experienced improved progression- free survival.

In ovarian cancer, it is estimated that the use of the HRD score could double the number of patients who may benefit from PARP inhibitor treatment. Meanwhile, a study presented at the European Society of Molecular Oncology meeting suggested that, in patients with prostate cancer, the HRD score identified 3 times as many potential responders to DNA-damaging therapies as did an evaluation of individual DNA repair gene mutations.

Jane de Lartigue, PhD, is a freelance medical writer and editor based in New Haven, Connecticut.

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