For the past few years, drugs exploiting synthetic lethality have gained attention as novel anticancer agents.
Breast and ovarian cancers with mutated BRCA1 or 2, essential components of a pathway for repairing DNA double-strand breaks, provide a fundamental example of how synthetic lethality works. Because replicating DNA requires repair of DNA double-strand breaks, these cancers rely on a key enzyme, PARP1, for replication fork progression. PARP1 inhibition of cells bearing BRCA1 or 2 mutations results in catastrophic double-strand breaks during replication and, ultimately, cell death.
Analysis and identification of drug–gene synthetic lethal interactions could also be exploited, investigators say, to design combination therapies and predict synergistic/sensitizer drugs.
In cancer and infectious diseases, particularly because drug combinations with distinct cellular targets can limit treatment resistance, synergistic drugs can be used at much lower concentrations to achieve the same biological effect, thereby limiting side effects.
But clinical trial failures for AstraZeneca’s PARP inhibitor drug candidate olaparib and Sanofi’s iniparib backburnered other trials for the drug candidate class. AstraZeneca cancelled a Phase III breast cancer trial after a study last October showed olaparib failed to benefit women with BRCA-related ovarian cancer more than chemotherapy and said it was waiting for additional results before moving forward.
Nevertheless, “After these failures, people are again looking more carefully at this population of BRCA1 and BRCA2 mutation carriers,” commented Susan Comchek, M.D., a University of Pennsylvania oncologist, who thinks that olaparib did poorly because it was tested in an untargeted population.
And currently despite earlier clinical setbacks with PARP inhibitors, several of these drugs continue to advance through clinical trials. These include olaparib in Phase I trial for solid tumors, Abbott’s veliparib for leukemias and solid tumors, CEP-9722 for lymphoma and solid tumors, and Clovis Oncology’s rucaparib in Phase I–II trials for BRCA1 and BRCA2 mutant cancers.
Prior to the clinical trial results with the PARP1 inhibitors, synthetic lethality was “a promising theoretical concept that people thought should work [in humans] because it works in model organisms,” said William Hahn, M.D., Ph.D., associate professor, department of medicine, Harvard Medical School and director, Center for Cancer Genome Discovery of the Dana-Farber Cancer Institute. Now, he continued, it’s been “taken all the way to the patient” and shown “to have a clinical benefit, and that’s why people are excited about it.”
But finding synthetic lethality relationships among potential drug targets remains challenging. Research groups are on the hunt using bioinformatics and small molecule or RNA interference (RNAi) screens to identify synthetic lethal relationships between known therapeutic targets.
In 2009, Dr. Hahn and his colleagues in the department of medical oncology at Dana-Farber Cancer Institute used systematic RNAi to detect synthetic lethal partners of oncogenic KRAS, mutated in a wide variety of aggressive cancers that respond poorly to standard therapies. KRAS has also remained refractory to efforts to develop effective, molecularly targeted therapies.
The investigators found that the noncanonical I-kappa-B kinase TBK1 was selectively essential for the cells with mutant KRAS. Suppression of TBK1 induced apoptosis specifically in human cancer cell lines that depend on oncogenic KRAS expression.
These observations indicate that TBK1 and NF-kappa-B signaling are essential in KRAS mutant tumors, and establish, the scientists said, a general approach for the rational identification of co-dependent pathways in cancer.
In 2010, investigators at Fox Chase Cancer Center reported that they had developed a protein network centered on the epidermal growth factor receptor (EGFR), a validated cancer therapeutic target. The scientists then used small interfering RNA screening to comparatively probe this network for proteins that regulate the effectiveness of both EGFR-targeted agents and nonspecific cytotoxic agents.
Screening of an initial library of 638 proteins revealed multiple proteins connected in the EGFR network such as protein kinase C or Aurora kinase A. These and other proteins synergized with EGFR antagonists to reduce tumor cell viability and tumor size, suggesting a potential direct path to clinical exploitation, the scientists said.
The Fox Chase team identified more than 60 proteins that cancer cells already “under assault with an EGFR inhibitor” rely on to survive. The investigators used RNAi screens in several cancer cell lines to knockdown, one by one, expression of the genes that produce these proteins. From the initial group of “hits”—genes that, when silenced, yielded increases in cancer cell death in EGFR inhibitor-treated cells—the team did additional validation testing with other small interfering RNAs to confirm the findings and isolate the most robust synthetic lethal relationships.
The entire study took more than three years to conduct, said Erica Golemis, Ph.D., professor and co-leader of the developmental therapeutics program at Fox Chase, and senior author of the study. Although it is a cumbersome process, she added, “RNAi screening is becoming a dominant way of approaching biological networks. We knew from model organisms that there was a dense network of genes. Using bioinformatics tools to intelligently mine this network provided us with a rich source of hits,” she said.
GEN asked Dr. Golemis what the most therapeutically promising synthetic lethal relationships discovered by the study have been. “The word promising depends on how you are handicapping this. For example, relationships involving an Aurora A inhibitor like alisertib (MLN8237), already moving from Phase II into Phase III trials, look promising. Our data supports combining a relatively late-stage drug like that and EGFR inhibitors,” Dr. Golemis said.
Based on this work, Hossein Borghaei of Fox Chase is currently leading a Phase I trial combining alisertib with erlotinib in non-EGFR-mutated lung cancer. A second trial, of alisertib combined with cetuximab and radiation for a subset of advanced head and neck cancers, has cleared institutional review board approval and is intended to open in several months.
Compared to pathway analysis to discover relationships, this type of analysis allows a functional determination of pathway analysis that is not obvious, explained Dr. Golemis. “We have a lot of interesting genes that have come up that have not been previously recognized as having a relationship with EGFR: for example, DDR2 is emerging as an interesting cancer target that is mutated in some EGFR-relevant cancers such as squamous lung cancer. Inhibition of DDR2 showed striking synergy when combined with an EGFR inhibitor.”
And despite the challenges in discovering synthetic lethal relationships among various molecular players and pathways, this mode of thinking about developing anticancer drugs may yield completely novel therapies.