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.