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Repare Therapeutics Using CRISPR to Develop Cancer Treatments for Synthetic Lethal Targets


NEW YORK – Precision oncology company Repare Therapeutics is homing in on synthetic lethality as a jumping off point for developing new cancer therapies.

Using a CRISPR-Cas9 genome editing-based screening platform, the company is aiming to discover novel pathways and patient subsets, and develop treatments that selectively affect DNA damage response mechanisms in cancer cells and kill them, while sparing normal cells.

The Montreal, Canada-based company was founded in 2016 by researchers Daniel Durocher and Frank Sicheri from the Lunenfeld-Tanenbaum Research Institute, and NYU Langone Medical Center Associate Professor Agnel Sfeir. According to Repare CSO Michael Zinda, the founding of the company brought together Durocher's work using functional genomics and CRISPR to study the DNA damage response, Sicheri's expertise as a structural biologist, and Sfeir's work on inhibiting DNA polymerase θ (Polθ) — which is involved in DNA repair — as a possible strategy for treating cancer.

Synthetic lethality is a mechanism that leads to cell death, and it arises when two or more mutations or epigenetic alterations are present in key genes, or the expression of those genes is somehow inhibited. However, for synthetic lethality to occur, more than one deficiency must be present. For example, PARP inhibitors were the first class of therapies to interrogate this process that the US Food and Drug Administration approved. This class of drugs have shown to work especially well in patients who carry germline mutations in either BRCA1 or BRCA2, which hobble DNA repair mechanisms in cells — treatment with PARP inhibitors causes further DNA damage that results in tumor cell death. More recent clinical trials have targeted the role of EGFR and BRAF, TP53 and BCL2, and PTEN and CHD1, in synthetic lethality.

In a synthetic lethal genetic screen, researchers generally begin with a cell line that contains a specific mutation that doesn't kill the cell but may confer a specific phenotype, and then systematically test other mutations at additional loci to determine which confer lethality.

Repare's technology platform, which is called SNIPRx, utilizes a unique genome-wide CRISPR library that was created by the company's researchers to screen isogenic cell backgrounds. Isogenic cell lines are often used to study the impact of experimental therapeutic compounds on different disease phenotypes, especially for cancer. An isogenic cell line is engineered from a parental line through the introduction of a targeted gene mutation and becomes a control line that can be compared to the engineered line as a reference.

"We use a normal cell background from the cellular lineage that the aberration we're looking at in a tumor was from," Zinda explained. "For instance, if the gene that we were looking at for synthetic lethality was lost in breast cancer, we would use human mammary epithelial cells."

Using the SNIPRx platform, Repare researchers knock out genes of interest and then use the CRISPR library to identify novel targets. "I think that's allowed us to see insights that you don't see when you're just looking across tumor cell lines de novo, because you can look at unique genetic alterations that aren't prevalent or don't exist in the tumor cell lines that are available, but also because we get better editing and more robust output that allows us to see targets that others aren't seeing," Zinda said.

Indeed, the company is using the knowledge it's generating through its CRISPR-based technology to find DNA damage response defects and genomic instabilities that are common across a wide range of cancers. Its researchers originally identified about 16 different genetic alterations that were linked with genome instability, Zinda said. Although some of these targets are specific to certain cancers, several of the targets are likely to be tumor-agnostic "where we would be looking at the genetic alteration, not necessarily specifically at a disease subset," he added.

Repare is building a pipeline of drug candidates for both novel and well-characterized targets. Earlier this month, the company announced it had raised $82.5 million in a Series B financing. The funds will be used to drive the progress of the pipeline and to continue with additional screens, Zinda said.

The project that's furthest in development is RP-3500, an ATR inhibitor. Repare is moving forward with RP-3500 in the ATM-null patient population — ATM-null status is caused by inactivation of the ATM gene and can result in resistance to apoptosis driven by p53. There's a well-established synthetic lethal interaction of ATM-null with ATR inhibition, he explained, pointing to Phase I data presented by different groups earlier this year at the American Society of Clinical Oncology annual meeting that confirmed anti-tumor effects of ATR inhibition in patients with ATM mutations.

Importantly, Zinda said, Repare used the SNIPRx platform to perform chemical synthetic lethal screens, in which researchers test a compound on cancer cells, knock out the genome, and then look for genes that, when lost, cause hypersensitivity to the compound.

"We used that method to find some novel insights into unique patient populations that we could go in with [the ATR inhibitor] that others aren't currently executing on and don't have insights into," he added. "So, we're bringing forward what we think could be a best-in-class molecule, along with additional insights on how to use it clinically and are really progressing that forward as fast as we can."

That compound is entering the preclinical stage of testing, and the company is hoping to start human trials in the second or third quarter of 2020, Zinda noted.

He also declined to specify what he referred to as the "unique" patient populations the company's researchers have found using the SNIPRx platform. "We haven't revealed what those patient populations are, so we're keeping that quiet until we get into the clinic," Zinda said. "But I'd say we found upwards of nine unique genetic alterations that we were initially looking at. We've expanded that out a bit since then."

The second project on Repare's list is a previously undisclosed program codenamed "Manchester," a CCNE1 synthetic lethal targeted therapy.

"It's a unique gene that, when inhibited, causes synthetic lethality with a gain-of-function cyclin E1 amplification," Zinda explained. Cyclin-E1 is a protein that is encoded by CCNE1. Overexpression of the gene has been observed in many tumors — it causes chromosome instability and may contribute to tumorigenesis.

Because the target is completely novel, Repare hasn't revealed it to anyone outside of a few selected investors and its board of directors, Zinda said. The company is aiming to formulate an actual molecule by the end of 2019 and to move into human trials by late 2020 or early 2021. 

"We would be proactively picking patients within that setting for cyclin E1 amplification in the key disease subtypes that we think are most important," Zinda added.

Finally, the company is progressing with its Polθ inhibitor. Polθ is a specialized A-family DNA polymerase that functions in processes such as translesion synthesis, DNA double-strand break repair, and DNA replication timing. Overexpression of the POLQ gene, which encodes Polθ, is a prognostic marker for an adverse outcome in various cancers.

The firm is aiming to move into the drug candidate phase for this target by the end of 2020, but this program is still in early stages and the timelines are a less clear, according to Zinda.

The company has established offices in Boston, where it houses its clinical bioinformatics and translational science teams, as well as some finance staffers. In total, about 40 of the firm's 50 employees work in the wet labs in Canada. Regulatory interactions with the FDA regarding its products will likely be run from the Boston office.

Repare is also looking at developing companion diagnostics to go with the therapeutics it's creating and is exploring the option of creating in-house CDx capabilities, partnering with firms with established diagnostics expertise, or both.

"For some of these [drug targets], there are already tests that are available from firms like Foundation Medicine or others that we believe we'll be able to use to help progress things forward," Zinda said. "For other, more novel, alterations that we've found, we're going to be working with some key external providers to create those companion diagnostics based on whatever the state of the art is that's necessary to bring them to the market."

The firm hasn't firmed up its strategy as to whether it will develop companion diagnostics prospectively or make a post-marketing commitment to develop them after the drugs are approved by the FDA, he added. That decision will likely depend on Repare's speed in getting the drugs to market and the market dynamics for specific indications.

The company is also using the SNIPRx platform to study mechanisms of treatment resistance driven by loss-of-function mutations. Understanding how the cells react to treatment will give Repare more insights into the interactions that cause synthetic lethality, which will help to better inform patient selection as the company's clinical trials move forward, Zinda said.

Improvements to the SNIPRx platform are also on the company's agenda. Although the technology currently uses the Cas9 nuclease, Repare has collaborations with different academic labs to analyze emerging CRISPR technologies and new CRISPR nucleases to see which ones can help it address challenges that aren't solvable with the current platform configuration.

But SNIPRx has already proven it has the potential to be more efficient and faster at matching patients to cancer treatments than current methods, according to Zinda. And, it has helped Repare identify both novel targets based on genetic alterations that haven't been identified before, as well as additional patient populations that might be able to take advantage of these new treatments.

Overall, he added, it's an interesting time for researchers and companies looking to exploit synthetic lethality as the next major frontier for personalized medicine. "We've just begun to understand the potential of this type of mechanism and the types of targets we might be able to take advantage of," Zinda said. "I'm really looking forward to the next five to 10 years as many more of these targets start to progress, and we can understand the full potential of this mechanism for helping patients."