Taking on DNA repair to tackle cancer

In 1996, Simon Boulton published his first ever paper. In it, he and his PhD supervisor described a new type of DNA repair mechanism. Working in yeast, Boulton had observed this pathway come into play when he disrupted a well-known form of DNA repair. The novel pathway was error prone and the pair had no idea what enzyme was mediating it — but, with it compensating for the loss of the blocked repair mechanism, it was clearly important for cell survival.

A quarter of a century later, we now know that the error prone repair pathway Boulton — now VP of Scientific Strategy at Cambridge-based biotech Artios Pharma — first discovered in yeast is conserved in humans. That human enzyme is called DNA polymerase theta, or POLθ, and earlier this year, for the first time, a cancer patient received a drug that inhibits it.

Not only that, Artios believes their POLθ inhibitor will be able to help treat a range of cancers.

“It’s one of those classic examples of how it takes a long time for all of the pieces to come together to be able to understand what that initial finding actually meant,” says Boulton, who also runs a research group at the Francis Crick Institute in London.

Indeed, the interceding 25 years have seen much change in the field of cancer and DNA repair. When Boulton was a graduate student, there was scepticism about developing drugs to target any of the multiple repair enzymes that constitute the DNA damage response (DDR) system. All cells constantly undergo DNA damage, and the DDR is vital for cell survival and integrity. Many thought that a drug able to interfere with a repair enzyme would be unacceptably toxic.

But Boulton’s PhD mentor, Steve Jackson, of the University of Cambridge, and others turned this notion on its head with the development of cancer therapies that inhibited the DDR enzyme poly-ADP ribose phosphorylase, or PARP.

PARP inhibitors showed not only that targeting DNA repair pathways could be safe, but that it could hugely benefit a range of cancer patients.

What’s more, in doing so, the developers of PARP inhibitors also introduced a new way of thinking about cancer therapy. They showed that if an individual’s cancer has defects in one DNA repair mechanism, the cancer cells’ survival often becomes dependent on another repair pathway. Critically, this makes those cells highly susceptible to drugs that block the second pathway.

“PARP inhibitors have been a trailblazer,” says Graeme Smith. Smith shared a bench with Boulton in Jackson’s lab, then went onto work at KuDOS Pharmaceuticals, the spinout company that created the first clinically approved PARP inhibitor. Smith has seen how large pharmaceutical companies deal with drug development, having accompanied KuDOS’ PARP inhibitor programme into AstraZeneca when it was acquired in 2008. Now back once more in biotech, as CSO of Artios, Smith says, “people want to see what’s coming behind the PARP inhibitors; to see that the DNA damage response offers more opportunity as an area of biology and ultimately of medical translation.”

Boulton and Smith both believe that being able to block POLθ-mediated DNA repair will offer oncologists another vital tool with which to capitalise on cancer cells’ frequently dysregulated DNA repair biology. The current first-in-human trials will evaluate the safety of Artios’ drug candidate and whether it is able to enter human cancer cells to block the enzyme. But down the line they envisage multiple possible applications for it.

That POLθ could emerge as the next outstanding DDR-related cancer target – and that it would have many potential uses – wasn’t, however, always obvious. Boulton, for his part, spent years developing a translational research programme around another repair mechanism. But in 2010, a radiologist from the University of Oxford approached CRUK to make the case that they should develop an inhibitor of POLθ. His two-pronged argument was based on two papers he’d published as a PhD student.

Finding the target

In 2007, Geoff Higgins moved to Oxford, as a CRUK Clinical Research Fellow, to embark on a PhD in which he would seek targets for drugs that would selectively sensitise cancer cells to ionising radiation. Fourteen years on, Higgins’ work as a clinician and basic scientist is still centred around finding ways to increase the effectiveness of radiotherapy.

Around 50% of all cancer patients receive radiotherapy as part of their treatment. “The key point here,” says Higgins, “is that we want to make cancer cells more sensitive to radiotherapy, and importantly, not make normal tissue cells more sensitive to radiotherapy, which is not straightforward.”

As a PhD student, Higgins and his supervisor Gillies McKenna reasoned that they should look at DDR-related genes that help cells survive the barrage of DNA breakages induced by radiotherapy. Reflective of the complexity of DNA repair, Higgins came up with 200 targets covering multiple complementary mechanisms. They then designed siRNA probes to downregulate the expression of these genes, applied them to cultured cancerous and non-cancerous cells, and irradiated those cells.

“When we knocked down POLθ,” Higgins says, “it made tumour cells more sensitive to radiotherapy, by increasing the amount of unrepaired DNA double strand breaks. But it didn’t have an effect on normal tissue cells.”

This result seemed to be explained by POLθ being expressed at very low levels in healthy tissues and – according to a handful of small, suggestive studies – it being upregulated in cancers. To confirm this, Higgins gathered published data from nearly 300 breast cancer cases and checked the enzyme’s expression. He found not only that POLθ was overexpressed in many tumours, but that high levels of it were associated with poorer outcomes in women who’d undergone radiotherapy.

“The implication was that if you could make a drug that inhibited POLθ,” Higgins says, “it could be used in patients, combined with radiotherapy, to control tumours more effectively and cure more patients – but without exacerbating the side effects of radiotherapy.”

With these findings in hand, Higgins, in 2010, approached CRUK to explore making just such a drug.

Mark Charles, who is now head of the medicinal chemistry and pharmacokinetics group at CRUK’s Therapeutic Discovery Laboratories (TDL), says that while today TDL often look to develop a portfolio of related targets, in the early 2010s, ”it was very much that a PI would come to us and say, ’we want to translate this discovery’.”

After a series of meetings, CRUK agreed to take on the project, and in 2012 TDL began the search for an inhibitor. Initially, there was some debate as to which of POLθ’s two enzymatic domains to target. The team plumped for the better characterised polymerase domain over a helicase domain associated with the N terminal of the protein.

With no structural data on POLθ then available, the TDL team designed a biochemical assay to detect polymerase activity and used this to screen their library of compounds. This led quickly to several lead compounds. “Once they committed to looking at it,” Higgins says, “the speed of progress was pretty astounding.”

Around this time, Boulton independently approached TDL with a new DDR-related target.

But he also made another essential contribution to this evolving DDR framework. That key insight in the development of PARP inhibitors – showing that cancer cells in which one DDR pathway was lost came to rely on another pathway – arose from the crucial observation when a cancer is caused by BRCA gene mutations, the cancer cells become heavily dependent on PARP-mediated DNA repair.

Boulton had helped show that in ovarian cancers where genes involved in homologous recombination-mediated DNA repair were disrupted, a heavy reliance on POLθ emerged. And that knocking down POLθ resulted in cell death. With this, and previous work undertaken at TDL, POLθ was no longer solely a radiosensitisation target.

A route to translation

By 2015, TDL had in-house lead compounds for two novel targets, including POLθ, that they felt could powerfully extend the use of DDR disruptors in oncology. Emboldened by the first clinical approval of a PARP inhibitor – the KuDOS-developed olaparib – discussions began as to how to further develop these programmes.

The main options were to either partner with big pharma or to follow the KuDOS model and spin out another company. CRUK put together a team of advisors, including Boulton, and chose the second option, a biotech that would specialise in DDR targets.

“I became a consultant, initially through CRT [Cancer Research Technology], to basically pitch the science to the investors,” says Boulton. Describing the multiple opportunities presented by TDL’s work quickly secured early interest from two investors – Schroders Ventures Health Investors and Merck Ventures – and Artios started to become reality.

“I came along in early 2016,” says Niall Martin. Martin was the former director of KuDOS and became CEO of Artios as the company was officially launched in June 2016. “It was a period when there was a lot of investment interest in getting into DDR,” he says, explaining that the company was able to quickly go beyond its seed funding and raise further Series A investment with several other investors joining at this early stage – this funding allowing it to in-license two lead programmes, including POLθ, from CRUK.

As Martin developed the nascent company’s infrastructure, Artios continued to work closely with TDL. Charles remained project lead for a number of years, further refining the lead compounds that had discovered, now aided by crystallographic structural data on POLθ and its binding sites. Once Artios had recruited a chemistry team, Charles says CRUK handed over the reins of the project to the company. But he and his colleagues have continued to work on the POLθ project jointly with Artios as well as discussing other opportunities with them.

With the formation of a biotech, however, Higgins and Boulton both faced a choice – what would their relationship with Artios be?

Higgins chose to become a member of the scientific advisory board and continue to collaborate closely on the use of POLθ inhibitors as radiosensitising agents. He says his decision naturally reduced the influence he could have on the work on the drug target he’d discovered as a PhD student, but the resources that have become available to his lab have massively accelerated academic understanding of POLθ as well as helping with key data relevant to drug development.

Many of the key experiments regarding POLθ and radiotherapy happen in Higgins’s lab, funded by Artios, and they hope to publish results of this work next year. They are also exploring the possibility of running combined studentships. “In terms of ultimately getting these drugs into patients,” Higgins says, “being able to do research with those kinds of resources takes it to a different level.”

Before Graeme Smith had been persuaded to leave AstraZeneca, Boulton had harboured notions of becoming Artios’s CSO. However, realising that such a role would inescapably become very demanding, Boulton decided he would not risk jeopardising his academic lab. “But,” he says, “I also felt compelled that this was a great opportunity to actually be involved in developing a small molecule inhibitor – or several inhibitors – that may have patient benefit.”

Consequently, Boulton proposed to the Crick that he work part-time at Artios in the role of VP for Science Strategy. At this point, Boulton explains, the Crick was a new institute with essentially no experience of its employees commercialising their work. There were concerns that such a role would reduce Boulton’s academic output.

Convinced he could make an essential contribution to drug development – mainly from a biology perspective but also as link to the wider DNA repair field – Boulton secured the position.

Still, he had anxieties about balancing this dual role. And he concedes that there were times when the company demanded a great deal of his time and energy. “But that balance shifted over time, once the company got up and running. And actually, it has been the most incredible journey,” he says. “In fact, the lab has been more productive than ever before in the last five years,” he says. “I think partly because Artios has influenced that to some extent.”

Making a medicine

With Artios’s core infrastructure put in place in 2016, Martin says 2017 was a year of consolidation, in which the company sought to clearly define its strengths and weaknesses, “to really identify what shape of company we wanted to create around DDR.”

A key part of this, Martin says, was establishing “how to partner with CRT, and the TDL labs within CRT, to really understand what we needed to do around POLθ to bring that project forward, and what we needed to do around other assets that we’d in-licenced.”

“From 2018 onwards,” Martin continues, “we started to build the science teams and really get motoring on the drug discovery side of the projects. Then, throughout 2019, we moved towards trying to get a candidate, particularly for POLq, that we could bring into the clinic.”

The compound had to be made more potent; it needed to enter and work inside cells.

That, of course, requires investment in drug-making infrastructure. The founding of Artios attracted $33 million in venture capital investment in September 2016, enabling it to dispel many scientific uncertainties around the POLθ target. Two years later, it attracted an $84 million Series B funding, including large pharmaceutical venture financing. Most recently, in July 2021 Artios’s C round pulled in $153 million from major European and US investors,

To do this within five years is fast, but the process has not been without its setbacks. “What we had in 2016 was very well validated ‘hit matter’,” says Smith. That is, compounds that we knew bound to POLθ, and with the structural data we knew where and how they bound. But the work had been done almost exclusively in test tubes. “So, the next stage,” Smith says, “was turning that hit into a drug.”

The compound had to be made more potent; it needed to enter and work inside cells. Then, finally, the compound needed to be an orally active agent. “Having a novel drug target like POLθ brings opportunities and challenges,” says Graeme Smith at Artios. “Bringing innovative chemistry to bear on a new target certainly adds highly valuable intellectual property; but any new molecules must work on the target inside the body and also not interfere with normal metabolic processes.” All these requirements took time and the team ran down several dead ends along the way. “It would be two steps forward, one step back,” says Boulton, “or one step forward, two steps back at some points.”

Eventually, though, ART4215 emerged and in September 2021 it was given to a cancer patient for the first time. This initial trial will enrol up to 206 patients across Europe and the US, all of whom have advanced cancer, and it will assess the safety, tolerability, pharmacokinetics, and clinical activity of this new drug candidate.

Where next?

If the trial is a success, Artios envisages multiple possible applications for this drug. Potentially the first would be as a remedy to the development of resistance to PARP-inhibitors. Despite the success of these drugs, it has become apparent that many patients’ cancers acquire resistance to them. In many cases, this may involve an emergent reliance on POLθ-mediated DNA repair. A POLθ-inhibitor might, therefore, prove to be an effective second line of treatment. Or, alternatively, combining POLθ and PARP inhibitors from the outset might prevent resistance from ever developing.

It also remains possible that tumours with a high dependence on POLθ will respond to a POLθ inhibitor as a standalone agent. For all these applications, Smith says Artios is also developing methods for analysing tumours and selecting those that will most likely respond to POLθ inhibition.

Then, of course, there is Higgins’s work on using such a drug in conjunction with radiotherapy. Higgins believes that lung, head and neck, and rectal cancers are the most likely indications for which POLθ-inhibition will be most beneficial. Once the overall safety of an inhibitor is established, he would like to see dose escalation studies in which a POLθ inhibitor is given alongside standard radiotherapy courses. Then, once safety is established in such setting, larger efficacy studies can commence.

“It has been great to see something go from a hit in a screen to first in human studies,” he says.

“For CRUK to initiate the projects in their labs,” says Martin, “and then for us to take on the baton, and move this novel target into the clinic, I think is fantastic. I think the core strengths of companies are in being ruthless and getting something into the clinic. It’s a slightly different skill set. It’s about that ability within a small company to translate and get something from A to B – B being dosing patients.”

ART4215 is the second Artios drug candidate to enter clinical trials this year. The first was an inhibitor of ATR kinase, another DNA repair protein. This drug candidate was the fruit of a programme developed by a separate drug development group at MD Anderson Cancer Centre and acquired by Artios at a much later stage of development. And in the last 12 months Artios has struck major collaboration deals with both Merck KGaA and Novartis to develop further targets in the DDR space.

On top of this, Smith says having an open line to a wide community of basic scientists is also invaluable. “It’s what other offshoots can you get?” he says. “And what other insights can you get around the biology of the small molecules you have?”

At the Crick, much has changed since Boulton first approached his employers with the proposal of working part-time for a biotech. The institute is now associated with 10 spin-outs, Boulton says, and launching such ventures “is now part of the ethos of the Crick.”

In fact, Boulton is today an ambassador for translation at the institute. In this role, he says he still has to combat some residual suspicions about translational work being less worthy than pure basic research. But mainly he’s occupied with passing on his experience to colleagues who have identified potential openings. Some conversations, he says, are about the process of securing investment or about strategising, others are more personal, reassuring basic scientists that they can pursue commercial avenues alongside their academic commitments.

Looking more broadly, Boulton says, “I’ve learned to appreciate that there’s a gap – a gap between when pharma is prepared to take the plunge, and when academics reach a certain point, and they can’t progress a project further, because they don’t have the technical capability or the financial backing. Really, pharma engagement happens once you’ve got a candidate molecule.”

Understanding, then bridging, that divide lies at the heart of turning good science into real world applications. “When the Crick was set up,” he says, “one of its defining aims was to improve health and wealth. Well, you’re never going to do that unless you translate.”

 

About the contributors

Niall Martin is CEO of Artios. He has extensive experience in the DDR field and in cancer therapeutics in general, both in small companies and pharma.

Prior to joining Artios, Niall was a co-founder and Chief Operating Officer at MISSION Therapeutics, a company focused on the commercialisation of research into ubiquitin pathways for the treatment of cancers and other diseases.

Prior to that, Niall worked as Head of KuDOS Pharmaceuticals in Cambridge, UK (a subsidiary of AstraZeneca) on a number of DDR projects into the AstraZeneca oncology pipeline.

Simon Boulton is VP of Science Strategy at Artios, where he assists the business development team in the identification and evaluation of new pipeline opportunities from the global academic and industrial DDR network.

Simon’s principal position is a Senior Group Leader at the Francis Crick Institute and he is also an honorary professor at University College London. Over the last 15 years his lab has discovered novel DNA repair genes and provided molecular insights into their impact on human diseases.

Graeme Smith is Chief Scientific Officer at Artios. He joined Artios from AstraZeneca, where he was Senior Director of Bioscience within the Oncology Innovative Medicines and Early Development division. Graeme gained his PhD from the University of Edinburgh and subsequently worked as a research fellow at the Wellcome/CRC Institute at the University of Cambridge in the laboratory of Professor Steve Jackson, FRS.

Geoff Higgins is an associate professor in the Oxford Institute for Radiation Oncology, having held a Cancer Research UK Clinician Scientist award since 2011. He is an honorary consultant clinical oncologist at Oxford University Hospitals NHS Trust and is a medical research fellow at Corpus Christi College. He previously undertook specialist medical training at the Edinburgh Cancer Centre before moving to Oxford as a Cancer Research UK Clinical Research Fellow in 2007.

Mark Charles is Associate Director at Cancer Research UK’s Therapeutic Discovery Laboratories.