A Healing Silence: Silencing and RNA interference technologies with Dr. Marie Wikström Lindholm, Silence Therapeutics

PharmaFEATURES interviewed Dr. Marie Wikström Lindholm, an oligonucleotide therapeutics, cardiovascular disease and lipid biology veteran currently working at Silence Therapeutics. Silence Therapeutics is working to advance small interfering (siRNA) treatments to mainstream pharmacology, including pipeline products for high-profile partnerships with companies such as AstraZeneca. Silence Therapeutics uses their own proprietary technologies to improve safety profiles and drug specificity. We talked to Dr. Lindholm to find more about the area.

PF: Good day, Dr. Lindholm. It is such a privilege to have the opportunity to talk to someone as successful in such a diverse background as you. Your own journey in science has been quite varied – from cardiovascular disease, to drug discovery, and now molecular design. What do you think is the common motivator that drove you to these areas? Are there any achievements you feel particularly proud of?

MWL: There are definitely achievements I look back on with pride – and thank you for the question. A common denominator in my “scientific history” is cardiovascular disease. It is not the sole thing that I am engaged in now – obviously I work in molecular design in general, but it is something I keep returning to. I think this is due to my interest in lipids since starting out as a graduate student – which drove my passion for learning more about lipid biology and their connection to cardiovascular pathology, as well as cardiometabolic disease. As an academic I worked on increasing our understanding of vascular wall macrophages, the composition of plaques, the cross-talk between lipid metabolism and inflammation – and how these can drive the development of disease. Despite this growing understanding, I did not feel I was making a direct enough impact in improving lives, or innovating solutions for the people who actually die of heart attacks at an early age. This drove me to embrace the opportunity to cross over to industry, where I started out as a scientist setting up a lipid analysis lab for a Danish biotech company, Santaris, working in Antisense Oligonucleotides (ASOs). My scope expanded to early discovery work on the design of ASOs against targets in dyslipidemias and cardiovascular disease. A few years ago I moved from early R&D for therapeutic ASOs to similar work on siRNAs, where I hope my team will be able to continue to improve the molecular design as well as bring the siRNAs to multiple different cell types and target organs. We remain somewhat limited with ASOs and siRNAs, which are still very focused on liver disease – or diseases which involve proteins connected with the liver in some way. This is because liver targeting, with the help of conjugation to GalNAc, is the most validated modality for therapeutic RNA interference (RNAi). However, closing the loop on the cardiovascular background, this limitation doesn’t prevent RNAi from being relevant for cardiovascular disease. I am one of the people that think that atherosclerosis is a liver disease – particularly because of the interplay between adipose tissue and the liver. There is a lot of cross-talk between what happens in the liver and the rest of the body, with a lot of disease-causing mechanisms related to it. Ironically, one reason for my initial interest in lipid biology was my disinterest in molecular biology at the time; I thought the area was overhyped – little was I aware about how much our knowledge of molecular biology could expand over the years. I count myself lucky, building on the insights I gathered in my time in academia, now in a position where I can help interfere with the progress of disease and very excited to see how much we actually can do with siRNAs in the near future.

PF: Your current position in Silence Therapeutics – which is very aptly named, by the way – is perhaps at the forefront of drug technology right now with its focus on RNA interference. What do you feel are the advantages of working with RNAi? Perhaps the nearly limitless possibilities it offers in targeting nearly any process in the human body?

MWL: While it is true that RNAi does offer nearly limitless theoretical possibilities, that is exactly what they are: theoretical. siRNA molecules alone have a limited capacity to enter cells. We require some kind of targeting moiety – our molecules cannot easily cross membranes without assistance. But this is also perhaps one of their advantages; while silencing can be effective, guiding RNAi with a targeting mechanism can eliminate non-specific uptake in cells the siRNA is not intended to reach, which can minimize adverse effects. This would be quite unlike widely accepted small-molecule drugs that have a plethora of side effects because they lack that precise nature, such as statins. And, with access to the entire human transcriptome and our increased understanding of it, we can select truly unique sequences that have strong knockout effects only on our intended target. Thus, RNAi does have the potential for true precision – both for targeting the right cell types, as well as only silencing the intended target.

PF: RNAi has faced a rather tumultuous journey as a technology. Subsequent to its discovery early in the millennium there was a rather long period of fading interest in it in the late 2000s and early 2010s. Do you feel this was because of limitations in delivery mechanisms? Specificity? Other challenges?

MWL: There were a lot of lessons to be learned before RNAi could truly progress. During the first decade of their discovery, siRNAs were delivered mainly in Lipid Nanoparticles (LNP). This modality can deliver a fair amount of siRNA to liver tissue, but isn’t completely specific and, as I understand it, also introduced complicated manufacturing at that point in time. It was also not particularly useful in delivering the agents to tissues beyond the liver. Since the early start for siRNA design, we have learned more about stabilizing the molecule, minimizing the immunogenicity and increasing the potency and duration of action. As such, the challenges faced by RNAi, and the subsequent unpopularity of the method until these were slowly being tackled, are unsurprising.

PF: Now that interest in RNAi has been renewed and big pharmaceutical companies are increasingly driving new partnerships with RNAi innovators, do you think any particular challenges remain?

MWL: Plenty of them. Particularly two key challenges, which are on the agenda for every scientific meeting I have attended for the last few years. The first would be to truly have efficacious and safe endosomal escape. This is because once the, usually conjugated, siRNA is taken up by the cell, the majority will remain entrapped in an endosome or lysosome. This means that a lot of material has to reach the cell for some of that to even manage to escape the endosome; improving in this aspect would be a true game changer. Alas, we have yet to find innovations that truly deliver on this promise and translate to significant dose reductions. It remains a big challenge as we need to find ways that can open up the endosome siRNA is in, while leaving others intact to prevent cell death – natural endosomes exist for a reason. The other challenge, naturally, is that RNAi still remains closely associated with liver disease. The community behind it is very keen to move on to other therapeutic areas as well, but hepatocytes remain the safest and most specific target for siRNAs so far; perhaps with future innovations, other targets will be much improved as well.

PF: What do you feel are the most significant differences between the two main categories of RNAi modalities – small interfering RNA (siRNA) and Antisense Oligonucleotides (ASOs) – and why has Silence Therapeutics chosen to focus on siRNAs exclusively?

MWL: I do possess my own experience in both areas, as I have mentioned. I worked on ASOs for a decade prior to moving across to siRNAs; there are some obvious advantages for ASOs, such as their validated use for splice switching. Beyond that, I have yet to see convincing data  that we will ever be able to make an ASO stable in circulation and within the cell, all the way until it reaches the nucleus to deliver its effect, without the help of a phosphorothioate (PS) “back-bone”. The PS backbone increases the risk for non-specific protein binding, contributing to a broad tissue distribution and, to some extent, dose-limiting toxicity for these compounds. With siRNA, we can reduce the number of PS linkages in the molecules with retained activity, thereby minimizing such non-specific effects. As such, I would say siRNAs are cleaner by nature – they require very specific targeting mechanisms to enter any cell, which means that they can be tailored and be truly precise.

PF: RNAi is not merely of interest to pharmacology, but to the biotechnology industry in general. We have even seen Monsanto make moves in the agricultural sector with RNA interference. What are your own thoughts about progress in such areas? As we’ve already established, RNAi provides immense flexibility by interacting with organisms at a very fundamental level.

MWL: I think the sky is truly the limit with this technology, as long as we can get into the right cells. Once we do breach the cellular barrier and the molecules separate into strands, it can leave a truly durable effect with a single treatment – but it will still be dose-dependent and not permanent. As such, I believe it offers an intermediate solution between, for example, most small molecules – which must be taken frequently, and gene therapy which would only need to be done once. Therefore there would be many areas where I imagine that would be put to use – both in pharmacology and beyond.

PF: Your current position is for molecular design in the RNAi field. As we all know, drug discovery is being revolutionized by improvements in computational methods – both with Artificial Intelligence, particularly machine learning, and quantum computing. Do you feel progress in these technologies will turbocharge RNAi in the coming decade?

MWL: I do think it would – and not just in one way, but on two fronts. It will help the field by assisting with target selection and choosing the right sequences, but also with molecular design – particularly modifications for optimizing our chosen sequences. Even now we test minor alterations to candidate sequences, but at a much slower pace than machine learning technologies could enable us to have. Our field just becomes so complex – particularly for all the permutations each sequence could have; it would be impossible for even the most organized mind to keep track of all of it: machine learning could.

PF: You will be one of the facilitators for our Medical Chemistry Strategy Meeting in London in 2022, where you will be speaking about the impact of AI in drug discovery. We will of course be delighted to host you and share in your expertise through a more personal medium. Are there any insights you’d like to share prior to the event?

MWL: I participated in a similar conference – three years ago. At that point in time, everyone was curious to see the potential of what we could do with AI in medicinal chemistry for therapeutic oligonucleotide design; but it was still very much in a conceptualization phase. Only now have we started to apply machine learning tools – and it is something that is going on across the pharmaceutical industry. Of course, in siRNA our datasets are much smaller than for small molecule medicinal chemistry – so we really need to examine what tools we are able to use in an environment that is not quite as data dense as small molecules. If you think about it, what we are doing may seem complicated, but it is quite less so than doing what the AI is tasked with. I look forward to sharing more at the Strategy Meeting.

Collaboration is key to solving the most important problems in science – as we have learned by our response against the pandemic. Join Proventa International’s 2022 Medicinal Chemistry Strategy Meeting in London to hear the latest insights on siRNA and other trending topics in Medicinal Chemistry – and perhaps even find your next strategic collaboration.

The views expressed in this article are Dr. Marie Wikström Lindholm’s in her personal capacity and do not necessarily reflect the opinions, positions or policies of Silence Therapeutics as a company, or any other entities Dr. Marie Wikström Lindholm is involved in a professional capacity.

José María De Uriarte Díaz, Head of Production, Proventa International

Nick Zoukas, Former Editor, PharmaFEATURES