A Word From the Wise

You’re both involved in your own work related to COVID-19. Could you tell us more about that?

Maarten: My lab was actually involved in our own consortium, similar to Perdita’s, called CoV-MS, which was looking at developing a short-term addition to the COVID testing toolbox. With my PhD student Bart Van Puyvelde, we were initially only aiming at the discovery phase – we wanted to see if we could detect some proteins related to SARS-CoV-2 in patient samples. But that ended up going so well that before we knew it, we were looking at how it could work in a clinical setting. We got it to a really promising point, but essentially there were too many hurdles to us moving it into the clinic. And that’s why I admire Perdita’s work so much – what she managed to do really is an impressive feat!

Even though our initial project didn’t continue as such, we have continued to work in this area. We had already been talking to SISCAPA, who were building peptide antibodies that essentially act as tweezers to fish out whatever it is you need to measure. Because our strength is really in academic optimization, we’ve been helping to build different protocols with SISCAPA – and that is actually what the NHS protocol is built around. At the moment, while Perdita has used this ingenious method to inactivate the virus, we are still trying to discover whether we can create an SOP that is perfect for the clinic and will work with any background – because we think we have a better chance of convincing clinical labs to give it a chance in Belgium in this case.

Jenny: My group has been involved in quite a few projects related to COVID-19 with a large number of collaborators. Of interest is a study of multi-systems inflammatory condition (MIS-C) in children, as well as other plasma studies focused on identifying mortality biomarkers. We’ve also been involved in the analysis of cells expressing different SARS-CoV-2 proteins – in fact, we are about to analyze the California variant (Cal20.C) and look at whether or not there is an underlying difference in the mechanism of infection. The final thing we’ve been working on is using remote blood sampling devices to look for COVID-19 induced seroconversion post-infection. We’ve then been analyzing those patients to figure out what the proteomic influences are in that process including those influences in COVID-19 long-haulers. So quite a lot!

How did you initially get involved in Perdita’s project?

Jenny: I got involved at the stage where the UK team had already started to generate some of the data – the infrastructure was already in place but they were trying to figure out which methods or instruments were best to pursue. As one of the external advisors on the project, I would meet with the team pretty much weekly to help troubleshoot and provide guidance because there was such an urgency to this project. We were mostly used as part of the decision-making process for the technical and analytical concepts that had to be decided. Of course, it was a unique situation brought about by COVID-19, because advisory boards do not usually meet this regularly. It was a super interesting process to be involved in and it was extremely productive.

Maarten: While we were working on our own test, we got to a point where we had to look for people with access to triple quad MS instruments and who were used to working with them. That’s when I sent out an open call to anyone who met the requirements, and we got to work with lots of instrument vendors and academic labs that had more expertise in certain areas than we did. This actually worked pretty well and we got a good idea of what the instrumental capabilities were around the world. It was at this point that Perdita really got to work on a similar (but much bigger) effort in the UK and managed to get funding from the NHS. So we kind of linked up at that point, and I helped to advise on certain aspects – it was perfect timing really because our project in Belgium was not destined to move into the clinic.

Why is it important to have MS testing for COVID-19 at all?

Jenny: The power of MS lies in multiplexing and the ability to quantify multiple proteins simultaneously, providing better analytics and additional clinical insight. Originally, the test was developed to improve COVID-19 testing capacity in response to a lack of reagents, but its ability to adapt to different variants will also be incredibly useful. Expanding this idea, we could see development of an assay comprising multiple tests for SARS, flu, and lots of other diseases that could be run simultaneously.

The other reason is simply to show it can be done! That is, to show it is possible to efficiently and effectively develop and deploy a protein clinical MS assay. Certainly, there are going to be more pandemics coming our way – with the help of MS we should be able to respond much faster next time, or more immediately, as new variants come out.

On top of this, there’s of course examples where MS can overcome analytical interferences or issues where antibodies don’t give you a correct concentration value. But my main interest lies in remote blood sampling devices, where patients can take their own blood sample at home, send it to a clinical laboratory for analysis and then the assay results reported to their physician for clinical decision making. I think this is a really crucial area in healthcare where MS can help.

Maarten: I’d agree with Jenny. For me, multiplexing is the most exciting aspect of MS. It’s simply a more versatile technique. With PCR, you need to synthesize a very specific nucleotide sequence. With MS – at least in routine tests – we are using simple chemical reagents. The information we can gather is also much broader. In theory, we should be able to tell patients exactly what variant they have, and even look at other viruses while we are there. If people feel sick at the moment and take a COVID test, they either get a positive or negative result. With MS, we would be able to tell them whether they have the flu or something else – we could even be looking at things like cancer and Parkinson’s. Perdita is again leading the way on the latter!

The other argument for MS is that it tells us exactly what is in our sample, as opposed to PCR which inflates the signal. And so, with MS, the risk of contamination is a lot lower. If we truly mobilize the power of MS, we will be much more prepared for future pandemics.
 

What are some of the challenges in translating such tests to clinical labs?

Maarten: Aside from having to convince doctors, I think the biggest challenge for MS is that it’s still too sensitive to the matrix. With PCR, you amplify the RNA and that’s the only signal left to be seen. With MS, we see everything – and that has both advantages and disadvantages. I like to use the metaphor that with MS we are trying to find tiny specks of gold in a riverbed – there’s a lot of sand that needs to be filtered through, and we need to have the right size holes to find what we are searching for.

Aside from this, the diversity of instrumentation is a major hurdle. With PCR, it doesn’t really matter which vendor you’re using. With MS, every clinical lab has a different LC, a different buffer system, a different instrument, and different software. Trying to convince people to develop an assay specifically for each vendor is a challenge. In this work with the NHS, they’ve managed to navigate the issue pretty well because they looked at the performance of different platforms in the P1 Phase and then naturally evolved towards the ones that out-performed others. Then, if a clinical lab doesn’t have those specific instruments, you can provide them with SOPs that are detailed and tailored to their set up.

The final challenge, of course, is that we are constantly competing with RT-PCR. The first question everyone asks is: “So you’re more sensitive than PCR?” No, of course we’re not because PCR detects just one molecule. The next question invariably is: “So you can run more samples than PCR?” Sorry, but no, we cannot look at 1 million patients a day. However, there are all these other amazing benefits that could really have a significant impact on the way we monitor health in the future.

Jenny: I think people still underestimate just how challenging it is to translate these new tests to the clinical lab. The tests need to be so much more rigorous because, all of a sudden, people’s lives are at direct risk – and that’s not a typical problem when working in an academic lab. So you need to know exactly where every chemical is coming from, looking at every reagent that has its own SOP, and you need to produce the same results every day. Even something as simple as changing pipette or reagent brand, which you might assume to be okay in an academic setting, you absolutely need to make sure it will be okay in a clinical chemistry environment.

I remain in awe of the UK team’s work in bringing an MS-based protein test to NHS clinical chemistry laboratories. To me, what’s so incredible is how they’ve managed to bring together so many research labs in the discovery phase, and additional labs in the clinical phase, while working with industry to develop an assay so quickly and to make key decisions in unprecedented time. There’s so much that needs to be considered when you are translating a new marker test to a clinical lab – it’s almost unbelievable that they managed to do it in such a short window of time.

How is the situation different in the US and Europe?

Maarten: I think it’s almost a cultural thing. When I talk to doctors in Belgium, they hear "mass spec" and immediately get skeptical. In the UK, there are a lot of clinical labs that are used to using MS already, so you’re already halfway there. Also, because every test is now benchmarked against RT-PCR, which works very well for what it’s supposed to do, people aren’t really looking for an alternative. Unless there was another shortage in reagents, people wouldn’t really turn to MS instinctively for this testing. So we need to get it as easy to use as possible to see a change in attitude.

Jenny: There’s a unique culture in the UK for collaboration, but I think there’s
another important point to stress here: you can only collaborate and produce work like this if there is a technical and scientific foundation on which to build. You can have all the collaboration in the world, but if you don’t have the right support, funding, and expertise already in place, such impressive and rapid developments are not possible.

With this NHS project, the UK team managed to bring together discovery labs who were experienced in proteomics already and were willing to pivot in this new direction, and they also had the clinical labs who had the technological capabilities and were experienced in running such tests.

What about the impact beyond COVID-19?

Jenny: My view is that every place a clinician has to make a decision, there should be a quantitative biomarker assay available to help them make that decision; that’s our focus as biomarker development researchers. If we manage to address this chasm between academic and clinical labs, I think this is definitely something we could see more of in the future.

I do also think remote blood sampling devices will become more commonplace in the future. We’ve seen it this year with COVID-19, where - particularly in the US - we’ve managed to adapt very quickly to telehealth. We were doing it already in some areas, but imagine how amazing it would be to be be able to send a blood sample device to the patient, and then they have a video call with a clinician who's already received their blood biochemistry data! This is where I see MS and protein assays opening up a lot of clinical usefulness. It could even help solve healthcare challenges such as the lack of available healthcare in underrepresented communities or provide resources in countries where there are fewer physicians.

Maarten: We are currently working on pooling samples. Imagine if you could do 100 patients in three minutes – that’s the perfect way to monitor any future outbreaks of coronavirus, through population screening. We could pick it up as soon as one patient gets infected. It’s not proven yet, but I’m excited to see where it goes.

I’d also like to mention multiplexing again. I can see a future where there’s an MS sitting in a clinic, running a test for COVID-19 perhaps, and then something from oncology comes in, something from hematology after that… and the MS is measuring them and spitting out a semi-automated report for the clinical biologist. It would be truly amazing, but I think it’s entirely possible. Once we get the SOPs sorted, I don’t actually think it will be that hard to convince doctors to make the switch once we show them that one MS can replace all these different tests. They would get their return on investment in a matter of months.

Just like with mRNA vaccines, which were sat there for a long time but suddenly had a huge push from COVID-19, MS needs time to develop in this area. It’s impossible to be the best right away. I think we’re at the earliest stages of MS being used as a diagnostic tool in the clinic, but the promise is so large that we need to continue trying.
 

In the first part of this feature, "Weighing Viruses," Perdita Barran shares how a network of eight academic labs in the UK have joined forces with twelve clinical laboratories based in the NHS to deliver a rapid and sensitive MS test for coronavirus in just four months.