Leaders in the Field: Salman Siddiqui on the way forward for breathomics
Published on: 6 Dec 2021, under Interviews
For this entry in our ‘Leaders in the Field’ series of in-depth interviews we spoke to Salman Siddiqui, Professor of Airway Disease and Respiratory Medicine at Leicester University. Salman was the translational lead for the East Midlands Breathomics (EMBER) MRC molecular pathology node and his group has been doing ground-breaking work for a number of years looking at breath biomarkers for asthma, amongst another inflammatory airway diseases, and markers of inflammation mechanisms in general.
Salman has recently accepted an exciting new role as Professor of Respiratory Medicine at the National Heart & Lung Institute at Imperial College London. We spoke to him about how future developments in breath testing could revolutionize the status quo in respiratory medicine.
You’ve been working in respiratory medicine for about 20 years now, what was it that drew you to that specialism?
I think one of the things that really pulled me to respiratory disease was the major unmet need. Respiratory disease is a major cause of both disability and mortality worldwide. Complex chronic diseases, like asthma and COPD, are really common and place a significant burden on healthcare systems.
We don’t really have very good ways of measuring, detecting and treating respiratory disease in a stratified way. I think breath-based diagnostics could transform how we approach respiratory disease – from a reactive approach, when the disease has already become really well incepted in the lung, to a more proactive approach and potentially even primary prevention. I think there is an enormous opportunity to help people by conducting active research in respiratory disease.
Why do you feel that inflammation is so important in the respiratory medicine field? And what do you think we can gain from investigating that more closely?
We now have this amazing opportunity in pulmonary medicine where we can dissect out the biology and understand the impact of that in humans using approaches such as single cell sequencing in primary cells and novel model systems using primary cells such as organ on a chip. What excites me about measuring and quantifying inflammation is that we have an opportunity to identify patients that have specific subtypes of inflammation (for example: type-2 inflammation in severe asthma), and then stratify treatments to them so that we get the most effective outcomes for our patients first time.
Currently patients often end up on the wrong treatments. If you’re on the wrong treatment with severe asthma, you might be on oral steroids for a year or two years unnecessarily, and oral steroids increase your risk of sepsis, blood clots on the lung, fracture, and cardiovascular disease. I think that measuring, quantifying and then targeting inflammatory disease in a precise way, offers an enormous possibility in pulmonary medicine.
“Through the nodes, we learned the importance of working with industry. Clinical academic industry partnerships offer the best platform for patient recruitment, delivering studies supported by quantitative and analytical expertise.”
When did you become aware of Owlstone, and in what context?
When I first met Billy Boyle [Owlstone Medical’s CEO], he told me about this little FAIMS sensor that had been developed to detect sarin, for a different industry. I immediately thought that technology had enormous opportunity to help quantify breath biochemistry. In years following that, my group then helped Billy set up some of Owlstone’s early studies and this led to an opportunity from the EPSRC and MRC to set up a new molecular pathology node in the UK.
The MRC had realised that molecular pathology was fragmented, and that there needed to be more of a close coalition between industry, academic and NHS partners. They commissioned and funded several UK molecular pathology nodes and I helped found EMBER in the East Midlands. Billy and Owlstone were really influential in how we shaped the node. Through the nodes, we learned the importance of working with industry. Clinical academic industry partnerships offer the best platform for patient recruitment, delivering studies supported by quantitative and analytical expertise.
The node pulled together 19 partners across the East Midlands, which included two universities, an NHS Trust, commercial pharma through a commercial partnership, and several analytics providers, including Owlstone Medical.
“One thing we learnt at EMBER was that the ‘single marker: single disease’ hypothesis of breath biochemistry is truly flawed. It’s really when you get a concatenated series of markers, that you can get very accurate prediction of different types of cardio-respiratory attack.”
What do you think, have been the key successes of EMBER?
We accrued 35,000 samples over five years across 16 studies and we’ve got about 30 publications that have come through the pipeline. We were also really successful in training people in molecular pathology and several have gone on to set up their own independent research groups in analytical chemistry or quantitative science.
One thing we learnt at EMBER was that the ‘single marker: single disease’ hypothesis of breath biochemistry is truly flawed. It’s really when you get a concatenated series of markers, that you can get very accurate prediction of different types of cardio-respiratory attack. What was striking was just how different the markers were between the different cardiorespiratory attack phenotypes. Not only were they very sensitive and specific but we also found some fascinating differences between disease. For example, you often think, there’s not much difference between asthma and COPD, but they’re like chalk and cheese. The asthma exacerbation state is characterised by the depletion of selected markers within a breath sample, whereas COPD is characterised by their enrichment.
These differences mean there’s much more potential to generate an AI algorithm that could separate out the acute cardiorespiratory exacerbation phenotypes. That’s really powerful, and I think we’ve got enough information now to then go on to do much more robust biomarker validation programmes with points of care sensors like FAIMS that are nearer the clinic. You’re not going to get a mass spec in the clinic anytime soon, but you will get FAIMS sensor and sampling devices like ReCIVA near the clinic.
Another area that we led on in my group was the delivery and development of breath biomarkers of type-2 inflammation using in vitro approaches and looking at how well they classified things like response to biologics and severe asthma. That has led to some exciting data that we’re writing up now.
“COVID has helped us reimagine medicine. I’m hoping that it will help us reimagine how we conduct research, hopefully at a more national scale, for the benefits of patients really.”
The COVID pandemic has had a particularly large impact for respiratory medicine. How has it affected your research and your priorities? How has it impacted your working practices in general?
I think COVID provided us with both an opportunity and a threat to our existing research, shutting down some areas while allowing us to explore ways to do research differently. Balancing that was truly difficult over the last couple of years.
COVID has provided UKRI with this massive opportunity to reimagine how research is done at a national scale. You can’t answer big medical questions in one group, in your own office or lab anymore. I think COVID taught us that when we embrace the challenge of nationalising research, bringing together the best people from the best groups into a framework, we can achieve some amazing things across the UK.
One of the fascinating things that we learned from COVID is that self-isolation and shielding does significantly reduce the risk of viral transmission. As a result of that, we found that there was a big tail off in asthma and COPD exacerbations in respiratory disease. When you’re trying to recruit into exacerbation trials for asthma biologics, you’re trying to recruit patients that had a certain number of exacerbation events over the previous year.
COVID has helped us reimagine medicine. I’m hoping that it will help us reimagine how we conduct research, hopefully at a more national scale, for the benefits of patients really.
What are your long-term career goals, and what are the key challenges that you need to overcome to achieve those goals?
In the longer term, my group are really focused on using both in vivo and in silico approaches to experimental medicine. We want to study immune mediated diseases driven by types of inflammation. With some of the high dimensional profiling techniques we now have e.g. Single cell technologies and gene editing in primary cells, we have this opportunity to really understand biology in a way that we’ve never had before.
Bringing breath into that equation, there are still questions to answer like where volatiles come from, why they differ between patients and how this relates to biochemistry and cellular mechanisms. It’s even possible that some volatiles could be part of a new system of crosstalk between inflammatory cells in the lung? There’s still a lot to uncover.
What’s exciting is once we really know what these markers are, we can then go back and reverse translate to understand what the impact of these volatiles are on the inflammatory cells. And then, find out which olfactory receptors, for example, are expressed in these cells, how selective they are for certain volatiles and what the impacts of the VOCs are on the cells themselves, and on different patterns of inflammation. That’s when we’re going to start to get more insight into causality and mechanism, rather than this broad approach that we have at the moment, which is really just measuring markers without knowing where they come from.
“Patient studies in the 1,000s are usually required to validate high quality diagnostic markers for clinical practice. So we need to do big studies, supported by the right level of funding, with breath as the primary focus, not an exploratory thing.”
What needs to change in the field to allow continued progress and to achieve the potential that breath has as a diagnostic and monitoring tool?
I think it comes down to a few key areas. The first is that we are at this exciting stage where we can scale – the technologies are there, and the sampling methodology is there. Really, we now need to be doing those large-scale studies that will give breath biomarkers greater credibility. Patient studies in the 1,000s are usually required to validate high quality diagnostic markers for clinical practice. So we need to do big studies, supported by the right level of funding, with breath as the primary focus, not an exploratory thing.
The second issue is sampling, there are still significant limitations in the analytical sensitivity of breath. You’re seeing volatiles that are really trace, they’re in the parts per trillion range, and more needs to be done on the instrumentation side to sample in a way that increases that sensitivity and on the mass spec side to maximise the sensitivity that we get from the sample.
The third issue is going backwards. Once you have robust markers, you need a way of understanding where those markers are coming from, and relevant systems to help you understand what the impact of those markers is on inflammatory cells.
“At Imperial I think there’s a big opportunity to set up the next EMBER, with a more strategic and substantive relationship with industry and companies like Owlstone. I think it’s going be exciting.”
You’ve recently accepted a new role as Professor of Respiratory Medicine at the National Heart & Lung Institute at Imperial College, London, congratulations! What are you most looking forward to, and what do you hope to achieve with this position?
What I’m most excited about in this context of breath biomarker research – is the opportunity to combine both volatile and non-volatile sampling. The integration of breath biochemistry with the information that we get from these liquid particles that are coming from the small airways is really fundamental. I think there are opportunities to image single particles with techniques such as optical trapping and Raman spectroscopy, which will then give us a much more complete profile of what’s in the breath. This will have application in other areas including infectious disease and viral transmission.
EMBER has finished as of this year. There are still a number of publications to get out, but funding has now wound down. At Imperial I think there’s a big opportunity to set up the next EMBER, with a more strategic and substantive relationship with industry and companies like Owlstone. I think it’s going be exciting. Anyone interested in collaborating in the future can reach me via email.
In 2020 Prof. Siddiqui’s group published a paper in ERJ Open Research investigating the feasibility of using Owlstone Medical’s ReCIVA® Breath Sampler with patients reporting acute breathlessness.
More recently Salman’s group has published a review paper looking at the VOC markers of inflammation and a study that investigated the feasibility of diagnosing COVID-19 infection on exhaled breath.
This blog post is part of our ongoing series of in-depth interviews with influential leaders currently working in breath research. Other ‘Leaders in the Field’ interviewees have included Professor Richard Yost, inventor of the triple quadrupole mass spectrometer, and Professor James Covington, a leading voice in VOC biomarker research.