1 00:00:00,180 --> 00:00:04,360 It should say something. Yeah. Okay. 2 00:00:04,360 --> 00:00:08,560 Can you just start by saying your name and what your current title is? 3 00:00:09,540 --> 00:00:19,079 Yeah. So I'm Andrew Kwok, I'm actually now a clinical lecturer at the Chinese University of Hong Kong and I previously did a PhD at Oxford University. 4 00:00:19,080 --> 00:00:25,020 So that was from 2018 and obviously during the COVID times as mine, I only just finished a few months ago, basically. 5 00:00:25,370 --> 00:00:28,860 Okay. Well, congratulations on finishing. Thank you. 6 00:00:30,030 --> 00:00:35,009 And so, first of all, can you just tell me a little bit about yourself from when you first got interested 7 00:00:35,010 --> 00:00:40,410 in in science generally and to specialise in the area that you're interested in that? 8 00:00:41,370 --> 00:00:48,359 Yeah. So I think with, as with a lot of scientists with COVID, it was a very accident, accidental thing. 9 00:00:48,360 --> 00:00:50,790 Well, I mean, okay, so first of all, the fact that the pandemic happened, 10 00:00:50,790 --> 00:00:54,749 you know, that in itself was already just a very sort of random event that way. 11 00:00:54,750 --> 00:01:01,680 Right. But originally I was interested in immunology that was as an undergraduate student. 12 00:01:02,280 --> 00:01:09,359 And then I did clinical school and I decided that I thought acute situations were really thrilling. 13 00:01:09,360 --> 00:01:15,509 So I thought that if I could try and find some research topic that would combine both of them, that would be the best. 14 00:01:15,510 --> 00:01:20,280 And then that's how I ended up. By acute situations, you mean kind of life or death relationship with the patient? 15 00:01:20,310 --> 00:01:24,510 Yeah. Yeah. So, so, yes, yes. So, so more emergency situations. 16 00:01:24,510 --> 00:01:34,169 Right. And so in that case, I looked up some projects on the university's website and it turns out that the lab that I was in at the end, 17 00:01:34,170 --> 00:01:41,700 so that was Professor Julian Knight's lab. So he has done a lot of work on sepsis, which is a life threatening condition when you get an infection, 18 00:01:41,700 --> 00:01:45,300 and that's usually due to your immune response going a bit haywire. 19 00:01:45,960 --> 00:01:49,860 So I thought, well, that seems to be a really good fit, right? So, so let me see. 20 00:01:50,130 --> 00:01:56,430 And he very kindly took me on. So that's what I was originally embarking the journey on, which was a PhD to work on sepsis. 21 00:01:56,910 --> 00:02:00,120 And then, you know, a year or so and obviously COVID started. 22 00:02:00,120 --> 00:02:05,210 And so given that sepsis is, you know, all that infectious diseases and immune responses, then, you know, 23 00:02:05,280 --> 00:02:10,950 actually, if you think about COVID, it's a bit of a very similar parallel topic or a bit of an extension. 24 00:02:10,950 --> 00:02:18,299 And in fact, you could very well say that technically people who get COVID, who get very, very ill, are essentially septic patients as well. 25 00:02:18,300 --> 00:02:22,980 So it was a very neat kind of marriage of the of the topics, and that's how I ended up getting into it. 26 00:02:23,280 --> 00:02:27,479 Okay. So so before we go on to talk more about the COVID project, 27 00:02:27,480 --> 00:02:35,820 let's talk a little bit more about sepsis and what your what the take of Julia night's lab was on approaching it. 28 00:02:35,820 --> 00:02:39,299 What? So what was it we didn't understand about sepsis? 29 00:02:39,300 --> 00:02:42,570 And what was your particular project aimed at trying to discover? 30 00:02:43,450 --> 00:02:47,489 Yeah. So the idea with sepsis is that it's an infectious disease problem, right? 31 00:02:47,490 --> 00:02:53,069 So if you think about then you split into two halves, then either there's a problem with the pathogen as the invading, you know, 32 00:02:53,070 --> 00:02:57,330 the bacteria or the virus, you know, the invasive aspect, or there's an ASP, 33 00:02:57,600 --> 00:03:01,470 there's an issue with the host response of the way the human system behaves. 34 00:03:01,830 --> 00:03:07,680 And so we looked at it from the perspective of the human right and we specifically looked at the immune response. 35 00:03:08,040 --> 00:03:16,919 So within that, the main problem that we faced as researchers, I think, was that sepsis is a bit of a broad, vague definition. 36 00:03:16,920 --> 00:03:23,010 So operationally it's very helpful because it defines the limits of what you can do as a doctor. 37 00:03:23,310 --> 00:03:28,770 So if you tell people that, okay, you know, we have a septic patient, that they're very ill, maybe they're going to need intensive care support. 38 00:03:28,770 --> 00:03:32,820 So, you know, you move, you escalate in terms of the amount of medical care you give the people. 39 00:03:33,240 --> 00:03:38,280 But what that doesn't really tell you is what the underlying biology is that's going wrong. 40 00:03:38,410 --> 00:03:42,480 Right? So that's so then you just have this broad umbrella. And so what our aim was to do, 41 00:03:42,990 --> 00:03:48,510 our aim was basically to see if we could understand the patient in groups with the condition 42 00:03:48,510 --> 00:03:54,809 a bit better by giving a proper biological mechanism behind different groups of patients. 43 00:03:54,810 --> 00:03:57,810 So to stratify them, so to speak, that was the idea behind the lab. 44 00:03:58,110 --> 00:04:01,110 So the idea being that different people might respond, 45 00:04:01,380 --> 00:04:06,330 they might catch the same bacteria or the same virus, but their body responds in a different way. 46 00:04:06,630 --> 00:04:10,230 What according to their genetic makeup. Right. 47 00:04:10,230 --> 00:04:17,580 Well, so that, you know, the genetics is then obviously a need to answer or any potential potential question to investigate, let's say. 48 00:04:18,120 --> 00:04:22,109 And I think, yeah, there's been a lot of genetics done in sepsis. 49 00:04:22,110 --> 00:04:24,420 I would say that none of it has been very fruitful. 50 00:04:25,110 --> 00:04:30,840 But yeah, you know, so we look at every layer, so everything from the genetics to just upstream of that and then, 51 00:04:30,930 --> 00:04:35,910 you know, all the way through to the immune system and so on. And I focussed quite a lot on the immune system. 52 00:04:37,370 --> 00:04:41,080 Okay. So it was a what? I'm sorry. I'm going to dive down into this a bit. Yeah, sure, sure. 53 00:04:41,360 --> 00:04:47,390 The immune system has many components. What are the particular components of the immune system that you've been interested in? 54 00:04:48,070 --> 00:04:52,309 Yeah. So that was a bit of a journey as well, right. Because so obviously, first of all, 55 00:04:52,310 --> 00:04:59,080 there was a lot of literature already on how different aspects of the immune system were dysregulated in the septic response. 56 00:04:59,510 --> 00:05:02,100 So for example, I think, you know, 57 00:05:02,120 --> 00:05:07,639 when people get vaccines with COVID that people may have heard of T cells and B cells being thrown around these kind of terms. 58 00:05:07,640 --> 00:05:08,629 Right, because of the pandemic. 59 00:05:08,630 --> 00:05:16,100 And so there was a whole literature about t cell dysfunction in sepsis, for example, and that the T cells were overactive or undirected. 60 00:05:16,110 --> 00:05:19,249 What was wrong? Yeah. Mostly underactive, I would say. 61 00:05:19,250 --> 00:05:25,290 Mostly underactive, but then. The way we looked at it was a little bit different. 62 00:05:25,290 --> 00:05:30,060 So our initial approach was to take blood from patients, total blood. 63 00:05:30,420 --> 00:05:35,130 And it turns out that the proportion of T cells that are in your blood is actually very, very low. 64 00:05:35,190 --> 00:05:40,470 Right. So so in the in the initial experiments that we were running, this is before I even joined the lab, 65 00:05:40,800 --> 00:05:43,620 the initial experiments from Juliane and others in the group. 66 00:05:44,640 --> 00:05:50,490 If you take the whole blood and then you just profile the total amount of RNA in the blood, 67 00:05:50,490 --> 00:05:57,330 and then you see if you can stratify patients with some various machine learning based algorithms and advanced statistical analysis and so on. 68 00:05:57,990 --> 00:06:02,280 Then you can it seems like we were getting meaningful subgroups of patients, right? 69 00:06:02,280 --> 00:06:08,190 Meaningful in the sense that certain gene expression signatures which were very reproducible, 70 00:06:08,490 --> 00:06:13,740 seemed to mark out groups of patients who would deteriorate much more quickly than others. 71 00:06:14,080 --> 00:06:16,860 Right. So it seemed like we were getting some meaningful biological signals. 72 00:06:16,860 --> 00:06:20,010 You know what I was saying about getting the biological mechanism behind the different groups, right? 73 00:06:20,400 --> 00:06:25,500 So that was that got us very excited. And that's basically how I joined the lab, right? Because I saw that I thought, hey, this is really meaningful. 74 00:06:25,500 --> 00:06:31,610 Let's dive deeper into it. So that initial finding was when you just took blood in bulk. 75 00:06:31,620 --> 00:06:37,799 Right. And so my question was very much, well, what are the cellular contributions to that signal that you're seeing? 76 00:06:37,800 --> 00:06:44,490 Which cells do the signals derive from which cells are therefore most likely, you know, malfunctioning in some way or another? 77 00:06:44,490 --> 00:06:47,540 How are they malfunctioning? Those are the questions that I wanted to address in the fleet. 78 00:06:47,550 --> 00:06:51,630 Right. So one so for ranked cells, have we got swimming around in our blood? 79 00:06:52,230 --> 00:06:57,629 Right. Right. So you could maybe broadly split it into what we call lymphoid and myeloid lineages. 80 00:06:57,630 --> 00:07:00,390 So lymphoid, you know, the T cells in the B cells, 81 00:07:00,390 --> 00:07:07,440 these are lymphocytes that people are both maybe have heard of and that those are the cells which are really exciting. 82 00:07:07,440 --> 00:07:13,979 And I think, you know, more historically, immuno, immuno immunologists were particularly excited about them in the sixties, in the seventies, 83 00:07:13,980 --> 00:07:19,980 because those were the cells where the exciting aspects of immunity seemed to reside in, 84 00:07:19,980 --> 00:07:26,400 such as the ideas of immune memory and immune specificity, the fact that you can target a pathogen very specifically. 85 00:07:26,400 --> 00:07:31,740 And then if you've had that infection once before, you know, a few months down the line, you see it again, you're able to respond very well. 86 00:07:31,740 --> 00:07:34,620 That's basically how the vaccines work, right? So that's the lymphoid side of things. 87 00:07:35,070 --> 00:07:39,750 And so in a sense, there's also a very much neglected other side, 88 00:07:39,750 --> 00:07:45,570 which is the myeloid lineage where you have cells such as things called granulocyte or monocytes. 89 00:07:45,900 --> 00:07:51,479 We ended up looking a lot at the granular science, but those cells I think are a little bit more poorly understood. 90 00:07:51,480 --> 00:07:56,730 And I think traditionally the remit has been more with the haematologists rather than the immunologists looking at that. 91 00:07:56,730 --> 00:07:59,610 And that's because the cells have been ditched by the immunologists to some extent. 92 00:07:59,610 --> 00:08:04,169 But I think in recent years there's been a lot more excitement in looking at those myeloid cells, 93 00:08:04,170 --> 00:08:07,409 which are which also another, you know, another bit of terminology. 94 00:08:07,410 --> 00:08:13,319 But if you broadly divide immunity into innate and adaptive, so adaptive being the immune system, 95 00:08:13,320 --> 00:08:16,139 which again has that specific function, has the memory function. 96 00:08:16,140 --> 00:08:23,940 So those are those lymphocytes, whereas the innate arm is the arm that responds more quickly and has a more non-specific response. 97 00:08:23,940 --> 00:08:26,990 And those are those myeloid cells more. So I would say. Yeah. 98 00:08:28,500 --> 00:08:36,030 And so you were looking to see if these myeloid cells were producing the distinctive signatures that had turned up in your analysis of whole blood. 99 00:08:36,870 --> 00:08:43,550 Yeah. So the first way we did it was what we tried to actually go in with a slightly more unbiased lens, right? 100 00:08:43,560 --> 00:08:48,600 So, so this was one of the more initial questions that I was challenged when I first started the application. 101 00:08:48,600 --> 00:08:52,950 So around the time I started there were these very exciting new technologies that 102 00:08:52,950 --> 00:08:57,269 were coming along called single cell RNA sequencing or single cell sequencing, 103 00:08:57,270 --> 00:09:03,960 we can call them. So that is to say, imagine if you could literally take every individual cell in your sample or your body, 104 00:09:04,500 --> 00:09:08,720 the sample material working with and you could actually profile all of them individually. 105 00:09:08,750 --> 00:09:14,729 Look at all of the RNA or DNA molecules, whatever your choices, all of those molecules in that individual cell. 106 00:09:14,730 --> 00:09:17,070 Right. So it's a very, very powerful technology. 107 00:09:17,070 --> 00:09:23,190 It's been around for more than ten years now, but then it's really taken off over the last five years or so, I would say. 108 00:09:23,550 --> 00:09:26,790 And so when I started the PhD, this was starting to become quite a hot topic. 109 00:09:26,790 --> 00:09:34,319 I wanted to, you know, really try it out as well. And the beauty of it is that it gives you a relatively unbiased lens into the question. 110 00:09:34,320 --> 00:09:43,560 Right, that you're asking. So because if you have your blood population of cells and you don't necessarily know which cells are the most relevant, 111 00:09:44,070 --> 00:09:48,600 you might have some guesses based on prior literature, but you can be sure you know 100% sure, right? 112 00:09:48,870 --> 00:09:52,319 You might want to use techniques such as this kind of single cell sequencing so that 113 00:09:52,320 --> 00:09:56,190 you can profile all of the cells and then you're sure not to miss any of the signals, 114 00:09:56,190 --> 00:10:00,030 per se, right? Yeah. And. 115 00:10:00,310 --> 00:10:05,380 Yeah. And so how far would you go with that? Well, it would fail. 116 00:10:06,010 --> 00:10:10,330 Yeah. Yeah. So because I was just starting, I'd never done this kind of work before. 117 00:10:11,080 --> 00:10:14,140 We we didn't get very far. We just ran some pilot experiments. 118 00:10:14,410 --> 00:10:18,879 It took more than a year to set up because in parallel, other than the lab side, 119 00:10:18,880 --> 00:10:22,300 other than the technological side, we were also basically setting up the clinical study. 120 00:10:22,300 --> 00:10:29,080 We'd had previous clinical studies in place, but there wasn't quite the ethics for us to take the kind of samples we wanted. 121 00:10:29,080 --> 00:10:34,990 So we actually spent a lot of time working out the ethics and the clinical study and then starting to actually recruit patients. 122 00:10:35,470 --> 00:10:41,830 Before we could even run some of the experiments. We got to the stage where we had some initial pilot data and then COVID hit. 123 00:10:43,060 --> 00:10:46,540 So you were you involved personally involved in recruiting the patients as well? 124 00:10:47,290 --> 00:10:52,540 Yes. So because of my clinical background, I basically did the entire study from scratch. 125 00:10:52,550 --> 00:10:54,730 Right. I wrote it up from scratch. 126 00:10:54,730 --> 00:10:59,380 And then I met all the people in the hospital, all the all the teams involved, to all the research nurses on the ground. 127 00:11:00,040 --> 00:11:07,750 And of course, as the research team, I wasn't actually meeting the patients directly, not in terms of the recruitment, 128 00:11:08,020 --> 00:11:14,560 but I was liaising very closely with that, closely with the research nurse teams who would then contact the patients. 129 00:11:14,800 --> 00:11:19,960 And then we also did a lot of work, for example, with patient groups, you know, patient groups with sepsis, 130 00:11:20,200 --> 00:11:24,489 so that we could understand from their perspective what they would want to be involved in, 131 00:11:24,490 --> 00:11:28,330 whether they thought this was useful at all, you know, engage them a bit of education. 132 00:11:28,910 --> 00:11:33,040 Yeah. Yeah. So I was doing a lot of that in the first year, actually. Excellent. 133 00:11:33,970 --> 00:11:37,840 So, yes, so we get let's get to to the arrival of COVID. 134 00:11:38,410 --> 00:11:43,840 Can you remember I mean, obviously, you come from from from Hong Kong yourself. 135 00:11:44,290 --> 00:11:56,259 Yes. So you must perhaps more alert to what was going on in Wuhan and spreading out into China, maybe a little earlier than some people were. 136 00:11:56,260 --> 00:12:05,169 And I think people I've interviewed have had a range of initial reactions from, Oh, it can be like sighs. 137 00:12:05,170 --> 00:12:10,420 It'll just go away, it won't come here. And other people saying, This looks really bad and we should we need to do something. 138 00:12:10,420 --> 00:12:14,830 So what what was your how did you first hear about it and what was your initial reaction? 139 00:12:16,170 --> 00:12:20,370 So I first heard about it towards the end of 2019. 140 00:12:20,430 --> 00:12:22,800 I definitely remember it was it was still December then. 141 00:12:23,580 --> 00:12:29,700 And I think the initial reaction was I wasn't too worried in the sense that it didn't seem too close yet. 142 00:12:29,700 --> 00:12:35,570 And you know, as with a lot of these things, you kind of have to just let things run their course to see how it pans out. 143 00:12:35,580 --> 00:12:39,510 It's just a bit impossible to predict. So in that sense, I wasn't necessarily very worried. 144 00:12:41,460 --> 00:12:46,650 I think I was also then then, you know, in another month or two's time, by the time January, 145 00:12:46,650 --> 00:12:50,400 February 2020 rolled around, it definitely seemed like it was a bit more serious. 146 00:12:50,400 --> 00:12:56,040 Right. I think at that point, I still wasn't very worried, at least to the extent that. 147 00:12:58,190 --> 00:13:06,550 I felt like I was personally quite prepared for issues of infection spreading through 148 00:13:06,560 --> 00:13:12,560 communities because I'd lived through sores myself and I thought that that was a. 149 00:13:14,030 --> 00:13:18,320 Preparation experience, if you if you if you will. You know, we we all survived through that one. 150 00:13:18,920 --> 00:13:25,850 But then, obviously. They were very different in the sense that this time, you know, it was a full on pandemic. 151 00:13:25,850 --> 00:13:29,780 Right. It really spread across the world. I think I didn't necessarily see that coming. 152 00:13:29,780 --> 00:13:35,150 But then I guess the question is for the people who say they saw it coming. 153 00:13:35,300 --> 00:13:40,630 You know, how how much predictive accuracy do you have if something else happens the next time around? 154 00:13:40,640 --> 00:13:43,730 Right. And, you know, you can always say that, oh, this one looks really bad. 155 00:13:43,730 --> 00:13:47,570 This one looks really bad. Is it always going to be really bad? It's very hard to say. 156 00:13:47,570 --> 00:13:56,050 Right. So I was. I think I was generally more worried during the thing than like in terms of any anticipatory anxiety. 157 00:13:56,080 --> 00:13:59,590 Yes, yes, yes, yes. Okay. We'll talk bit more about that later. 158 00:13:59,800 --> 00:14:09,880 So at what point did Julian and the lab decide that you were ideally placed in the way to to tackle, 159 00:14:10,360 --> 00:14:14,020 you know, to use the techniques that you were using to tackle COVID itself? 160 00:14:14,980 --> 00:14:23,080 Yes. In fact, before the virus actually hit the UK in January 2020, when things were actually still quite normal in the U.K., 161 00:14:23,290 --> 00:14:30,369 we were already looking into it because Julian had some collaborations with a group in Beijing, 162 00:14:30,370 --> 00:14:35,320 which was a virology group, and so they were obviously, you know, working hard on the problem already. 163 00:14:35,650 --> 00:14:42,969 And so we had some discussions and communications and we had sort of some ideas of what we could offer on our side, you know, 164 00:14:42,970 --> 00:14:44,810 leveraging what we'd done on sepsis before, you know, 165 00:14:44,830 --> 00:14:49,720 whether there were similar similarities and whether we could parallel up parallels, any kind of work. 166 00:14:50,050 --> 00:14:54,720 So we'd already put in a little bit of thought there. And then, of course, COVID actually hit, right? 167 00:14:54,730 --> 00:14:59,430 And so. I think we were. 168 00:15:00,410 --> 00:15:05,480 Not necessarily ahead of the game, but it was just because of that collaboration that it just prompted us to think quite early, 169 00:15:05,540 --> 00:15:14,240 you know, before it even hit the UK. And so, I mean a study was set up with the title combat. 170 00:15:15,430 --> 00:15:18,470 You just tell me what that, what that stood for. 171 00:15:18,530 --> 00:15:22,580 And we'll talk a bit more about how it how it came together. 172 00:15:23,120 --> 00:15:30,299 Yeah. Yeah. So the combat was the name for the consortium, the COVID Multi-omics Blood Atlas. 173 00:15:30,300 --> 00:15:38,270 So the COVID being COVID right, the multi omega pot is where when I was saying talking about single cell sequencing earlier on. 174 00:15:38,270 --> 00:15:45,169 So this idea that if you can sequence molecules and get an unbiased view, right, as in so you don't know what the bag of molecules are, 175 00:15:45,170 --> 00:15:47,180 you just sequence all of them first and then see, 176 00:15:48,050 --> 00:15:55,129 that's when in biology we call that a lot of omics because it's and that's to say it encompasses the whole thing, right. 177 00:15:55,130 --> 00:15:59,180 So your, your genome, right. Is your whole whole genetic makeup. 178 00:15:59,180 --> 00:16:02,540 Right? Or you can see the transcriptome, which is the way the genes are expressed. 179 00:16:02,540 --> 00:16:06,620 And that's how all of the genes are expressed as the transcriptome rather than each individual one. 180 00:16:07,010 --> 00:16:08,209 And so that's the omics. 181 00:16:08,210 --> 00:16:15,020 And so it was an idea of multi-omics in the sense that we had layers of data which were all encompassing at the level of the DNA, 182 00:16:15,020 --> 00:16:18,110 at the level of the RNA, at the level of the proteins and so on and so forth. 183 00:16:18,620 --> 00:16:22,249 And because we were heavily focussed on blood sampling, so that was the Blood Atlas. 184 00:16:22,250 --> 00:16:27,260 So we were building this entire atlas of how the human was responding to the 185 00:16:27,260 --> 00:16:31,760 virus through a blood window and with these many different layers of the data. 186 00:16:33,660 --> 00:16:44,100 So. So the idea was to take blood from COVID patients and what compare that with people with other infections or people with no infections. 187 00:16:44,550 --> 00:16:54,129 How did that work? Yeah. So one of the strengths of the set up and I think our cohorts was that we had obviously the single, 188 00:16:54,130 --> 00:16:57,900 you know, basic comparison is you compare people with COVID with healthy individuals. 189 00:16:58,260 --> 00:17:05,040 Right. And then there was a tricky thing as to how you could get age appropriate controls. 190 00:17:05,040 --> 00:17:08,729 Right? Because actually a lot of the people who are being hospitalised with COVID or 191 00:17:08,730 --> 00:17:12,930 especially getting critical illness were people on the older age or older spectrum. 192 00:17:12,930 --> 00:17:15,930 Right. It wasn't as many 20, 30 year olds. There were some. 193 00:17:15,930 --> 00:17:21,240 But that was, you know, fewer, fewer proportion at a lower proportion for sure. 194 00:17:21,810 --> 00:17:27,270 So then there was a very tricky thing of having to find older, healthy controls. 195 00:17:27,270 --> 00:17:33,450 And actually we had some recruitment drives where we distributed posters to various colleges asking for various professors, 196 00:17:34,110 --> 00:17:37,499 you know, of slightly more advanced ages to participate. 197 00:17:37,500 --> 00:17:40,920 And it was it was quite it was actually we got quite a doozy asking responses. 198 00:17:41,400 --> 00:17:45,030 And so what do you need? It from them was a blood sample. 199 00:17:45,210 --> 00:17:51,930 Is that right? Yes. Oh, it. That was it. Yes, that was it. But it was you know, it was not easy to be able to find such a targeted age group in a way. 200 00:17:51,950 --> 00:18:01,109 Right. So that was one route we had. And then we also had a contrast between people who were very ill from COVID and people who are less ill. 201 00:18:01,110 --> 00:18:09,240 So that ranged from individuals who were hospitalised but didn't necessarily need much additional medical support other than just sort of monitoring. 202 00:18:09,960 --> 00:18:13,560 And then we had people were critically ill in intensive care from COVID. 203 00:18:13,560 --> 00:18:15,030 So those who were actually septic. Right. 204 00:18:15,390 --> 00:18:20,010 And then we had some individuals who were in the community who caught COVID, didn't even need to be hospitalised. 205 00:18:20,010 --> 00:18:25,079 So we had the whole we spend a whole range of severities and then we still had a couple of more 206 00:18:25,080 --> 00:18:31,620 comparisons where we managed to source some cohorts of patients who had previously had flu, 207 00:18:32,880 --> 00:18:36,740 the flu infection and were critically ill as well in intensive care. 208 00:18:36,750 --> 00:18:42,030 So that provided a very, very good control to the COVID critically ill COVID patients, 209 00:18:42,030 --> 00:18:44,999 because then you had two groups of patients which were both critically ill, 210 00:18:45,000 --> 00:18:48,990 but from different pathogens, and you could see how the immune response was going differently. 211 00:18:49,380 --> 00:18:53,250 And then there was a final one where we had some or all cause or, you know, 212 00:18:53,250 --> 00:18:58,920 mostly bacterial causes really of septic patients who were also very, very ill. 213 00:18:58,920 --> 00:19:02,550 And again, they were not caused by COVID, but illness. 214 00:19:02,700 --> 00:19:06,509 And we could compare those immune responses again with the individuals who had COVID. 215 00:19:06,510 --> 00:19:13,680 So we had a whole range of comparisons. So combat, as its name suggests, was a consortium. 216 00:19:14,160 --> 00:19:17,700 I mean, I've I've seen the publication that came out at the end of this, which we'll talk about. 217 00:19:17,700 --> 00:19:22,320 It's got a lot of names on it. How was that consortium put together? 218 00:19:23,400 --> 00:19:27,600 So I think it was very organic, right? I think a lot of things really started in Julian's lab. 219 00:19:27,600 --> 00:19:32,190 And between us, the two of us, you know, having meetings are just talking about, well, what are we going to do about this? 220 00:19:32,580 --> 00:19:38,489 But it soon became clear that we would need just a lot of on the ground support logistically. 221 00:19:38,490 --> 00:19:44,190 Right. And especially if you consider the context, which is that this was a an acute public health emergency. 222 00:19:44,200 --> 00:19:49,829 Right. I mean, I think that's one of the things that made it particularly impressive was, you know, it's there you know, 223 00:19:49,830 --> 00:19:57,299 we were very proud to be part of and proud of achievement, essentially, which is that it was hectic already enough as it were. 224 00:19:57,300 --> 00:20:05,770 Right. So in a way, the list of names. Includes, I think, just everyone who was even more peripherally involved in the project. 225 00:20:05,860 --> 00:20:11,470 For example, all of the all of the a lot of the ground stop and the hospital who participated and contributed back. 226 00:20:11,650 --> 00:20:18,120 But, of course, also a lot of the key players, such as the research nurses who put in a lot of hard work best, we had, you know, 227 00:20:18,130 --> 00:20:24,750 sample processing teams which were equipped to deal with coded samples, 228 00:20:24,750 --> 00:20:28,270 as I say, equipped because, you know, this was at the beginning of the pandemic. 229 00:20:28,270 --> 00:20:31,389 We were much more worried about the pathogen than we currently are now. Right. 230 00:20:31,390 --> 00:20:36,010 So, you know, then at that point, things had to be done at very high biosecurity levels and so on. 231 00:20:36,010 --> 00:20:36,390 And so, you know, 232 00:20:36,400 --> 00:20:42,580 we had sample processing teams in place and then the teams which would actually generate data and then data analysis teams and so on. 233 00:20:42,940 --> 00:20:44,829 So it was it was quite organic in the beginning. 234 00:20:44,830 --> 00:20:50,889 But as the project grew, you know, we just reached out to more and more people and then I think people were obviously keen because it was, 235 00:20:50,890 --> 00:20:55,720 it was such a big thing and it was it was a great scientific opportunity as well. 236 00:20:55,960 --> 00:21:01,300 And so that's how the team just grew. And then eventually it got to the point where, well, this is clearly the size of a consortium. 237 00:21:02,950 --> 00:21:04,899 And you personally, I mean, again, 238 00:21:04,900 --> 00:21:10,740 I've looked at the contributions of all these different people and your name tags up under most of the that the headings. 239 00:21:10,740 --> 00:21:15,210 So were you playing a coordinating role. Yeah. 240 00:21:15,220 --> 00:21:21,370 So I think I was I was definitely involved in basically every facet of the, of the project, as it were. 241 00:21:21,640 --> 00:21:25,540 I wasn't really the coordinator per se in the sense that I wasn't supervising the project. 242 00:21:25,550 --> 00:21:27,610 So that was really much more of Julian's role. 243 00:21:28,240 --> 00:21:33,010 But in terms of then all of the ins and outs of because if you think about the way the study came about, 244 00:21:33,070 --> 00:21:36,820 so it's a combat was the name of the sort of the study, the group, right. 245 00:21:37,810 --> 00:21:42,880 The majority of the patients were recruited under that initial study that I'd set up in the first year of my people. 246 00:21:43,720 --> 00:21:48,280 So. I was probably I was the best place person to know everything about the study write. 247 00:21:48,280 --> 00:21:51,399 You know, I'd written it up from scratch. I had designed it up from scratch like that. 248 00:21:51,400 --> 00:21:56,080 So I knew where all the ethics, you know, what it was all about, what the framework was. 249 00:21:56,350 --> 00:22:00,700 I knew all the research teams, so it was very, very close liaising with them. 250 00:22:00,700 --> 00:22:01,030 In fact, 251 00:22:01,330 --> 00:22:10,209 in the study we I don't even know what the actual number of COVID patients we've got in the Biobank now is because we've been continually recruiting. 252 00:22:10,210 --> 00:22:12,760 But I very distinctly remember the first two patients, 253 00:22:12,760 --> 00:22:20,350 which I basically cycled the blood samples from the hospital to the lab because that was how on the ground it was at that point. 254 00:22:20,350 --> 00:22:27,579 Right. So so I was involved in everything from, you know, those initial bits with the study to then of course generating the data and then analysing. 255 00:22:27,580 --> 00:22:33,040 And so even though I wasn't coordinating, I was basically in I can imagine like all of the meetings it was it was meetings 256 00:22:33,040 --> 00:22:37,119 constantly in addition to obviously the round the clock scientific work. 257 00:22:37,120 --> 00:22:45,069 Right. So, yeah. Mm hmm. And and so, I mean, is it too soon to jump to the the outcome? 258 00:22:45,070 --> 00:22:49,180 No, I don't think it is. What what what? 259 00:22:49,180 --> 00:22:52,450 Once you know, I think we should talk a little bit about the analysis. 260 00:22:52,450 --> 00:22:58,600 So you collected huge amounts of data, as you say, in this rather unbiased way, which just finding out what was there. 261 00:22:59,710 --> 00:23:03,790 How did you go about the analysis? Right. 262 00:23:04,210 --> 00:23:07,810 So yeah, I guess there are maybe two things that are worth sort of flagging up. 263 00:23:08,140 --> 00:23:12,700 One is that they're a more practical, logistical thing. 264 00:23:12,700 --> 00:23:17,499 But it was it's to say that we had a lot of analysis teams because there was so much data, 265 00:23:17,500 --> 00:23:21,900 as you said, that we needed many people and a lot of different expertise. 266 00:23:21,910 --> 00:23:27,670 It was multi-omics, right? So there was data from, you know, gene expression that was data from protein and so on. 267 00:23:27,670 --> 00:23:30,700 And I wasn't necessarily an expert in all of them. 268 00:23:30,820 --> 00:23:37,000 And in fact, I don't think any of us were really right. So we had to really split the task up and divide and conquer that way. 269 00:23:37,420 --> 00:23:45,219 And then what was very interesting was that around the same time as how well these things develop in parallel, right? 270 00:23:45,220 --> 00:23:51,940 So we we started to have these technologies to probe biological samples in this data heavyweight in the lab. 271 00:23:52,240 --> 00:23:57,970 And so then at the same time, people were coming up with very interesting computational methods to analyse the data. 272 00:23:58,300 --> 00:24:01,959 And so one of the more interesting things to highlight was that and strength, I think, 273 00:24:01,960 --> 00:24:10,240 of the study was that we were trying out some very novel analytical methods to try to integrate the many different layers of data. 274 00:24:10,960 --> 00:24:14,500 And so there were, you know, a number of people on, on that team. 275 00:24:14,500 --> 00:24:16,629 And I was part of that team. I wasn't leading that team. 276 00:24:16,630 --> 00:24:25,540 But, you know, we tried a lot of new mathematical ways to to combine the layers of data in something that would be meaningful rather than just, 277 00:24:25,540 --> 00:24:29,950 you know, an abstract mathematical notion as well. So that was a very, very exciting opportunity. 278 00:24:31,010 --> 00:24:37,240 Yeah. And from looking at the paper, you really work very hard on the visualisation side of it, 279 00:24:37,520 --> 00:24:44,780 making those the results clear or the analysis clear through different kinds of data visualisation. 280 00:24:45,620 --> 00:24:49,879 Yes. And I think this is something that I learned quite a lot from Julian as well, I think, 281 00:24:49,880 --> 00:24:54,450 over the course of years, which is that the data needs to be presented very clearly. 282 00:24:54,450 --> 00:25:00,079 Right. There needs to be not not only does there need to be no ambiguity, but it needs to really flow. 283 00:25:00,080 --> 00:25:03,920 Right, because otherwise it's hard to follow the story as given how complex it already is. 284 00:25:04,030 --> 00:25:07,069 Right. If I was just describing, I'd describe the multi-omics. 285 00:25:07,070 --> 00:25:09,140 I'd describe how many cohorts of patients we had. Right. 286 00:25:09,410 --> 00:25:15,670 You know, if you imagine just intersecting those two things, you already have a big, you know, a large combination of variables there. 287 00:25:15,680 --> 00:25:18,240 Right. So imagine how difficult it is to follow that. Right. 288 00:25:18,260 --> 00:25:22,280 It's like if you're watching a TV series and you have many different characters except, you know, 289 00:25:22,280 --> 00:25:25,609 it's all condensed in this paper as well with all this data you're trying to interpret. 290 00:25:25,610 --> 00:25:33,410 So. So, yeah. So that was, you know, we did spend a lot of time on that to polish the, the presentation such that in the final format, 291 00:25:34,040 --> 00:25:40,640 there would be common threads that you could sort of follow to help you really to guide through that the reading of the story. 292 00:25:42,020 --> 00:25:46,400 And what were the key headlines of the of the findings from the study? 293 00:25:48,100 --> 00:25:54,910 So the key headlines we will highlight, too, I think one of them was that. 294 00:25:55,180 --> 00:25:59,710 So if you think about COVID, I will SARS-CoV-2 write the virus itself. 295 00:26:00,580 --> 00:26:08,739 Very often when we think about immune responses, there is some amount of tailoring of your immune response to the type of a pathogen. 296 00:26:08,740 --> 00:26:14,890 So that is to say a virus usually elicits a antiviral immune response and then you have antibacterial ones and anti-fungal ones and so on. 297 00:26:15,190 --> 00:26:21,670 And because of the uniqueness of our cohort, the fact that we had those many different comparative groups and then we had different pathogens, 298 00:26:22,030 --> 00:26:29,170 what we could really see was that COVID would elicit, in fact, of course, as expected, atypical antiviral response. 299 00:26:29,410 --> 00:26:36,069 But what was quite interesting was that the severity of illness did not seem to track that antiviral response. 300 00:26:36,070 --> 00:26:46,470 So it was other things, right? And of which we identified a very specific set of genes which belong to what we call that, like, you know, 301 00:26:46,510 --> 00:26:55,780 an entire program or module of genes which seem to belong to a pathway where a very central regulator was a gene or a protein complex known as AP one. 302 00:26:56,590 --> 00:27:03,850 Now, to be completely honest, I think it's still a little bit unknown as to how that in the end really impacts your response. 303 00:27:04,060 --> 00:27:09,310 But that was one of the more novel pieces that we could get from combining so many different layers of data, 304 00:27:09,310 --> 00:27:12,129 which I think other people have also seen now. 305 00:27:12,130 --> 00:27:18,400 But then this was one of the more initial central reports of of this COVID, this aspect of the COVID response. 306 00:27:18,610 --> 00:27:26,379 And it's so different people have variations in that that kind of percent of of genetic 307 00:27:26,380 --> 00:27:30,730 material that you're talking about which influence severely the disease impacts. 308 00:27:30,730 --> 00:27:34,510 And. Yes, yes. And this was a very uniquely COVID thing. 309 00:27:34,510 --> 00:27:34,870 Right. 310 00:27:34,870 --> 00:27:42,759 Because you could say, you know, people with flu, that the other flu cohort that we had, they were similarly ill and that was also a viral illness. 311 00:27:42,760 --> 00:27:48,940 And yet they didn't have this response. So this was very unique to the kind of immune response to COVID, which was what we were trying to get at. 312 00:27:48,940 --> 00:27:53,650 Right. So we were able to do it through this kind of multi-omics layering. 313 00:27:54,070 --> 00:28:00,280 And I think the second thing maybe then to highlight rather than the biology, but more something from the technical aspects. 314 00:28:00,760 --> 00:28:08,470 So what I was briefly alluding to earlier, but I think in a way, the the paper was also a. 315 00:28:09,850 --> 00:28:14,780 A demonstration of the success of using some of these more novel analytical algorithms. 316 00:28:14,850 --> 00:28:21,850 Right. So it was a bit of a technical achievement. And as as one of the examples, we use many, many different methods, 317 00:28:21,850 --> 00:28:31,570 but one of the examples we use the kind of tensor decomposition method, which is to say, if you imagine your many different datasets. 318 00:28:31,840 --> 00:28:35,799 Right. So where you have each dataset, you can imagine there are two dimensions, right? 319 00:28:35,800 --> 00:28:40,480 One dimension is the number of samples that you have. Right? So, you know, you have a table, right? 320 00:28:40,480 --> 00:28:44,260 You have a table where the columns of the samples, let's say, and the rows are the measurements that you take. 321 00:28:44,260 --> 00:28:45,970 Right. So a nice 2D table. 322 00:28:46,300 --> 00:28:52,840 But then imagine you had many of these kind of data sets of the same patients, the same samples, but the measurements are all different. 323 00:28:52,840 --> 00:28:55,960 Right? So one is, you know, blood cells, one is the blood proteins and so on. 324 00:28:56,410 --> 00:29:02,209 And if you combine all these tables and make it 3D, then then you have what's mathematically called the tensor, right? 325 00:29:02,210 --> 00:29:07,720 And so how might you go about decomposing that tensor to find structure in the data? 326 00:29:07,720 --> 00:29:10,870 So that's, you know, not a trivial question to answer, right? 327 00:29:10,870 --> 00:29:14,739 So we were able to really apply these kind of methods to these datasets. 328 00:29:14,740 --> 00:29:19,960 And I think that was a real demonstration of the power of some of these new algorithms. 329 00:29:19,990 --> 00:29:26,500 Do you and I should perhaps fast is beginning it, but it sounds like a silly question. 330 00:29:26,500 --> 00:29:36,850 Obviously it's it's good to know why things work the way they do but but what was the the hope or the expectation that by acquiring this 331 00:29:36,850 --> 00:29:49,030 knowledge in the world of research and and drug development might be able to do in future to to actually tackle these kinds of conditions. 332 00:29:50,110 --> 00:29:53,860 Yeah. So I'll give you two examples. 333 00:29:54,160 --> 00:29:58,690 One not immediately related to the study, but it'll make sense. 334 00:29:58,690 --> 00:30:07,929 But so there are a lot of anti COVID treatments now which are given based on our understanding of the 335 00:30:07,930 --> 00:30:12,219 biology of the immune system and not necessarily aspects which are unique to COVID individually. 336 00:30:12,220 --> 00:30:17,360 But they were trialled because they've been very well understood those aspects of the immune system for many years now, 337 00:30:17,360 --> 00:30:22,240 and they've been used in many other different settings and therefore they will, you know, are already licensed products basically. 338 00:30:22,420 --> 00:30:27,879 And so people trialled them on COVID patients and you know, some of them work, some of them didn't. 339 00:30:27,880 --> 00:30:31,750 And then the ones that have worked, they're obviously now currently being used. 340 00:30:32,050 --> 00:30:37,270 But that's all thanks to things like dexamethasone, the sterile steroid dexamethasone, which. 341 00:30:37,450 --> 00:30:39,670 Right, dexamethasone. But I was thinking. 342 00:30:39,940 --> 00:30:47,019 Yeah, I was thinking maybe it's like even more niche ones, things like drugs called Elysium Mab, which inhibits a very specific IL6 receptor pathway. 343 00:30:47,020 --> 00:30:47,160 Right. 344 00:30:47,200 --> 00:30:54,850 And you know, that's only thanks to knowing how il6 signalling really works, what it really means in the immune system and inflammatory response. 345 00:30:55,210 --> 00:30:57,160 And that was, you know, years, decades and decades of work. 346 00:30:57,160 --> 00:31:05,139 And in a way, what we are doing, what we did and what we continue to do right, is to build on these kind of fundamental aspects. 347 00:31:05,140 --> 00:31:13,180 You know, what is the what are the systems in biology that work that make humans work the way they do? 348 00:31:13,610 --> 00:31:19,239 And by understanding these things, eventually you will crack these you will get these kind of insights, like the whole sex pathway and so on. 349 00:31:19,240 --> 00:31:21,880 And then you have these kind of drugs right now. 350 00:31:21,910 --> 00:31:28,540 Obviously, the study, I don't think, you know, we didn't go straight from this study to a drug that's a really, really long process. 351 00:31:28,540 --> 00:31:32,229 But then to highlight, as I was saying earlier, that AP one pathway, which, you know, 352 00:31:32,230 --> 00:31:37,299 I think is probably a story which would be worth following up, it's just that I'm post patient and haven't followed it up. 353 00:31:37,300 --> 00:31:41,980 But so one of the thoughts would be that Long-covid is obviously a big issue, right? 354 00:31:42,830 --> 00:31:48,100 A lot of people have it. It's something like 5% or maybe even more people get it. 355 00:31:49,330 --> 00:31:54,040 And I think it's really poorly understood. Right. Exactly what's going on now in our cohort. 356 00:31:54,490 --> 00:32:02,080 You remember I said that we had some individuals who were ill with COVID but didn't need to be hospitalised. 357 00:32:02,080 --> 00:32:08,290 And in fact, some of these individuals were probably in what we call the convalescent phase already of the illness. 358 00:32:08,290 --> 00:32:12,790 They were already recovering. But what was very interesting was when you looked in these patients, 359 00:32:12,790 --> 00:32:19,840 it seemed like they would still show signatures of that COVID response in terms of that AP one program that I was explaining. 360 00:32:20,110 --> 00:32:27,129 And in fact, in some cases that seemed to be even more highly activated, that program than in the acute phase of the illness. 361 00:32:27,130 --> 00:32:30,580 And yet this program was not activated in other aspects of critical illness. 362 00:32:30,580 --> 00:32:35,920 Right. So you can see how now you're starting to get hints of, well, 363 00:32:35,920 --> 00:32:39,670 is this going to be one of those pathways that you really need to probe into 364 00:32:39,670 --> 00:32:44,709 and understand what its relationship is with longer term sequelae of COVID, 365 00:32:44,710 --> 00:32:50,590 for example? How does that relate to the the virus? How does it relate to the rest of your immune response, the interaction of that together? 366 00:32:50,980 --> 00:32:56,650 And so, you know, these are the kind of fundamental things which maybe in another five years, ten years or something, you know, 367 00:32:56,650 --> 00:33:01,770 as people follow it up, you get to the point where then you can say, Oh, look, maybe we have some druggable targets here and there. 368 00:33:01,870 --> 00:33:06,609 This is the pathway that we should really act on to treat people. So that's one example. 369 00:33:06,610 --> 00:33:10,329 But one can imagine that with such an enormous dataset, actually, 370 00:33:10,330 --> 00:33:16,960 you've generated enough new questions for lots of people to explore for some time to come. 371 00:33:17,980 --> 00:33:22,620 Yeah, no, for sure. And I think so. So that's where there's strengths and limitations, right. 372 00:33:22,630 --> 00:33:31,930 But with these kind of studies, I think the one of the biggest limitations ultimately is that we're talking about observational data, right? 373 00:33:31,930 --> 00:33:37,900 So we have many different patient groups and we collect the data and it's observational, but it's not necessarily perturbation. 374 00:33:37,990 --> 00:33:45,399 So we haven't given people any drugs or we're not trialling things on mice in the lab or something like that. 375 00:33:45,400 --> 00:33:52,540 Right? So you can never be 100% sure where the various effects that you observe are necessarily causal. 376 00:33:52,840 --> 00:33:54,729 And so that's where, you know, you have to go back to the lab, 377 00:33:54,730 --> 00:33:59,830 you have to develop your model systems and then build on the questions that we've really come up with in the study. 378 00:33:59,830 --> 00:34:02,950 But of course, this was, you know, such a big project on its own already, right? 379 00:34:04,570 --> 00:34:09,640 Yeah. So did that become the topic of your your dphil? 380 00:34:10,960 --> 00:34:17,350 And suddenly chunks of it. Yeah. So, so I would say about yeah. 381 00:34:17,350 --> 00:34:26,229 About a half to two thirds. So of it was of of the of the thesis ended up being on this work and then the rest of it was on other 382 00:34:26,230 --> 00:34:31,600 sepsis work which I actually ended up going back to basically after completing the combat project. 383 00:34:31,720 --> 00:34:37,570 Yeah. So what was the timeline of it. When, when did you regard the the Copan project as complete. 384 00:34:39,490 --> 00:34:46,330 Yeah. Well let's say yeah, that's a good question. I mean, you know, combat finished combat was released earlier this year. 385 00:34:46,330 --> 00:34:53,530 Right. And of course, we were months before that it had already been completed and been in the pipeline for being published. 386 00:34:55,120 --> 00:35:06,219 But I spent about the last let me think a year and a half I think it last the last year and a half of the Ph.D. back to working mostly on sepsis, 387 00:35:06,220 --> 00:35:09,280 I would say mostly because I was still doing various things on on on COVID, 388 00:35:09,490 --> 00:35:13,870 just not necessarily on the combat project, but all the strands that we were still trying to follow up on. 389 00:35:14,350 --> 00:35:25,809 So yeah, I think, you know, in a way I thought this was a very big stroke of luck for me in the PhD in the sense that it was such 390 00:35:25,810 --> 00:35:30,969 a ridiculously good learning experience and what an amazing opportunity in terms of the science, 391 00:35:30,970 --> 00:35:34,930 you know, meeting the people that I did and learning from everybody, you know, in the team, that was a huge privilege. 392 00:35:36,350 --> 00:35:40,180 Yeah. You're not the only person who's said so. 393 00:35:40,220 --> 00:35:45,950 Some of them were slightly reluctant to say it, but that COVID did open up amazing opportunities. 394 00:35:45,950 --> 00:35:48,229 But there are a number of people in their research, 395 00:35:48,230 --> 00:35:57,980 and sometimes it seems it seems almost unfair to to mention that when a lot of people have, you know, have had a hard time with it. 396 00:35:57,980 --> 00:36:03,170 But clearly, in the in the research area, it did open it opened lots of doors. 397 00:36:04,470 --> 00:36:11,030 You know for sure. I think I do talk about that a fair bit with, you know, other people, you know, my friends, my family or anything. 398 00:36:11,030 --> 00:36:14,839 I because people always ask me, right, you know, they say, well, how is it, you know, during that time? 399 00:36:14,840 --> 00:36:21,440 Because it must have been really rough. And I always tell them that it was rough from, you know, in many ways, obviously the lockdowns and everything. 400 00:36:22,160 --> 00:36:27,830 But I said that honestly, I wouldn't complain to the extent that I was so lucky in the sense that the work well, 401 00:36:27,830 --> 00:36:31,459 I know so many of my other friends who are so heavily affected. 402 00:36:31,460 --> 00:36:36,020 Right. You know, their projects can run and so on. And then of course, the pandemic itself was also raging. 403 00:36:36,020 --> 00:36:39,679 You know, people were worried about their personal safety and health. Right. Myself as well. 404 00:36:39,680 --> 00:36:43,129 But, you know, so there were so many all the things everyone had to contend with. 405 00:36:43,130 --> 00:36:46,280 I count myself as having been so lucky in that period. Definitely. 406 00:36:47,240 --> 00:36:53,060 But it was. Yeah, you did. You were rough. What was your personal life like through that? 407 00:36:53,120 --> 00:36:56,240 Through that period? What kind of hours were you working? Where were you living? 408 00:36:56,840 --> 00:37:01,850 How did you cope with with the social distancing regulations, all that kind of thing? 409 00:37:03,140 --> 00:37:08,990 So for me, it was a it was such a surreal experience because because of the lockdown. 410 00:37:10,670 --> 00:37:14,749 There was basically not much contact with anybody. 411 00:37:14,750 --> 00:37:22,010 Right. So it was just going to work. And only a select few of us who were still going to work in the lab were allowed in anyway. 412 00:37:22,020 --> 00:37:25,549 So I was I was given one of those essential worker status letters. 413 00:37:25,550 --> 00:37:30,470 I still remember that. I think I still have a copy of that because I thought it was such a strange thing. 414 00:37:30,480 --> 00:37:33,950 It was such a strange feeling to be holding that piece of paper and then thinking, okay, well, 415 00:37:33,950 --> 00:37:38,090 I'll take the bus in the morning, you know, at seven and then get into the lab and then get the day going. 416 00:37:39,230 --> 00:37:44,180 It was very much round the clock work for many months. 417 00:37:44,660 --> 00:37:55,580 And, you know, I remember having had conversations with team members with some sort of, you could say quite hilarious comments being thrown around, 418 00:37:55,580 --> 00:38:01,909 such as saying, well, if I were a management consultant, I hope that, you know, I wish that this could go even even even more quickly. 419 00:38:01,910 --> 00:38:05,680 But then, you know, we were already working really at the limits, right? 420 00:38:05,690 --> 00:38:08,810 As in we were going full throttle. So. 421 00:38:08,980 --> 00:38:13,550 So it's very, very intense. The rough one. 422 00:38:13,670 --> 00:38:19,430 One of the roughest parts was the fact that I just didn't have much social contact 423 00:38:19,430 --> 00:38:27,650 because most of my friends also had left Oxford either just as things had, 424 00:38:27,890 --> 00:38:32,360 you know, started getting bad or right after lockdowns had happened. 425 00:38:32,750 --> 00:38:36,500 But then because of the stuff I was doing, you know, I had to be there to do it right. 426 00:38:36,980 --> 00:38:44,960 So I was basically completely on my own for months for that that whole stretch between March to July, 427 00:38:44,990 --> 00:38:50,450 August time before before the first sort of opening up right in the UK and. 428 00:38:51,840 --> 00:38:55,200 I mean, I think in a way I was able to keep going because I was so busy. 429 00:38:55,500 --> 00:38:58,829 But it was very, very strange. It was definitely very strange. 430 00:38:58,830 --> 00:39:03,510 And I think I guess I was kept sane by just, you know, making sure that I would still talk to people, 431 00:39:03,510 --> 00:39:07,290 even though I didn't necessarily have the physical contact. I would still call people. 432 00:39:08,220 --> 00:39:09,330 I again, 433 00:39:09,330 --> 00:39:16,530 maybe I was lucky in the sense that I had that essential worker status and at least I saw a few people in the lab rather than if you completely, 434 00:39:16,530 --> 00:39:21,510 you know, work from home or couldn't work. Of course, there were many more who were much more unfortunate that way. 435 00:39:22,140 --> 00:39:26,820 And where were you? Where were you living at the time? So I was just living in the city. 436 00:39:27,060 --> 00:39:33,660 I was not that close to the lab. Well, so this is what sort of what a lockdown does, right? 437 00:39:33,990 --> 00:39:38,700 My normal morning commute would take while the daily commute would be 45 to 438 00:39:38,700 --> 00:39:43,380 45 minutes to an hour from where I left it to the lab on about an enduring. 439 00:39:43,560 --> 00:39:46,890 Yes, but I change at some point. 440 00:39:47,400 --> 00:39:55,049 And then with COVID, it became something like 20, 25 minutes at half the time, literally, because there were just no people around. 441 00:39:55,050 --> 00:39:58,230 Right. So no stops or anything. You just it was a straight shot kind of. Yeah. 442 00:39:58,230 --> 00:40:04,110 So that was that was a very noticeable what even a flat to or a college room or what sort of. 443 00:40:04,110 --> 00:40:08,399 Yes, I was I was in a flat. I was I was renting a flat with a college friend. 444 00:40:08,400 --> 00:40:12,990 But then he'd gone home on your own. Yes, exactly. 445 00:40:12,990 --> 00:40:16,170 Exactly. Yes. He'd he'd returned to Italy and so I was on my own. 446 00:40:17,380 --> 00:40:20,460 Yeah. And your family were your family in Hong Kong? 447 00:40:21,060 --> 00:40:23,640 Yes. So my entire family was in Hong Kong. 448 00:40:24,390 --> 00:40:29,490 And I think especially during 2020, Hong Kong didn't have a particularly rough time, so I wasn't very worried. 449 00:40:30,330 --> 00:40:35,310 And this was another thing that I always mentioned to other people, but I said that I was, 450 00:40:35,550 --> 00:40:39,900 in a way, as scary as it was, you know, personal safety public health wise. 451 00:40:41,130 --> 00:40:48,180 I was very fortunate that my grandparents weren't around. I felt like I wasn't as stressed in that way because I think we were all very acutely aware, 452 00:40:48,180 --> 00:40:52,360 very early on about how the elderly were by far the ones most at risk. 453 00:40:52,360 --> 00:40:58,650 Right. So I felt like that would have been a very, very big stressor if, for example, I'd been living with my grandparents, I would have, you know. 454 00:40:58,920 --> 00:41:03,970 Yeah, but living on my own. I didn't have that baggage necessarily and. 455 00:41:05,620 --> 00:41:11,200 And and so. Yes. So you completed your your PhD. 456 00:41:12,220 --> 00:41:15,850 Have you go back to clinical work now or are you are you still doing this research? 457 00:41:16,540 --> 00:41:19,659 Yeah, so I am actually. I'm with the Chinese University of Hong Kong now. 458 00:41:19,660 --> 00:41:29,410 And so they've been very supportive of the junior staff who are aspiring to do both clinical work and research work like myself. 459 00:41:29,830 --> 00:41:34,510 And so I'm in a position where I spend about three quarters of my time doing clinical work, 460 00:41:34,810 --> 00:41:39,370 but then the other one quarter of the time I'm actually attached to a lab and so I'm doing the 461 00:41:39,370 --> 00:41:44,290 research there and now I'm sort of more full time into that analysis rather than the wet lab work, 462 00:41:44,290 --> 00:41:48,189 because it's a bit hard to combine clinical work where you have very heavy contact time. 463 00:41:48,190 --> 00:41:53,079 You have to see the patients day in, day out kind of thing and then also try to run experiments at the same time. 464 00:41:53,080 --> 00:41:56,020 Right? The only way you could do that is basically probably run the experiments at night. 465 00:41:56,020 --> 00:42:04,690 And I think I find it a lot easier to sit in front of the computer to do some analytical work in the evening rather than still be in the lab, 466 00:42:04,690 --> 00:42:13,210 you know, slaving away with the pipettes. Yeah. And are you continuing with the same ideas that you worked through during your Ph.D.? 467 00:42:13,900 --> 00:42:21,370 So it's been a bit of a stretch. I've actually made a switch to neuroscience, but then, yeah, so radically different. 468 00:42:21,370 --> 00:42:25,149 But I think actually at the end of the day, to me it's all biology. 469 00:42:25,150 --> 00:42:31,810 And one of the key things is still thinking about the genomics aspects, the multi-omics that, you know, we were talking about with combat. 470 00:42:32,140 --> 00:42:38,170 And so really applying those kind of lenses to interrogating neurobiological questions rather than immunological questions. 471 00:42:38,410 --> 00:42:45,790 So that's one. But I think certainly longer term, one thing that I'm actually very interested in is the idea of neuro immune connections. 472 00:42:45,790 --> 00:42:49,959 So in recent years, we've there's been quite an explosion, I would say, 473 00:42:49,960 --> 00:42:54,760 of understanding that there are actually many links between the nervous system and immune system. 474 00:42:55,210 --> 00:42:59,050 And these are many things that we're not really aware of consciously on a day to day basis. 475 00:42:59,050 --> 00:43:05,140 Right. But these kind of cross talks are probably very relevant biologically, and I think there's a huge amount to be discovered there. 476 00:43:05,140 --> 00:43:09,490 So who knows? But maybe that's the kind of stuff that I'll be getting into in the years to come. 477 00:43:10,690 --> 00:43:13,870 That sounds really exciting. I shall have to come back to you again. 478 00:43:13,910 --> 00:43:20,840 But you've done some more work on. So. 479 00:43:23,250 --> 00:43:29,520 Yeah. Oh, yes. Sorry, I just on the question that I'd written about the another published your science paper. 480 00:43:29,900 --> 00:43:37,920 I should have mentioned that earlier that looked at predicting outcomes in sepsis from using the the kind of data that you collected during combat. 481 00:43:39,590 --> 00:43:44,210 Oh, yes. The. Yes. Yes. More recently released one. 482 00:43:44,270 --> 00:43:48,410 Yes, very. Yes, I think it was. Yes, yes. Yes. That's in the last month or so. 483 00:43:48,460 --> 00:43:56,000 Yeah. Yeah, yeah. So so that was work that was led by any kind of agamben's, which is a post-doc in Julian's lab. 484 00:43:56,000 --> 00:43:59,190 And then, you know, he was building on the. 485 00:44:00,440 --> 00:44:10,799 So that was. It was more more clinically translational related than mechanistically biologically related, I would say. 486 00:44:10,800 --> 00:44:13,950 Right. But yes. So so now we're going back to sepsis, right. Rather than COVID. 487 00:44:14,100 --> 00:44:21,399 Yes, yes. But. Right at the beginning, we were talking about how you could take some blood, just whole blood from patients, 488 00:44:21,400 --> 00:44:26,440 and then you could stratify them into at least two groups that's called amino groups one and two, right? 489 00:44:26,440 --> 00:44:31,150 Where, let's say group one does more poorly. They deteriorate more quickly. 490 00:44:31,160 --> 00:44:35,799 Right. And one of the questions we were interested in was to say, 491 00:44:35,800 --> 00:44:46,060 have we captured essentially an axis along which individuals with infectious disease present in terms of their severity and, 492 00:44:46,450 --> 00:44:50,169 you know, obviously some kind of biological meaning because we're using gene expression as a readout. 493 00:44:50,170 --> 00:44:54,640 Right. And so we did this. We derived this originally in sepsis patients. 494 00:44:55,030 --> 00:45:02,560 So then the question was, can we extend this over to other settings of either critical illness or infectious disease? 495 00:45:03,280 --> 00:45:09,009 And so what that new project was about was this generalisation. 496 00:45:09,010 --> 00:45:18,220 And we basically managed to take a lot of publicly available datasets as well as dataset that we generated ourselves and show that, 497 00:45:19,720 --> 00:45:23,770 yes, that original description that we had, we called them the sepsis response signatures. 498 00:45:23,770 --> 00:45:28,239 You could in fact recapitulate that signature in COVID patients and flu patients 499 00:45:28,240 --> 00:45:34,360 and sepsis patients or even potentially in patients who didn't have infection. 500 00:45:34,370 --> 00:45:40,870 So just an idea of, you know, critical illness. So we we seem to have identified a kind of blood gene expression, axis of severity of illness. 501 00:45:41,050 --> 00:45:47,410 Much like how, you know, if you have a cough and a fever, you think, and then eventually you need oxygen support. 502 00:45:47,410 --> 00:45:51,680 You think that the person who needs oxygen support probably has the worse illness than just the cough. 503 00:45:51,680 --> 00:45:56,140 Right. Except we've got this on a biological axis. So that was the kind of work that we were trying to do. 504 00:45:56,500 --> 00:45:58,360 And along with that, 505 00:45:58,360 --> 00:46:08,769 there was a very big technical challenge as to how you could actually do this analysis in these different datasets in a robust manner, 506 00:46:08,770 --> 00:46:13,870 which would be, you know, it wouldn't give you a false result just because you moved to a different technical platform, a different data set. 507 00:46:14,050 --> 00:46:19,420 And so that was a huge challenge that Eddie overcame. And so thanks to some amazing work that he put in there, 508 00:46:19,630 --> 00:46:25,510 I think we're able to apply this kind of framework now a lot more generally to a lot of different settings and datasets. 509 00:46:27,070 --> 00:46:32,530 So that holds the promise that you could simply take a blood sample from somebody who looked a bit 510 00:46:32,530 --> 00:46:40,720 poorly and have a sense of how closely you needed to monitor them because of how far it might develop. 511 00:46:41,230 --> 00:46:44,559 Right, exactly. Definitely. So that's definitely one of the ideas. 512 00:46:44,560 --> 00:46:52,810 So, you know, again, maybe two quick points on that. The first is that this is something that we imagine to be clinically imminently translatable 513 00:46:52,810 --> 00:46:57,879 because the basis of this is actually just measuring the expression of seven genes in the blood. 514 00:46:57,880 --> 00:47:00,880 So it's a very small we've managed to shrink it down to a very, very small number. 515 00:47:00,880 --> 00:47:04,750 So, you know, we started off with profiling everything, right? The omics, the unbiased nature. 516 00:47:05,080 --> 00:47:11,200 But of course, you know, you go from that big sea of data to wanting to pinpoint what some of the specific factors. 517 00:47:11,200 --> 00:47:13,509 And we've managed to successfully narrow down seven genes. 518 00:47:13,510 --> 00:47:17,649 So you can imagine if you wanted to measure seven in a patient's blood, that's not too difficult. 519 00:47:17,650 --> 00:47:22,180 Right. You could turn that around within an hour or two. And so that might be something you could do by the bedside. 520 00:47:22,180 --> 00:47:24,010 So we find that to be very exciting prospect. 521 00:47:24,550 --> 00:47:30,040 The second thing, a very key, I think, extension beyond just saying, oh, these patients are going to do poorly. 522 00:47:30,040 --> 00:47:37,749 Is that so? This is work in a study, in a in a manuscript, which we are which is now under review. 523 00:47:37,750 --> 00:47:41,530 Right. So we're hopefully going to be releasing yet another one to follow up on this work, 524 00:47:42,100 --> 00:47:50,979 which goes beyond the the data predictions to really understanding some of the underlying biology I was talking about right at the beginning. 525 00:47:50,980 --> 00:47:54,280 What are the biological mechanisms or features that underlie these groups of patients? 526 00:47:54,280 --> 00:47:57,550 And I think we've really managed to get a good crack at that, I would say. 527 00:47:58,360 --> 00:48:07,120 So hopefully that data comes out soon. But basically with that knowledge now we get closer to those pathways. 528 00:48:07,120 --> 00:48:13,719 As I was saying, you know, with IL six or the AP one and so on, with COVID, we have a similar kind of framework that you could work on in sepsis. 529 00:48:13,720 --> 00:48:21,490 And for that matter, in terms of the degree of severity in an infectious disease case, infectious disease patient. 530 00:48:21,970 --> 00:48:24,210 And so then the excitement is beyond just that. 531 00:48:24,230 --> 00:48:30,250 You could say, oh, these are the patients who would deteriorate, but then we can really highlight specific pathways which we think we should target. 532 00:48:30,520 --> 00:48:37,749 So if you have something clinically actionable there, then I think that's really the beauty of doing that bench work that the, 533 00:48:37,750 --> 00:48:45,580 you know, understanding the fundamentals of immunological biology and then bringing it all the way to the clinical use. 534 00:48:46,330 --> 00:48:52,600 Really fantastic. Right. I think we've we've more or less got the hope that they at the end. 535 00:48:53,410 --> 00:48:59,799 I've just got a final question really to ask whether the experience of working through the 536 00:48:59,800 --> 00:49:05,170 pandemic and working on this project has changed your attitude or your approach to your work? 537 00:49:05,170 --> 00:49:08,830 And and is there anything you'd like to see change in the future? 538 00:49:10,740 --> 00:49:17,399 Yeah, I think. Yeah, you know, that's a quite a reflective question. 539 00:49:17,400 --> 00:49:20,969 I feel like I've definitely thought about that a lot and talked to people a lot about it, 540 00:49:20,970 --> 00:49:27,640 but I think you've maybe caught me a little bit off guard at this moment, specifically in time, I would say that, um. 541 00:49:30,570 --> 00:49:33,930 Maybe I'm a little bit less uptight about. 542 00:49:36,630 --> 00:49:43,260 Certain aspects of the research work after the experience because it was sort of very nerve wracking to go through it. 543 00:49:43,260 --> 00:49:46,320 But then it feels like, you know, we've all come out the other end. 544 00:49:46,670 --> 00:49:48,659 Now, on the other hand, you could maybe say that, you know, 545 00:49:48,660 --> 00:49:52,560 I feel I've been lucky enough to you know, we've been lucky enough to come out the other end. 546 00:49:52,680 --> 00:49:56,210 It's been a very, very traumatic experience in many ways for the entire world, I'm sure. 547 00:49:56,220 --> 00:50:04,250 Right. So. So. And the other thing is that, you know, is this just a matter of having gone through the idea that, 548 00:50:04,250 --> 00:50:08,120 you know, maybe you relax a little bit more after that? It's a bit hard to tease that apart. 549 00:50:08,360 --> 00:50:11,929 And so I guess that, like you say, I should just say that this may be part of what you're saying, 550 00:50:11,930 --> 00:50:19,670 that with the degree of responsibility that you had as a Ph.D. student was, I would have said in excess of what you would normally expect. 551 00:50:21,530 --> 00:50:24,649 Maybe. But I think, you know, when I was doing, I did think about that. 552 00:50:24,650 --> 00:50:28,090 Right. You know, I was just in the thing. You know, these were the things that we need to do. 553 00:50:28,100 --> 00:50:32,600 These were the directions that we were going to go, let's just do it right. You know, I was just fully, fully, fully engaged. 554 00:50:32,930 --> 00:50:39,860 And I think maybe you could say this thing hasn't changed, but I still think I guess that's in general how I approach my work, my life. 555 00:50:39,860 --> 00:50:44,080 You know, I'm enthusiastic about the things I do, right? So so I pick and choose carefully, right. 556 00:50:44,090 --> 00:50:49,069 You know, but if I'm if I've made that decision to choose that, then then I will put myself into it. 557 00:50:49,070 --> 00:50:52,880 Right? So, so I think and so in that sense, it was a very rewarding experience to. 558 00:50:54,980 --> 00:50:58,990 In terms of things that could be done differently, I think? 559 00:51:00,020 --> 00:51:02,210 Well, again, this is a it's a tricky one. 560 00:51:02,510 --> 00:51:08,650 And, you know, looking back, obviously, there were many things that we could have either done better or quickly, 561 00:51:08,660 --> 00:51:14,180 more efficiently, had complementary approaches to help what we actually did. 562 00:51:15,320 --> 00:51:17,959 So, you know what I was saying about how you profile a lot of patients. 563 00:51:17,960 --> 00:51:22,610 You have all these data that you observed in different groups, but it's very hard to understand what causes what. 564 00:51:23,060 --> 00:51:29,570 And you might easily make the point to say, well, why don't you build a model, you know, have a mouse model and then, 565 00:51:29,960 --> 00:51:34,400 you know, try to actually interrogate some of the questions that you generate from your data. 566 00:51:34,640 --> 00:51:37,940 So in a sense, that's an obvious improvement step, right? 567 00:51:38,120 --> 00:51:42,949 But at the same time, what I also mentioned earlier, which was that, you know, this is already such a huge project on its own, right. 568 00:51:42,950 --> 00:51:47,690 It was it required such a huge team, so many people, so much dedicated effort. 569 00:51:47,990 --> 00:51:50,809 It's easy to say, like, well, why don't we actually add this thing? 570 00:51:50,810 --> 00:51:56,450 But it turns out it's already enough of a sometimes that's that's a separate project like let's say. 571 00:51:59,480 --> 00:52:04,820 Okay. I think that's great. Thanks very much indeed. Thank you, Cody.