In the Cancer and COVID-19 CME event hosted by Penn Medicine and featuring Dr. Anthony Fauci, Dr. E John Wherry, PhD, Chair of the Department of Systems Pharmacology and Translational Therapeutics at the Perelman School of Medicine at the Hospital of the University of Pennsylvania discusses the elevated inflammatory response, evidence of T cell activation or exhaustion, and long term serological immunity of COVID-19. He elaborates on the immunotypes linked to different clinical presentations and links between clinical treatments and specific immune cells.
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So I want to talk just briefly about the immune responses in Kobe 19 patients and describe some of our recent results, some of which were published in some of which have just been submitted. S o. I have some disclosures, none of which are relevant to the studies that I'll present. So what do we know about Kobe? 19 immunology. We've heard a little bit of this from Dr Fauci and others so far. We, uh, know that there's an elevated inflammatory response, and we've heard a little bit about how this may impact from the vascular manifestations and also some of them, you know, pathology that make her. But we also know that there are mixed responses to anti inflammatories, and we heard this already about Dex methods own, perhaps not having a benefit and maybe even causing harm if treated too early in disease or in patients. Um, with not a severe inflammatory symptoms. We have good evidence in the literature of T cell activation in some patients, but there's also evidence that perhaps t cell hypo function, or T cell exhaustion in the literature, and so we don't really know which way the immune response is going in a given patient. We know that there's long term serological immunity in some patients some, and they're starting to be emerging evidence of cellular immunity that is, memory T cells in some patients that recover from disease. But we really don't understand the relationship yet to the acute immune responses. There's been some associations proposed between the severity of acute disease and perhaps their ability of serological memory or impacts on cellular memory. But it's unclear exactly how this relationships pan out. We also understand relatively little about the temporal kinetics of disease, and I'm not gonna talk very much about the innate immune response. But but certainly there's emerging data suggesting that differences in the innate immune response and interfere on pathways may impact the ability to mount adaptive immune responses. But in general, we still don't understand the temporal kinetics of the immune response because we don't really understand the temporal kinetics of infection, pathogenesis and disease. Very well, we do know that there are antibody producing plasma blast that are found in the blood of acutely ill patients on board. Most of our hospitalized patients actually do have antibody many when they present to the hospital. But yet these patients are still sick on convalescent plasma or antibody therapies. Show promise anecdotally. But you just heard that on larger trials. Some of these studies still have sort of mixed outcomes, and the benefit is unclear. So it's not entirely clear why patients have antibodies and when adding additional antibodies to these patients might provide benefit. We also really don't yet understand why Children are aren't a sica's most adults and whether they respond the same way to cove in 19 disease or start scoping to infection. So the bottom line is that we're still searching for trying to understand what a typical immune response Thio stars. Kobe to infection is in Kobe 19 patients. So in late March, working with several partners on campus, we decided to build a translational immunology profiling pipeline, really adapted from our work in cancer immunotherapy and and turn that engine towards Kobe. 19 patients. We have amazing partners in critical care, including New Lemire, who really was instrumental in getting these studies off the ground and who also treated many of the patients who we studied for free immunology and pathology. We also partner with Mike Bettes early on Thio build this profiling pipeline and enlisting many of the key scientists in our labs here who ended up being first authors on several papers that came out of this work. We acquired samples, process them and then fed them into what we're calling a deep immune profiling pipeline. And I'm gonna show you show you mainly flo site commentary data from this pipeline today. But there are many other platforms that are currently being used. What I want to describe just in a couple of slides is a covert that we developed again starting in late March. And and really what? The analysis. I'm going to show you his patients that were recruited into this cohort until about mid May of covert still recruiting. But the analysis that I'll show you stopped at 152 149 hospitalized Kobe patients, most of whom are I see you but somewhere floor patients. Ah, 125 of those we have deep I mean profiling data on. But we compared these Kobe 19 patients thio covert of recovered donors who are at least two weeks from last symptom on also the healthy donors. Now the courts are not perfectly age matched in the pandemic. It was difficult to do that. But there there at least overlapping. They are gender balance and match for other things, to the extent that we could match them. So one of the things we wanted to do was ask what the immune response looks like in these patients, and we started out using a baseline of our understanding of antiviral immune responses in humans and especially CD eight T cell responses. Because those T cells are important for intracellular pathogens and viruses. And we used a trick that has been used to study antiviral immune responses in HIV infected patients. Influenza infected patients where patients receiving live attenuated vaccines and that is thio. Use these markers and marker called CD 38 in combination with H L A D R and use up regulation of both markers toe identify punitive virus specific T cell responses. Now on those settings. Many people have shown that virus specific T cells during acute infection up regulate both of these markers and can be identified in this sort of quadrant of the Filosa commentary gate in the upper right now. What you see here is in healthy donors or even the recovered donors. There's very little Baseline CD, a T cell activation. But in our Kobe 19 patients, you see stark activation of CD eight T cells. In some cases, whether you use these markers or other markers of activation, more than a third and sometimes even higher than 50% of the circulating CD A T cells are highly activated in ways that suggest we have an antiviral T cell response. We will also notice there are other Kobe 19 patients that actually look indistinguishable from our healthy controls. And in fact, the Green Line here indicates the 90th percentile of our healthy controls, and you'll see that there are at least some Kobe 19 patients that seem not toe have t cell activation profile. You can do this in higher dimensional space, and we're looking at just under 30 different markers by close Saitama Tree here, and you can then project that high dimensional data in various ways and yet essentially a landscape map for how the overall T cell compartment has been perturbed by SARS. Kobe to infection. This Kobe 19 patients and what you'll see is that heat map of the diversity of of the activation profile and CD A T Cells is actually pretty similar between the healthy donors and the recover donors. There's some subtleties here that I'm happy to discuss, but in the Kobe 19 patients, you see a massive reorganization of the T cell activation profiles. And in fact, a lot of this activation FINA type of the CD 38 h led our cells is right down this sort of middle valley here, and you can pick this apart and look at the different sort of regions of these maps. And there's different regions actually tell you something about the biology of the T cells that are responding, and you can pick through this a little bit more to figure out which kinds of T cells were responding and importantly, in which patients, Because we have about 50 or 60 parameters of clinical data on these patients. What we learned from this is that there's tremendous activation of CD eight and CD four T cells in most Kobe 19 patients. This activation profile is similar to our higher than what we see in many other acute viral infections. We see activated C V A T cells but actually a particular type of affect. ER CD eight T cells that those that express markers like transcription factor, T bed or other other molecules were actually relatively low despite this activation, in contrast, on the CD four T cell side, that activation subset is highly enriched and in fact is more abundant than you find normal normal settings. We also see an altered or a lower percentage of these so called circulating follicular helper cells that help the cells make antibody. Um, and this is interesting considering the type of humorous response that we've seen some patients. So that led us to try to understand what was happening on the B cell side of the equation. And if you look in these acutely infected patients at their B cell compartment, what you find is an incredibly robust response of circulating plasma blasts in the blood of these patients. In normal, healthy humans, you see very few of any circulating plasma blast. These air cells that are are typically coming out of germinal centers. Their job is simply to make antibody. Once the germinal center response has started to calm down, these cells exit and their present in the blood for a very short period of time on their way to the bone marrow world, where they will set up residents for the rest of their life. Now, this kind of peak of a plasma blast response eyes indicative of making a robust antibody response on you can see that sometimes we have 30 even 40% of your circulating B cells. Are these plasma blast? Not in all patients. Again and again, you see some patients down here below the screen line. But to put this in context, what you see, if you're acutely infected with influenza virus is something in the range of maybe 10 to 15% of your circulating. These cells would be in this plasma class compartment in patients that are acutely infected with Ebola. The last time we had Ebola patients in the U. S. You see that there you can start to get to the range that we see in Kobe. 19 patients in the hospital. So this is an extraordinarily high percentage of circulating plasma blast that suggests that there is some ongoing be so response to current. In fact, you can look there are antibodies to the stars. Kobe to spike in most of these patients. The Plaza blast response does not correlate with that circulating antibody response just to the spike protein. That may be because many of these plasma blasts are also making antibodies to other parts of the coronavirus, the nuclear protein or other proteins. Or because there's some bystander activation of plasma blast. Because of the inflammatory response. Now we collected a lot of immunological data. In fact, we had 550 discreet immune features on DWI. Also collected about 50 clinical features. That's very difficult to look at in two dimensional space like data. I was just showing you. So we built a mapping algorithm, actually project all of that information in two dimensional space and also related to disease severity. And what you're seeing here is the aggregate signal of immune features that give you, ah horizontal component component one and immune features that contribute to the diversity of the patient response and component to, and you can see a little bit that there's more severe patients on the right hand side of this Aziz, the symbols get darker and the triangles are patients who succumb to disease. And indeed, if you look at the relationship between this component. One is composite immune, signature and the horizontal direction. There is a relationship between an increase in component one and more severe disease. In fact, you can project back onto this map individual features of the immune response. So CD four T cell activation actually contributes to both component one and component to whereas that unusual affect her like population. And, I said was low income in 19 patients actually really is only contributing to patients immune features in the heart and the vertical direction so component to but not contributing in the horizontal direction. And overall, what this lead us to is the realization that there are different immunity types of response. There are patients that actually are very driven by this horizontal feature, which is activated C four and C t A. T cells. These defector like city for diesels that also expressed this chemokine receptor c x three cr one and that have very robust plasm. Less response. This immune feature correlated very strongly with disease severity in the vertical direction. However, we have different immune features. We have this defector like CD eight T cell population, but not the effect of C four T cell population and proliferating B cells. We also see um, or coordinated immune response in this vertical direction for component to that component to is not associated with disease severity. Interesting. Low. Interestingly, though, you do see that there are patients who succumb to disease all around this map of relating immune features. Disease severity Now I kept pointing out on the previous slides. Uh, these patients that actually sit below the screen line. And indeed, about 15 to 20% of the Kobe 19 patients who are hospitalized with severe disease have very little evidence of immune activation that is T cell or plasma blast activation. So I wanted to ask, Where do those patients fall on this map of immune features? And they actually fall in this region sort of in the in the middle, but a little bit on the lower side. And in fact, they're immune. Features are negatively correlated with this component one or component to or disease severity over time. Yet at least one of these patients still succumb to disease thes patients, many of them, not all of them have antibody to the stars. Kobe to spike in the hospital. So it's not that they have no immune activation whatsoever, or that antibody is actually a residual cross reactive antibody from previous coronavirus infections. We don't know the answer to that yet, but this gives us the picture that there are three different ways that the adaptive immune response can manifest. Uh, reaction to stars Kobe two. You have one that is very robust, highly activated and maybe imbalanced immune responses. And, um, you know, type one more balanced immune response where you have activation of C four and C T A T cells, but less that over activation in the Munich Type two and then a third immunity type where there's very little activation of the adaptive immune response. I think this has potential implications for different treatments. So even when these immune it type three patients are present later in disease course, perhaps these patients still might be patients. You want to reserve treatment with X and methods own because we're we really don't have an active, adaptive immune response. But that's, ah, a little bit of speculation on my part. So the last question I wanted to address is what happens in these pediatric patients when they don't get severe disease, or in the pediatric patients that present with this Miss C presentation that Dr Fauci mentioned this multi inflammatory syndrome of Children. And so we did the same thing and build a pediatric cohort with our colleagues at Children's Hospital Filadelfia 30 patients, half of whom had this Miss C presentation for the pediatric world. This is a fairly large cohort, even though it's small by most standards. What we saw is that in the pediatric patients, we had some level of T cell activation using some of the same criteria. But in fact, these Miss See Children had much mawr activation of their T cell compartment than did the non Missy covert patients. Pediatric patients. In fact, the Miss See Children had t cell activation that rivaled our most severely ill adult patients, sometimes a tow, highest end of that spectrum. You could do the same thing where you project these data onto this landscape map of immune responses, and you can convince yourself that perhaps in the area of immunity type three, there are fewer of these miss see patients. The triangles now in this case, and perhaps some of the acute respiratory distress that we see in Children maps to this immunity type three area, or at least low immunity. Type two component to what is interesting about the Miss See patients is. Actually, they seem to resolve their symptoms very quickly. And in fact, that's the clinical experience that while Miss C presentation is quite scary. Initially, patients recover very, very rapidly, and in fact, in a handful of patients we have blood draws about a week apart, and you can see that this immune T cell activation in the sea is very robust at the first blood draw. But is returning towards baseline actually close to baseline by the second draw. And that correlates, or at least is associated with a decrease in clinical measures of disease severity, including CRP and Prochaska tonin levels in these patients. And just the last point I wanna make is an observation we made because of this deep profiling platform. The identification of the cell type that seems very interesting and perhaps is connected to some of the immune connections to thrombosis that that Adam talked about a few minutes ago. And so this is this population of CD eight T cells that expresses the chemokine receptor c x three cr one. This chemokine receptor recognizes a key McCain C x three c. L one and this access is quite interesting to consider. In this case, this access has a role in my Lloyd cells and mostly set a toxic lymphocytes, including CD A, T cells and K cells and a couple of other types of cells. This chemokine receptor is expressed by CD A T cells that are involved in patrolling the vasculature, and in fact, the Chema kind itself is up regulated and expressed in an interesting way by activated and the thallium. These CD A T cells that are marked by this chemokine receptor are also MAWR, site of toxic and often more terminally differentiated. And in fact, this chemo kind, receptor axis and Chema kind. Access has a clear role in cardiovascular disease in athletes sclerosis, where genetic variance in this pathway actually are associated with disease. Now, the number of the frequency of this population of cells expressing this scheme counter sector is not different across disease, whether it's in adults or in Children. However, what we see, especially in the Miss see patients, is a dramatically elevated activation of T cells expressing this chemokine receptor. So in miss See you see almost half of the circulating C B A T cells that expresses chemokine receptor expressed these activation markers. Or you could do this by other activation markers compared to the pediatric Kobe patients, where it's only about 10 to 15% and you can see this being robustly different in the sea. X three Sierra one positive cells in the sea patients Now we wanted to ask whether this had any relationship to disease presentation, disease manifestation. And so what we did is ask whether there was a relationship between the activation state of these chemokine receptor positive T cells and the need for a physician to treat with basil active medication. And in fact, regardless of whether the presentation was a missy or non missy patient, there is a much higher likelihood of treatment with basil active medication. If there is a high percentage of these activated c x three cr. One positive circulating CD eight T cells. We wanted to ask whether the pediatric setting actually give us any insight into adults. In fact, in a very similar analysis and there's again a relationship numbers are a little bit better here, but still a little bit on the low side. But if patients have a high percentage of activated 63 CR one positive CD A T cells, they're more likely to have clocked complication during their time in the hospital. So let me just summarize very quickly I won't read through all of this. But just make a couple of points that we see tremendous clinical and being heterogeneity in Kobe, 19 patients that manifests in the type and features of activated C D foreign CD A T cells. There's a massive plasma blast response rivaling what we see in acute Ebola and dinky infection. Although we don't know the specificity of that response yet, some of this immune activation is incredibly stable over time. Some of these patients have activated to your B cells for many weeks longer than you seem typical acute viral infection. We think that some of the immune features might actually give us some insights into how to treat patients with different drugs, although that requires direct testing. And then we identified this unusual or this this c x three cr one positive CD, a T cell that might be vascular patrolling and founded associated with the pathogenesis of missy in Children. And that led to potential insights in adults related to this cell type. So we think this kind of immune profiling might allow us to identify links between the way the immune system is behaving and the way we may want to test different treatments in Sarah's Kobe to patients Kobe, 19 patients. So I'll stop there. Thank you for your attention and look forward to question is a little bit later.
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