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MMRF » 2018 Vaccine Development Conference #04: Decoding The Human Immune System [2018-06-27. Mark M. Davis. HVP/USC]

2018 Vaccine Development Conference Session #04: Decoding The Human Immune System: The Potential [2018-06-27. Mark M. Davis, Marie-Paule Kieny. HVP/USC]

2018 Vaccine Development Conference – Session #04: Decoding The Human Immune System: The Potential — Mark M. Davis, Marie-Paule Kieny.


Organized in conjunction with the Human Vaccines Project, the 1st Annual Conference on the Future of Vaccine Development was a one day event which took place at the USC Michelson for Convergent Bioscience on June 27, 2018.

By bringing together some of the world’s leading scientists in the fields of immunology, genomics, bioinformatics, and bioengineering, the Future of Vaccine Development annual conference aims to explore how the convergence of new technologies across disciplines is impacting the future of vaccine development. The conference will also honor the three inaugural winners of the Michelson Prizes for Human Immunology and Vaccine Research, both via their respective presentations and the remittance of their prizes during the Awards dinner ceremony following the conference itself.


  • Mark M. Davis, Phd, Director and Avery Family Professor of Immunology in the Institute for Immunity, Transplantation and Infection, Stanford University.
  • Marie-Paule Kieny, PhD, Director of Research @ Inserm (Institut national de la santé et de la recherche médicale), former Assistant Director-General for Health Systems and Innovation at the World Health Organization (WHO).

Marie-Paule Kieny: So our next speaker is Mark Davis. So Mark is the director of the Stanford Institute of Immunology, Transplantation, and Infection, and Howard Hughes Medical Institute Investigators. He’s well-known for identification in the 1980s of elusive T-cell receptor genes and his group has made many subsequent discovery about T-cell receptors and how they function in both biochemical and at the surface of living cells. Of course, like the previous speakers, Mark’s contribution to immunology have been recognized by many honors and awards, including a recent election of membership at the Royal Society in London, the National Academy of Science, and the National Academy of Medicine. So congratulations for all this and we look forward to your presentation for 20 minutes.

Mark M. Davis: Yeah, hopefully I won’t let you down. So I came at this from a somewhat different angle and I just wanted to show that because I think there are much broader implications than vaccines, which is that the immune system is involved in a huge number of different pathologies and different diseases. You could go on and I think there are many that we don’t even know are immunological because the people studying those diseases aren’t immunologists and generally most people are still traumatized by the first immunology lecture they ever heard. You mention the subject and they get out the garlic, and the crucifixes, and just try to ward you off from telling you anything. And yet the public wants immunology.

There you go. There’s probably a whole immune booster aisle at Whole Foods. This is just what you see at the airports a lot. This is totally fake and it’s fake because there are no standards. There’s no standard for whether or not you should boost an immune system, and in fact, we do boost the immune system of cancer patients quite regularly now with checkpoint inhibitors, and some of them have got very severe autoimmune diseases as a result, so you could boost too much, but unless we actually develop standards for what is actually a healthy immune system.

So that’s what first got me into this is saying how can we define metrics of immunological health? If you go into a doctor’s office and say, “I worry about my heart,” they’ll have all kinds of stuff they can sell you which may or may not be actionable and never is the whole story, but they’ve got a whole set of stuff that is available, and is authorized, and validated. If you go in the same doctor’s office and ask, “How’s my immune system?” They’ll look at you as if you’re some kind of nut. “Are you sick?” And they have nothing they can do for you.

So really we know all medical knowledge is now on a cloud and there’s the immune system right there, clear as day, and why is it clear as day? Well, because it’s just incredible how there’s no modern immunology in basic medicine, that these are the two main assays that people do in the clinic involving the immune system, basically white blood cell counts, which is all of 1915, and complete blood cell counts, which is a glorified white blood cell count, five whole categories, 1959. In 1959, we didn’t even know that lymphocytes made antibodies. Many people thought lymphocytes were some useless cell that plowed around, probably had an osmotic effect in terms of the blood, but we didn’t really know anything.

So it’s just amazing that here since 1960, there have been something like 12 Nobel prizes awarded for immune studies, and yet, zip is getting into basic medicine. Now of course, cancer in other areas that more directly involve the immune system have gotten on the sick to some extent, but we are right now in a situation where there are way more innovative experiments being done in cancer immunotherapy than we have mouse data to support, so essentially you go through. I have ten different things. I’ll make all possible combinations of those things and see what works.

And why is that? Well, it’s because the immune system is complicated and so we had to develop a simplified model, namely the inbred mouse, and that’s been great for understanding the basics of the immune system. In fact, I don’t think we could have gotten anywhere without the mouse model, but we’re now in the situation where we’re curing mice right and left, or as Pedro Lowenstein said, “For the mice in the audience, I have wonderful news, that we can cure your autoimmunity, cure your cancer.”

So I think it’s time to move beyond the mouse system. I don’t think it’s over anytime soon. It’s still an incredibly useful and accessible system. We still have lots of mice, but there’s been this disconnect between clinical data, like all vaccines work in mice almost and none of them work in humans. That’s a slight exaggeration, but in recent days, I hear many of those tales. I’m sure Wayne knows more than I do. And so we really have to study the human immune system directly. This is where I’m coming from. I avoided medical school and I think there are a lot of patients that should be grateful for that event or nonevent, but it’s certainly interesting. There’s certainly lots of important problems.

The other thing that occurred to me was that we needed a strategy other than just making a mouse sick and curing it, and that brought me to a systems immunology style approach and we’ve been working on that for the last 11 years and there are lots of reasons to do that, but one of the things that I really thought was important was to develop a facility that could do what genome centers do. Genome centers do mass sequencing of genomes. That’s how we got the human genome and all these other genomes, and I remember people at that time, that Jim knows more than I do, they were saying, “No, we can’t do big science. That’s going to destroy research as we know it.” No. It was absolutely the right decision.

These are data that we want to get in a pipeline, in an industrial approach, and so for that reason, we developed this Human Immune Monitoring Core at Stanford, now over 11 years ago, and it’s just been great in terms of providing immunological data that’s done by experts, not by your students and postdocs, and reproducible high technology. We’re able to use the latest technology to do that and then we integrate this into large grant efforts from NIH, and now also the Gates Foundation, and the Parker Foundation, have been funding the groups of investigators.

So this is like a human vaccine project in one institution largely where we have expert clinicians, particularly in vaccinology. Corey Decker’s been working with us now over ten years. She recruits patients, bleeds them, gives them vaccine, bleeds them some more, brings them back year after year if that’s part of the thing, and then samples go to the Immune Monitoring Core and we collect all this data, but we always get much more blood than we need for these assays and this provides material for a whole bunch of science labs at Stanford particularly but also informatics analysis, microbiome studies, technology development, genomics, et cetera, just making human samples available easily to basic scientists really, really enables them to do human work.

Most of these people could not do human work unless someone gave them samples. They just don’t have the bandwidth to make the clinical connections properly. This is now systemizing and working really well. We have hundreds of papers published.

Why do we do vaccines? Well, not because we want to develop a better flu vaccine but because flu vaccine is something you could give to everyone regardless of age and it’s a good stimulant in the immune system, and also in terms of the last point, it has the advantage of also being a crappy vaccine so there are lots of nonresponders. We didn’t have to go to hepatitis B. We just went to flu. It’s right there and you don’t need to do thousands of people to get a few nonresponders. They’re right there, especially elderly people.

So anyway, without going into that, we have quite a few studies of this that we’ve done in a systems way. I don’t want to dwell on those. I don’t have the time to do that but I just highlight a few things.

I’m very proud that there was just so much literature extolling the connection of some gene polymorphism with some disease no matter how trivial the connection was. I just thought we really needed to do something more rigorous and that was a twin study where we combined the power of systems immunologies, we call it, with the ability to look at monozygotic and dizygotic twins in a population and really say on balance, is the variation in this trait heritable or not heritable?

And it turns out about 75 percent of the 200 traits in the immune system that we looked at are not significantly heritable. There might be a small genetic component but it’s basically not an item. Only a few things were really there. There was a lot of data in this paper but I just want to highlight this because I think it’s particularly interesting that the 210 twins that we looked at, 16 pairs were monozygotic twins were discordant for cytomegalovirus and so we asked what’s the effect of cytomegalovirus on the disposition of the entire immune system of these people, and this is what we would call an immunome, and it turned out almost 60 percent of all the 200 variables were changed by CMV in these monozygotic twins, so CMV has an enormous effect on the immune system and not just in the effect.

We had a separate study that we were doing at the same time with a longitudinal cohort that we’ve been plugging away at for 11 years now focused on aging and whereas the older people in the cohort, there wasn’t a significant influence of flu antibody response to vaccine between CMV negative and positive or there was a lot of noise here, but what was interesting is that our control cohort of 20 year olds, perfect in every way, actually the CMV positive young adults had superior flu vaccine responses than the CMV negative, so CMV is acting seemingly as an adjuvant to the flu response.

In this same paper, we had a colleague, Paul Thomas, had a very striking mouse experiment that go along with this where if you infected mice with cytomegalovirus, and then five weeks later, infected them with flu, the ones that had been previously infected with cytomegalovirus gave a hugely lower titer of flu, a four log lower titer of flu. They were almost entirely protected from the flu, and that effect wore off over time but still it’s very interesting or it supports the idea. Billions and billions of people around the world are infected with CMV and most of them are just fine.

We think of CMV as a pathogen ’cause it will kill you if somebody just irradiated your immune system, but if you’re lucky enough to have avoided that, it’s probably a good thing, at least while you’re young. When you’re old, all bets are off, but you shouldn’t just think of it as a pathogen. It’s probably doing a lot of good for many more people than it’s doing bad for.

And then I want to switch here to talking about my almost first love, T-cell receptors, and how we are always the missing piece in the systems immunology repertoire, and James gave a great overview of how important, and how vast, and how complex that is. This is our own version where we focus on T-cells and particularly the problem with T-cells is getting at their T-cell receptors, and so Arnold Han, a clinical fellow in the lab, developed this very simple, high-throughput way of getting single cell T-cell receptor sequence data and also phenotypic data where you can tell, okay, this was an expanded clone of T-cells here in terms of the same sequences, multiple cells, and then what are the phenotypes of those cells? Do they make IL2, do they make FOXP3, et cetera, et cetera? So we can look at the sequence diversity and the phenotype at the same time.

And one of the things that came out of their earliest studies here was how clonal expansion really clues you in to what’s important in a response. So this where colon carcinoma’s TIL cells and these are CD4 cells where we sequenced 600 individual CD4 cells from this colon carcinoma versus 300 from adjacent, normal adesimal tissue, and then what you can see with the color wheel here is there’s massive colon expansion. Ten percent of all the CD4 sequences were one sequence, and it wasn’t that these cells with the same sequence all came into the tumor. It’s almost certainly that one cell with that sequence came into the tumor and then was very excited by what it saw. It saw some antigen and then clonally expanded.

We followed this up with another great technique. Our colleague, Chris Garcizevalt, a way in which you could display 10 to the ninth different peptides in the same MHC in a yeast library and then screen that library with a T-cell receptor of interest in a soluble, multivalent form, and on a good day, you can find the antigens, and this is an example.

In this colon carcinoma study that just came out a little while ago, we found two different antigens using T-cell receptors and that we had sequenced in this approach, and this was a shared one that two different patients basically had T-cells. They weren’t identical in sequence but they recognized the same peptide essentially. We also found a neoantigen in one of the patients, so there’s a mixture of neoantigen-specific T-cells and self-specific unmutated things, and this is a proof of principle that this whole system can work.

The other problem is that for T-cell receptors, you just get one sequence out of billions and billions of possible sequences. There are way more T-cell receptor sequences than there are antigens that T-cells recognize, so a big problem is how do you find the T-cell receptor sequences that recognize the same antigen. So they’ll be different between different people. Even identical twins have only about one or two percent overlap in terms of actual sequence identity, so looking at sequence identity in T-cell receptors is not the answer. You need to find the rules for recognition.

And so what a really brilliant graduate student, Jake Glanville, in the lab did was he took a panel of peptide MHC tetramers, used them to isolate specific T-cell receptors, specific T-cells from different people, and then compared the sequences, and what immediately came out of this was that we could see conserved three or four amino acid sequences in the CDR3 of the beta chain of these T-cell receptors, and basically, it’s an immunogenesis experiment without the immunogenesis, which is one of the most painful things you can do in molecular biology. You let the natural variation in T-cell receptor sequence tell you what’s important for this given specificity that you’ve defined by using this particular peptide MHC label.

And it turned out that these conserved sequences were exactly the residues that bound the peptide in the MHC groove in all these cases where we had a structure that we can go to. So this immediately said that, for instance in this case here, you see this conserved sequence but you also see this other stuff here that’s kind of similar but different. It turns out this doesn’t matter brcause this is structural. This is the sides of the CDR loop. What’s really important is this contact region and that’s why it’s conserved, so if you design, as Jake did, an algorithm, which he calls GLIPH, that can take thousands of T-cell receptor sequences and look for ones that share just the motif, just the three amino acids or so, plus there are some other rules that go into this, you might have a system by which you can crunch thousands of T-cell receptors and look for shared specificities. The sequences are not identical, but that doesn’t matter. As long as they share motifs, they will share a specificity.

And I have to hurry along, I’m sure. So we did this for CD4 T-cells from TB-infected people, lightly infected people, and it was really nice that we took almost 6,000 sequences to start with. We crunched them. We got 100 different groups, specificity groups, we call them, and these were the ones that were most shared between three or more people, and we could also see that with HLA type that if people shared a particular TCR motif, they also shared an MHC allele, which was fantastic because this is a South African cohort and they expressed 69 different Class 2 alleles. It would have been a nightmare to look at all those individually, but since we had this strong indication of what the MHC was, we could go right to reporter constructs and right to a collection of peptides that Alex Eddy had curated for CD4 responses in TB and we could find the peptide MHC target for every one of those five groups.

And so this says the algorithm works and that means you can use the algorithm just by itself to cruise through sequences and understand the diversity of a particular T-cell response either in a group or in a collection, and so what we’re doing now for flu and other diseases like TB, we’re assembling disease-specific TCR-omes so that we could have a very large collection of specificity groups in a given disease for a given MHC. So if somebody comes in with that MHC, infected or vaccinated, you could then gauge the diversity of their response just by looking at this index, just this database that we’ve been developing. Right now, we have something like 30,000 unique flu-specific sequences that we’re using.

And just in general, what we’re finding is that this clonal expansion that I first showed you in the colon carcinoma is absolutely characteristic of T-cell responses, particularly CD8 clonal expansion. We see them in lyme-infected people. We see them in MS patients. We see this in chronic fatigue patients, versus normal people have very few in the blood, very few clonally expanded CD8 cells. They’re really rampant in just about every disease we’ve looked at or in a vaccine response.

So very lastly, I want to tell you about how an artificial lymph node has long been a goal in vaccinology and for the obvious reason that it takes so long and costs so much to get a single vaccine into a single person, years, and years, and millions, and millions, of dollars. If you could do this in vitro initially and you can do it on a much broader scale. You can look at hundreds of vaccine candidates. You can look at thousands of adjuvants and that’s exactly what we want to do.

But artificial lymph nodes have not happened yet, so we went another route to say let’s just take a real lymph node, namely a tonsil, that something like half a million tonsils are whacked out of innocent little children every year and we can catch some of those. They’re usually just thrown away, so if you’re standing there with an ice bucket, you can get a chunk of tonsil, and Lisa Wagger really made this work where you can basically stimulate the tonsil with live attenuated flu vaccine, for example, you get a real response. You get germinal centers. These are clusters of B cells and then there’s a T-cell zone here just like in a lymph node typically, but more importantly, the proof of the pudding is we get flu-specific antibody responses in terms of these ELISA assays. We also get plasma blasts and lots of sequences and somatic mutation just like you’d hope.

If you looked at affinity of these antibodies, it would be quite decent affinity, flu-specific T-cells, mostly HA head but some stem as well, so there’s hope there. We also have done this with RSV fusion protein where we can also get decent antibody responses.

We can manipulate the system so one of the common problems that people have with human work is the inability to do mechanistic experiments, in many cases. I don’t think that’s absolute but that’s what most people think. This is mechanistic experiments in spades. You can manipulate the genes. You can manipulate the molecules. You can manipulate the cells and we’ve done some of that.

If you remove the dendritic cells from the culture, nothing happens, although if you remove memory cells, it’s actually okay. Nothing bad happens. Anyway, we’re picking that apart.

So all these stories are I think really helpful both in understanding human immunology, in working towards what we hope will be an immunometer, the metrics of immunological health in general. We go along with this study we just heard about and others I know of where the preimmune status seemed to be the biggest correlate with a good vaccine response versus a bad vaccine response. I think this tonsil organ system will be a really valuable system for a vaccine development adjuvant, a development mechanistic studies of one of the most basic things that happens in an immune response, adaptive immune response, and probably there’s lots of innate stuff going on, too.

And I think I will go to the last slide and thank the people. Peter Brodein really led the twin work. Jacob and Huang-Huang did the TB work. Arnold Han and others did the single cell T-cell sequencing, and Lisa Wagger and others have really powered through the tonsil organite system, so I will stop there.


Marie-Paule Kieny: Thanks a lot, so you are first one and I’ll take only one question. Go ahead.

Audience: On the tonsils, both of those are probably recall responses with the flu and RSV?

Marie-Paule Kieny: Can you speak up?

Audience: Have you generated a primary response in anything?

Mark M. Davis: We can get a bit of a primary response with some HIV antigens, but they’re IGM. They’re not very high affinity, but what we can do, because we can freeze down lots of aliquots of the tonsils and we can work just those frozen aliquots, what is on the list right now is can we jump from one aliquot to another? Can we start a response, a primary response, and then boost it by adding more cells from the same individual, from the same tonsil, and I think that should be possible.

Marie-Paule Kieny: Thank you very much.

Transcript curation: Alison Deshong

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