6.2 Dennis Burton — How Does HIV Evade the Antibody Response?

Dennis Burton: [00:00:00] First of all, like many have said, it's a great honor to be invited to be here, and thanks to Bob [Gallo], John [Coffin], Mila [Pollock], and Bruce [Walker] for the invitation. I didn't have any personal slides. I'll just tell you briefly my history, academic history, if you like. I studied chemistry at Oxford and then did a PhD in NMR in [00:00:30] Sweden, went back to Oxford and started working on antibodies and their effector functions, got a job in Sheffield, in the north of England, and worked on antibody effector functions, their interactions with FC receptors. We actually showed the site of interaction with those.

Then I went on sabbatical to Scripps in 1989 and to work with Richard Lerner (b. 1938) on developing recombinant [00:01:00] antibodies from libraries. Obviously, I never went back, for well-known reasons. As soon as we got that technology to work, I started to apply it to human antibodies. The first thing we applied it to was HIV, and that's how I got into HIV and vaccine development.

The title I was given here was the first one, which is, "How does HIV evade the antibody response?" [00:01:30] That refers to how the virus defeats the antibody. Actually, I'm much more interested in the reverse, "How does the antibody defeat the virus," and that's broadly neutralizing antibodies. I'm just going to have one slide on the first of those two clauses and then all the rest is on the second half. How does HIV evade the [00:02:00] antibody response? There are many different factors, but the obvious ones, that it's the spikes, the sole target for neutralizing antibodies, there's a great paucity of such structures on the spike structure and that tends to elicit rather poor B cell responses, but the real killer is the nature of the envelope spike, this structure. (1, 2, 3, 4) We now have that. We speculated for many [00:02:30] years on it, but thanks to the work of James Binley, Rogier Sanders, and John Moore in generating a recombinant form of this trimer, and then of Ian Wilson, Andrew Ward, Dmitry Lyumkis is actually here, I think, somewhere, who did the cryo-EM, and Peter Kwong, we now have a very good view of this molecule. This is where all our problems start and end, in a way, and it's a beast. It's a very tight structure. The [00:03:00] protein surface is largely on the inside, and then even without the glycans, and then on top of that, you build this huge shield of glycans.

Just looking at this, you can well appreciate that antibody recognition, antibody is a pretty large molecule, is going to be very, very difficult, and especially when you ask for broad neutralization because you're asking for antibodies that are able to recognize somewhat conserved [00:03:30] regions of the envelope spike. It could have been, and you might have thought that broad neutralization wasn't possible. The principle that it was possible was demonstrated pretty much around the same time by our lab and by Hermann Katinger. (5) It was demonstrated, not with sera but with monoclonals.

We generated this antibody, [00:04:00] b12 in 1994, and we sent it to various different labs to run their neut assays. One of the clearest cut results came from David Ho's lab. When he got this data, he was really amazed. He called me up, and this was unbelievable, that a single monoclonal could neutralize all these different viruses that were really quite dispersed in terms of [00:04:30] sequence.

That was really the point at which, for me, anyway, we started to think about vaccines, because now we thought, "Well, if you have broadly neutralizing antibodies, then you have the opportunity—produced in natural infection, you have the opportunity to immunize with those and re-elicit them, and that could lead to a vaccine."

This work I did actually with Carlos Barbas (1964–2014). [00:05:00] Here is his—one note, I just actually took this off the Amazon site just a couple of hours ago, and this is a link to Cold Spring Harbor. Carlos and I—actually I bailed out after about four years, and two weeks in November here is quite tough. I don't suppose I should say that, but it is. Anyway, I did this with Carlos [00:05:30] for about four years, and he kept doing it for many years. We taught this, Phage Display. (6) Of course, Carlos, unfortunately, passed away a couple of years ago, tragically, because he was a really truly brilliant scientist.

Anyway, we did a lot with this antibody, including all sorts of in vivo studies. We worked with Ian Wilson. This is where our collaboration with Ian started, [00:06:00] with a graduate student, Erica Saphire, worked between Ian and my lab. (7) She solved the structure of this antibody, actually as a whole human IgG, and that's still the only structure of a whole human antibody that's available, as far as I know. Immediately, you saw unusual features, and these have been seen time and time and rediscovered many, many times.

It was clear that the level of [00:06:30] mutation, somatic hypermutation was quite high, and the antibody had this unusual finger here, this H3 that really came off the surface. That's true of many of these broadly neutralizing antibodies. It's probably related to the fact that the whole protein surface of this thing is covered by this glycan shield, and you need to find a way to get underneath the shield. [00:07:00] With this antibody and those from Hermann Katinger, we had a little set for quite some time of four broadly neutralizing antibodies.

These don't look so impressive today in terms of potency or breadth, but remember, at that time, we only had clade B, and they did very well against clade B. They do less well against other clades when you start to go global, but you can see here the coverage and the potency. [00:07:30] Very often now folks start by saying, "God, how miserable this set of antibodies are," but again, I would say, you've got to start somewhere, and this is where it started.

Once we got these antibodies, as I said, in these antibodies, we started to think about vaccines. (8) I apologize for this, pulling this whole abstract, but I really [00:08:00] wanted to make most of the points that are here. First of all, we did do protection studies, so we knew these antibodies worked in vivo. This is 1997. "The challenge in antibody-based vaccine design is to elicit such antibodies to the viruses involved in transmission. At least two major obstacles exist. The first is that very little of the envelope spike surface appears accessible for antibody binding, [00:08:30] probably because of oligomerization and a high degree of glycosylation."

This is long before we had any structures. I think that's really been borne out, and that was borne out by thinking a lot about a lot of biochemical data, really, that indicated that.

"The second is that the mature oligomer constituting the spikes appears to stimulate only weak antibody responses." That's still very, very much [00:09:00] a problem. Variation was not seen as so much a problem. And that's still debated. You would think that variation causes a big problem, and sometimes folks will argue it is, and it may be. But we actually still don't know whether the difficulty in hitting some of these conserved sites is because there's all this variation or not.

But here's the most important line here. "Vaccine design should focus on the presentation [00:09:30] of intact mature oligomer"—that's very much ongoing—"increasing the immunogenicity of the oligomer"—that's very much ongoing today—"and learning from the antibodies available that potently neutralize primary viruses." To me, it's amazing that 20 years later, so much of what we do, anyway, is still contained within those thoughts. It's just taken that long to get all the information and data that really allows us [00:10:00] to move in these directions.

Looking particularly at that last line, again, this got me thinking about difficult pathogens, generally. I proposed in 2002, that one could take these antibodies, like broadly neutralizing antibodies from HIV, and that these could be the clue to vaccine design against difficult pathogens.  [00:10:30] I argued that one could study these at a structural level and come up with combinations of immunogens that, when given to uninfected individuals, would re-elicit, if you like, these sorts of protective antibodies. (9)

I called this at the time, "reverse vaccinology." I should have been more careful because then Rino—and I published—and then Rino Rappuoli (b. 1952) sent me an email and he said, [00:11:00] "Well, look, I already coined this phrase," and he had for his genetic approach. (10) I had to drop that particular name, which I felt was very unfortunate, because that's what exactly I thought that we were advocating. Normally, you put a vaccine into people and you get antibodies. I was saying, you go to a person, you take out the antibodies and you work backwards to a vaccine, so I thought that was a nice name for it. Anyway, [00:11:30] Rino rescued us recently by suggesting that we call this now reverse vaccinology 2.0. (11) He calls his 1.0. I figured, if he says it's okay, it's okay. He's also Rino.

There was a problem with this whole approach, particularly with regard to HIV, and I think this approach is also very much being adopted elsewhere. This is the basis of [00:12:00] attempts to generate a universal flu vaccine. I think you'll see it'll also become successful in malaria, we'll see. But the big problem we have with HIV was we had these very small number of antibodies, not really enough to do the kind of molecular work that we were advocating. It really became necessary to get more antibodies. We spent a long time working on this. Eventually, we broke through. [00:12:30] We, the field, broke through, and the reasons are twofold. The first one's often totally neglected, and that is that we got much better cohorts. Instead of just looking at random folks, we went out then—with IAVI (International AIDS Vaccine Initiative) we looked at nearly 2,000 donors, and found those with the best broadly neutralizing sera in order to make broadly neutralizing antibodies. And that's key, it really is key. [00:13:00] A lot of that was made possible by high throughput technologies to look at sera neutralization against panels of viruses. And then better methods were developed for isolating human monoclonals largely based on single B cell technologies, direct neutralization and affinity selection. Actually, the first, the approach, the non-biased approach is actually that that's given us the most novel broadly neutralizing antibodies over [00:13:30] time.

This was how we first broke through. (12) And this was this pair of antibodies, PG9 and PG16, that were about an order of magnitude more potent than the existing antibodies at the time, with great breadth, about 70%, which is pretty good for a single antibody. This was in 2009, and the way we did it is shown here. Again, this was really dependent upon having [00:14:00] access to high throughput technologies for screening purposes, for plating out cells and then for screening supernates.

What we did was, we took one of these donors that had a very good broad neut sera, one of the 1,800, we plated them the B cells out of one B cell per well, roughly, we activated the B-cell, and then [00:14:30] we tested the supernates after about a week in a micro-neutralization assay, so that's 30,000 micro-neutralization assays. That found two wells that were giving good neutralization on a couple of indicator viruses, we rescued the genes, and that gave us these antibodies, PG9 and PG16. That really showed that there was much better stuff in there in these [00:15:00] donors.

That's led over time to a huge movement, on the left here, of ever increasing potency. This is an antibody, probably, one of the best available that we got a couple of years ago that has a potency that's comparable with the best antibodies against polio virus or whatever you'd care to name, and a coverage of about 80% of global isolates, which is pretty good for a single antibody. [00:15:30]

These antibodies have become so potent and so broad that they've attracted interest in the therapeutic modalities. For example, we showed with with Dan Barouch that this antibody, PGT121 was able to bring the viral loads in macaques very quickly down to undetectable. In the case some animals, it remained undetectable out to beyond [00:16:00] a year.

There's been great interest in these antibodies from therapeutic and also cure angles. These antibodies mostly come from the VRC (NIH Vaccine Research Center), from Michel Nussenzweig, and from ourselves. A number of these have already hit the human phase one and a number are about to do so, so it'd be quite interesting to see if these have a therapeutic efficacy, particularly if they have some [00:16:30] role combined with other modalities and cure strategies.

Our interest has always was been vaccines and we needed to understand how these antibodies interact with our sole target, the envelope spike. (13) These are composite of EM, negative stain EMs from Andrew Ward's lab showing mostly antibodies that we've isolated and one or two there is from the VRC. Those two are from [00:17:00] Michel. Most of them are from us, that's from [unintelligible 00:17:03]. This is really I think, amazing finding actually. The bottom line of all of this is, it shows you the power of evolution, because despite this glycan covering, if you give the antibody system time, that is years, then it can find ways to get recognition [00:17:30] under that shield over a large part of the molecule. We now group these different broadly neutralizing antigenic regions into five: the apex, a region of high mannose sugars here, the CD4 binding site, a region between gp41 and gp120 and close to the membrane, the membrane proximal, external region.

I'll just comment on two of these with single [00:18:00] slides in terms of structure, because there are some common motifs here. Looking first at the apex, this is an unpublished cryo-EM structure that we have. Actually, this is a cartoon of the cryo-EM structure that we have, a work we've been doing with Andrew Ward, J. H. Lee and Raiees Andrabi in my lab. (14) Basically, the theme to note [00:18:30] here is that here's the protein surface, it's on the V2. This is right along the threefold axis at the top of the envelope spike. This long HCVR-3 and two V2 strands comes between these glycans. There would be three of these. At its tip, it has a very negatively charged loop, negatively charged with tyrosines and sulfated—sorry, sulfated tyrosine and aspartate. And it recognizes a group [00:19:00] of—particularly lysines in a basic sync. It recognizes from multiple protomers, so the antibody is trimer specific.

But here is a very interesting theme and one that's repeated for these broadly neutralizing antibodies, is that they don't necessarily require absolute conservation. That's one of their tricks. So what you have here is a sequence of lysines. It's actually quite variable. Sometimes one lysine comes up, sometimes another. [00:19:30] But what these antibodies recognize, all they require is a certain degree of positive charge in this general region. If that's achieved, then they will bind with high affinity and they will neutralize. The virus has a lot of trouble escaping these things in a simple way. This extends to the fact that this type of antibody as shown by [00:20:00] Beatrice [Hahn] will even neutralize chimpanzee viruses, no other broadly neutralizing antibodies will. Then if we look at the CD4 binding site, this is a real lesson in evolution of the antibody system. These are antibodies first described, obviously, by the VRC, John Mascola and colleagues. And this antibody is—what they do is they [00:20:30] imitate CD4 as far as they can. This is gp120, green, CD4 binding site in yellow, the outer domain of CD4 in orange, that's the terminal domain that's interacting. Now, I'm going to bring in the antibody molecule. The VH domain of the antibody now sits very much where [00:21:00] the CD4 immunoglobulin domains sits. The details of—and this requires a certain germ line, it actually requires one called VH1-2—and the details of interactions is actually molecularly come out quite similar.

But now you have a problem—you see it feels the same space but now you have a problem because CD4 is one immunoglobulin domain-wide, and antibody  [00:21:30] is two, so it's got to find a way to get the light chain in. How does it do that? Well, it puts a lot of requirements on the light chain. First of all, it has to have a very short LCDR3, these are normally nine or 10. This is only five, it's always five and then it also has to have a series of mutations and or deletions in the loop here L1 and framework in order to accommodate a glycan [00:22:00] which sits right over the CD4 binding site. If the antibody can evolve all these features, then it can get in there and it's very potent.

But from some time ago, as we even before this we understood these antibodies with this complexity—this one's particularly been studied by Peter Kwong and the VRC this type—but even before we got there, we started to realize [00:22:30] that the HIV vaccine problem and recognizing these shapes is going to be very, very difficult. The classical approaches of simply mimicking the killed or attenuated virus are not going to cut it. A long time ago, actually, we proposed that it was time to look beyond the molecules of natural infection. (15) That one had to [00:23:00] think anew about vaccine design. You always just think "We'll just try and mimic exactly, we'll just take the same molecule that's on the surface." You obviously need something that's the same shape, but it does not necessarily mean you have to take the whole caboodle that comes on the surface of the pathogen. And increasingly that, as well, has evolved into a strategy. [00:23:30] 

There's one further complication to all this noted by Mitco Dimitrov, and related to the last slide, which is that many of the—if you take a broadly neutralizing antibody and go back to a germline version, it no longer reacts with envelope. (16) Then you have a problem. How are we even going to trigger broadly neutralizing antibodies? Because you've got to start somewhere, you've got to trigger the lineage. [00:24:00] That's greatly influenced the vaccine field, I'm sure that Bart'll say a lot more about lineages and so on.

But now I think that, and this again is revolutionary thinking actually in a way from the field in terms of vaccine design. Vaccine design to date is, you get the same vaccine three times, usually or maybe twice, but [00:24:30] it's the same molecule that goes in boom, boom, boom. For HIV, it's become apparent that that won't work, and what we're going to have to probably do is have a set of vaccines, of different immunogens, so one, two, three, maybe four different immunogens. And that's going to be the only way I think we're going to take the antibodies that were given in the naive repertoire to broadly neutralizing antibodies. [00:25:00] Normally, that process will take years in natural infection, we have to do it in much shorter time. I think we can if we can really get control of affinity maturation.

These are various possible strategies, you could imagine, you could take clade A, then B and C, put those in some sequential arrangement. You could look at natural infection and try and mimic that in certain waypoints. Or you could [00:25:30] take this approach, which would, probably is one we favor, which is you deliberately go for the germline initially, you rationally boost, and then you finish off with something that looks like the natural trimer. This is one that, at least in our CHAVID (Scripps Consortium for HIV/AIDS Vaccine Development) and CAVD (Collaboration for AIDS Vaccine Discovery, we've focused on more than anything else.

I'll just finish up showing you what we're doing. [00:26:00] Much of this is the brainchild of Bill Schief. What he did, first of all, was through computation and selection, design molecules which presents in a nanoparticle, which will specifically activate the VH1-2 gene that's important for CD4 binding site antibodies. Furthermore, hopefully, select for that short L3, so kick things off in the right direction. [00:26:30] That's what this design was all about. Since then, we've gathered evidence, albeit in somewhat biased—models, one not so biased, I'll show you—that this is indeed possible. This shows you in a knock-in mouse, particular bias model, having the germline versions of the VRC-R1 class antibodies that you can activate the right [00:27:00] germline. (17) This shows that humans have the right combinations, the right germlines with the short LCDR3 in their repertoire. (18) They're a pretty good frequency. There's about 100 of these per lymph node. This recent paper shows that you can drive things beyond the initial stage, you can activate and go about [00:27:30] halfway or more than halfway, maybe two-thirds of the way using designed immunogens. (19) This paper from Fred Alt, Bart and John shows a similar type of conclusion. (20) This one shows you that you can activate germlines with a lot of competition in a Kymab mouse with Allan Bradley. (21) And this one shows things in a completely different system the PGT121 antibody system [00:28:00] that you can drive affinity maturation all the way from germline to complete. (22)

Finally, then, this is our—I know, honestly, this is the last slide. [laughter] This is our overall strategy and I guess what I would just say is that the field has had great success here. We still need to learn a lot here, particularly in terms of durability of responses. That to me is one of the biggest problems we have now with protein [00:28:30] immunogens. Natural infection, Bart and John Mascola have done great things here, all of this is fed into here. We have many immunogen designs and strategies now. We're in a very exciting phase where these are being evaluated, and at least a handful of vaccines are going into humans in the next year 2017 I think. These animal models are crucial for iteration. [00:29:00] I'll just acknowledge the fact that I've spoken of many, many different collaborations and all of this is funded very generously by the CHAVID and CAVD from the Gates Foundation, and from the Ragon Institute. I'll take questions, thank you.

[applause] 

Harriet Robinson (Moderator): Questions? [00:29:30]

Wasif Khan: Great work of number of people here. I have two questions. One is how do you predict the intermediate stages or the immunogen design, how is the design done? The second question, perhaps more important, is that there may—So antibody response probably is produced [00:30:00] against many more peptides and antigens encoded by the virus, and if—dilution effect, for example, if there are antibodies which are much more against other things than neutralizing antibodies, or, further, that the memory develops against some other epitopes, which are not neutralizing.

Dennis: Right. Oh, yes. I got a microphone. To take the second question [00:30:30] first, you generate 90 odd percent of your, or 99% of whatever of your antibody responses, against crap. It doesn't do anything for you. That's the normal way of things. It would only be a problem if you then were distracted, as it came at the end of your question. To avoid that sort of problem, we tend to present an epitope, and then we'll do a resurfacing in the next stage so that [00:31:00] the only thing it's seeing constant is the epitope that we're targeting, so we resurface. That's how we try to deal with that. We're not 100% clear how important that is.

What matters is the good stuff, not if you have vast libraries of bad stuff. The other question was about how we design the boosts and this particularly [Bill Schief's] work. There, we often make use [00:31:30] of antibodies that are at some intermediate stage. You can take a germline, for instance, and you can take it some distance towards a broadly neutralizing antibody, and then you can look for an immunogen that binds to that so then you can shepherd things. We're always looking—We have a gradient of immunogens that start with the things that bind very well to the germ line, to those that bind very [00:32:00] well to the final trimer on the virus. It's all very logical, but it doesn't necessarily [unintelligible 00:32:08] afterwards.

Wasif: The final primer is actually a trimer?

Dennis: Yes. It's the associate trimer. It's the favored trimer at the minute engineered versions thereof. John.

John Mellors: Dennis, it's brilliant work. One anxiety, I have that's a hangover from—

Dennis: You only have one? [laughs] [00:32:30] 

John: Many. One anxiety that I have is there's a hangover from drug development is minor variance. Can you comment on how many mutations away the virus is from escaping the neutralization of many of these bnAbs?

Dennis: Generally, you could probably escape any single bnAb (broadly neutralizing HIV-1 antibodies) [00:33:00] with a point mutation. Some of them might really cost you a lot of fitness or they might-- but generally speaking, not that much probably. That's where the strategy is always look to induce multiple antibodies. And polyclonal—we're not trying to induce monoclonals, we're trying to induce a series of antibodies that look like [00:33:30] that monoclone plus a whole thing repeated with another epitope. That's the ground design.

John: The key issue is you won't know. There's no system because of the diversity of the variance that will predict in advance.

Dennis: What you're saying would be the greatest problem for a therapy approach.

John: Yes.

Dennis: That's why I'm still [00:34:00] vaccines because I think the diversity problem is much less of a problem if you're looking at protection than it is against if it's therapy.

Harriet: Okay. One quick question.

Emilio Emini: Yes, one question. You mentioned earlier, Dennis, and we've talked about it before that you don't get engagement of by the germline antibodies of the trimer, right? Of the envelope.

Dennis: Very often. Sometimes you do, yes.

Emilio: Yes. [00:34:30] The question is, obviously in the context of an infection, it's got to start somewhere?

Dennis: Right.

Emilio: You do, in theory, get it?

Dennis: Oh, I think you do. I think you can find a trimer that will bind to any germline version. You can find Burston work. You can find a trimer, but the problem of immunizing with that trimer alone, and it might work and we and others are testing that. The problem would be, you still have a whole bunch of other distracting potential epitopes on it [00:35:00] and then we don't know how distracting those are.

Emilio: No, no. That's fine, but you can, in theory, if you've got the right structure, start with the trimer though it's- [crosstalk]

Dennis: Yes. absolutely. Okay.

Harriet: Thank you very much. Our next speaker.

[applause]

[00:35:18] [END OF AUDIO]

Citations

1. Day, Cheryl L., Daniel E. Kaufmann, Photini Kiepiela, Julia A. Brown, Eshia S. Moodley, Sharon Reddy, Elizabeth W. Mackey, et al. “PD-1 Expression on HIV-Specific T Cells Is Associated with T-Cell Exhaustion and Disease Progression.” Nature 443, no. 7109 (September 21, 2006): 350–54. doi:10.1038/nature05115.
2. Julien, Jean-Philippe, Albert Cupo, Devin Sok, Robyn L. Stanfield, Dmitry Lyumkis, Marc C. Deller, Per-Johan Klasse, et al. “Crystal Structure of a Soluble Cleaved HIV-1 Envelope Trimer.” Science 342, no. 6165 (December 20, 2013): 1477–83. doi:10.1126/science.1245625.
3. Lyumkis, Dmitry, Jean-Philippe Julien, Natalia de Val, Albert Cupo, Clinton S. Potter, Per-Johan Klasse, Dennis R. Burton, et al. “Cryo-EM Structure of a Fully Glycosylated Soluble Cleaved HIV-1 Envelope Trimer.” Science342, no. 6165 (December 20, 2013): 1484–90. doi:10.1126/science.1245627.
4. Pancera, Marie, Tongqing Zhou, Aliaksandr Druz, Ivelin S. Georgiev, Cinque Soto, Jason Gorman, Jinghe Huang, et al. “Structure and Immune Recognition of Trimeric Pre-Fusion HIV-1 Env.” Nature 514, no. 7523 (October 8, 2014): 455–61. doi:10.1038/nature13808.
5. Burton, Bennis R., Jayashree Pyati, Raju Koduri, Stephen J. Sharp, George B. Thornton, Paul W. H. I. Parren, Lynette S. W. Sawyer, et al. “Efficient Neutralization of Primary Isolates of HIV-1 by a Recombinant Human Monoclonal Antibody.” Science 266, no. 5187 (November 11, 1994): 1024–27. doi:10.1126/science.7973652.
6. Barbas, Carlos F., III, Dennis R Burton, Jamie K. Scott, and Gregg J. Silverman. Phage Display of Peptides and Proteins: A Laboratory Manual. Cold Spring Harbor: Cold Spring Harbor Laboratory Press, 2001.
7. Saphire, Erica Ollmann, Paul W. H. I. Parren, Ralph Pantophlet, Michael B. Zwick, Garrett M. Morris, Pauline M. Rudd, Raymond A. Dwek, Robyn L. Stanfield, Dennis R. Burton, and Ian A. Wilson. “Crystal Structure of a Neutralizing Human IgG Against HIV-1: A Template for Vaccine Design.” Science 293, no. 5532 (August 10, 2001): 1155–59. doi:10.1126/science.1061692.
8. Burton, Dennis R. “A Vaccine for HIV Type 1: The Antibody Perspective.” PNAS 94, no. 19 (September 16, 1997): 10018–23. doi:10.1073/pnas.94.19.10018.
9. Burton, Dennis R. “Antibodies, Viruses and Vaccines.” Nature Reviews Immunology 2, no. 9 (September 2002): 706–13. doi:10.1038/nri891.
10. Rappuoli, Rino. “Reverse Vaccinology.” Current Opinion in Microbiology 3, no. 5 (October 2000): 445–50. doi:10.1016/S1369-5274(00)00119-3.
11. Rappuoli, Rino, Matthew J. Bottomley, Ugo D’Oro, Oretta Finco, and Ennio De Gregorio. “Reverse Vaccinology 2.0: Human Immunology Instructs Vaccine Antigen Design.” Journal of Experimental Medicine 213, no. 4 (March 28, 2016): 469–81. doi:10.1084/jem.20151960.
12. Walker, Laura M., Sanjay K. Phogat, Po-Ying Chan-Hui, Denise Wagner, Pham Phung, Julie L. Goss, Terri Wrin, et al. “Broad and Potent Neutralizing Antibodies from an African Donor Reveal a New HIV-1 Vaccine Target.” Science 326, no. 5950 (October 9, 2009): 285–89. doi:10.1126/science.1178746.
13. Burton, Dennis R., and Lars Hangartner. “Broadly Neutralizing Antibodies to HIV and Their Role in Vaccine Design.” Annual Review of Immunology 34, no. 1 (May 20, 2016): 635–59. doi:10.1146/annurev-immunol-041015-055515.
14. Lee, Jeong Hyun, Raiees Andrabi, Ching-Yao Su, Anila Yasmeen, Jean-Philippe Julien, Leopold Kong, Nicholas C. Wu, et al. “A Broadly Neutralizing Antibody Targets the Dynamic HIV Envelope Trimer Apex via a Long, Rigidified, and Anionic β-Hairpin Structure.” Immunity 46, no. 4 (April 18, 2017): 690–702. doi:10.1016/j.immuni.2017.03.017.
15. Burton, Dennis R., and Paul W. H. I. Parren. “Vaccines and the Induction of Functional Antibodies: Time to Look beyond the Molecules of Natural Infection?” Nature Medicine 6, no. 2 (February 2000): 123–25. doi:10.1038/72200.
16. Jardine, Joseph G., Takayuki Ota, Devin Sok, Matthias Pauthner, Daniel W. Kulp, Oleksandr Kalyuzhniy, Patrick D. Skog, et al. “Priming a Broadly Neutralizing Antibody Response to HIV-1 Using a Germline-Targeting Immunogen.” Science 349, no. 6244 (July 10, 2015): 156–61. doi:10.1126/science.aac5894.
17. Jardine, Joseph G., Daniel W. Kulp, Colin Havenar-Daughton, Anita Sarkar, Bryan Briney, Devin Sok, Fabian Sesterhenn, et al. “HIV-1 Broadly Neutralizing Antibody Precursor B Cells Revealed by Germline-Targeting Immunogen.” Science 351, no. 6280 (March 25, 2016): 1458–63. doi:10.1126/science.aad9195.
18. Briney, Bryan, Devin Sok, Joseph G. Jardine, Daniel W. Kulp, Patrick Skog, Sergey Menis, Ronald Jacak, et al. “Tailored Immunogens Direct Affinity Maturation toward HIV Neutralizing Antibodies.” Cell 166, no. 6 (September 8, 2016): 1459-1470.e11. doi:10.1016/j.cell.2016.08.005.
19. Tian, Ming, Cheng Cheng, Xuejun Chen, Hongying Duan, Hwei-Ling Cheng, Mai Dao, Zizhang Sheng, et al. “Induction of HIV Neutralizing Antibody Lineages in Mice with Diverse Precursor Repertoires.” Cell 166, no. 6 (September 8, 2016): 1471-1484.e18. doi:10.1016/j.cell.2016.07.029.
20. Sok, Devin, Bryan Briney, Joseph G. Jardine, Daniel W. Kulp, Sergey Menis, Matthias Pauthner, Andrew Wood, et al. “Priming HIV-1 Broadly Neutralizing Antibody Precursors in Human Ig Loci Transgenic Mice.” Science353, no. 6307 (September 30, 2016): 1557–60. doi:10.1126/science.aah3945.
21. Steichen, Jon M., Daniel W. Kulp, Talar Tokatlian, Amelia Escolano, Pia Dosenovic, Robyn L. Stanfield, Laura E. McCoy, et al. “HIV Vaccine Design to Target Germline Precursors of Glycan-Dependent Broadly Neutralizing Antibodies.” Immunity 45, no. 3 (September 20, 2016): 483–96. doi:10.1016/j.immuni.2016.08.016.
22. Escolano, Amelia, Jon M. Steichen, Pia Dosenovic, Daniel W. Kulp, Jovana Golijanin, Devin Sok, Natalia T. Freund, et al. “Sequential Immunization Elicits Broadly Neutralizing Anti-HIV-1 Antibodies in Ig Knockin Mice.” Cell 166, no. 6 (September 8, 2016): 1445-1458.e12. doi:10.1016/j.cell.2016.07.030.

Index

• 1.5 John Coffin — The Origin of Molecular Retrovirology
• 2.4 Robert Gallo — Discoveries of Human Retrovirus, Their Linkage to Disease as Causative Agents & Preparation for the Future
• 4.3 Beatrice Hahn — Apes to Humans: The Origin of HIV
• 6.3 Bruce Walker — Role of T Cells in Controlling HIV Infection
• 6.4 Barton Haynes — Development of HIV Vaccine: Steps and Missteps
• 6.5 Emilio Emini — Issues in HIV Vaccine Development: Will the Future be any Easier than the Past?
• 8.1 John Mellors — MACS and Beyond: Epidemiology, Viremia and Pathogenesis
• 8.2 David Ho — Unraveling of HIV Dynamics In Vivo
• Alt, Frederick W.
• antibody, immunoglobulin (Ig)
• B cell
• b12 (IgG1b12)
• Barbas, Carlos F., III (1964–2014)
• Bill & Melinda Gates Foundation
• Binley, James M.
• blood — banks, donors, plasma, screening, transfusions, clotting factors (factor VIII), PBMCs
• bnAb (broadly neutralizing HIV-1 antibody)
• cDNA clones, cDNA library
• chemistry, chemists
• chimpanzee (Pan troglodytes)
• cohort study
• Cold Spring Harbor Laboratory (CSHL)
• Dimitrov, Dimiter S. "Mitco"
• gp120
• gp41
• HIV vaccine
• IAVI (International AIDS Vaccine Initiative)
• in vitro vs. in vivo
• influenza
• Khan, Wasif N.
• Kwong, Peter D.
• Lerner, Richard A. (b. 1938)
• Lyumkis, Dmitry
• macaque, rhesus macaque
• malaria, Plasmodium
• Mascola, John R.
• mice
• microscope — electron and optical
• models (model systems, model organisms, modeling)
• Moore, John P.
• natural selection, evolutionary selection, evolutionary fitness
• NIH Vaccine Research Center (VRC)
• NMR (nuclear magnetic resonance)
• Nussenzweig, Michel C.
• Oxford University
• polio, polio vaccine
• Pollock, Ludmilla "Mila"
• Ragon Institute
• Rappuoli, Rino (b. 1952)
• Sanders, Rogier W.
• Schief, William R.
• Scripps Research Institute (TSRI)
• Session 6: Immunology and Prevention
• simian immunodeficiency virus (SIV)
• simultaneous discovery (multiple discovery)
• structural biology
• Sweden
• University of Sheffield
• Ward, Andrew B.
• Wilson, Ian A.