Michael Malim: [00:00:00] Well, good morning. First of all, thank you very much to John [Coffin], Bob [Gallo], and Bruce [Walker] for convening this meeting and inviting me. It's quite a humbling experience really to speak after some of the people we've listened to so far. I'm very grateful for the opportunity. I will start with a few reminisces, and then I'll tell you about our work that led to the identification of APOBEC3 restriction mechanisms, [00:00:30] and then a little bit at the end about where that is taken our work since then. I'll start off. This is me in the mid-'80s.
Michael: This is actually the varsity golf team at Oxford University. When I wasn't—
Audience: Which one?
Michael: Which one?!
Michael: There you go, a little bit, yes. The hair was a bit darker then, but. [laughs] When I wasn't frittering away my time chasing the white golf ball around a golf course, I was getting really hooked on reading about HIV research. I didn't work on HIV. Actually, I wasn't even a virologist at the time. I just remember reading these papers from Flossie [Wong-Staal], and Joe [Sodroski] and Bill Haseltine, and Bob [Gallo], and so forth. It was absolutely gripping. On top of which, of course, it was this imminent global health threat, [00:01:30] the HIV/AIDS pandemic. It was absolutely, it was just a gripping time to witness, and I decided that when I finished my PhD, what I wanted to do was go to the US and start working on HIV, which I did.
I went to Duke University and work with Bryan Cullen (b. 1951) for a few years. Then I moved to the University of Pennsylvania, and started working on one of the proteins that Flossie talked about this morning, which ultimately became called the vif protein. The two similar papers that showed this protein was a regulator of viral infectivity, are here. [00:02:00] There's one from Flossie's lab, first author my friend Mandy Fisher, who now works in (Imperial College) London. (1) And the other paper from Malcolm Martin's lab led by Klaus Strebel. (2) What both groups showed very convincingly, was that this protein was a very important regulator of virus infection. That's pretty easy to demonstrate in primary T cells: a virus that lacks a functional vif gene is unable to grow. This is obviously a good or worthwhile project to get into. You've got a nice substantial phenotype to sink your teeth into. [00:02:30]
Now, one of the curiosities in this field was that while primary cells and certain cell lines showed an absolute dependence upon vif for HIV replication, there were another flavor of cells where it was completely dispensable. This was a conundrum for some time for the very, very important observation.
Another very important observation came from Joe [Sodroski]'s lab in '92, which trying to address this issue of why the virus would grow in some cells and not others. (3) They determined that the phenotype that imprinted viruses, [00:03:00] where the phenotype was determined by the cell in which the virus produced. In contrast, the TRIM5 that we heard about this morning, which is a target cell phenotype, the vif phenotype is determined in the cell that produces a virus.
Now there are two models for why you could have these two differential phenotypes or two simple models. One is that, non-permissive cells or the cells in which you require Vif to grow, those could potentially contain an inhibitor of viral infection, and this role would be to counteract that. (4) Alternatively, [00:03:30] the cells where the virus can grow without Vif, they could contain a cellular factor that perhaps mimics the activity of Vif. (5) To distinguish between these two phenotypes or two ideas, you can fuse the cells together and see which one dominates, and you recapitulate the non-permissive phenotype, which suggested that the role of Vif —or it was suggested to us that the role of Vif was to suppress an innate inhibitor of viral replication.
Another very important observation was that, [00:04:00] the species specificity of Vif. Looking here at an SIV from an African green monkey, the Vif protein works very well in cognate African green monkey cells, and it is non-functional in human T cells. Taking all that together, we thought that we knew that Vif worked in cells that produced virus. We thought that it suppressed the activity of some protein in those cells, and it did that in a species-specific manner, again, arguing about a virus-host interaction. I'm not going to say anything more about the species angle [00:04:30] because Michael Emerman is going to give a very elegant presentation later on that particular subject.
Now, we obviously ultimately interested in trying to identify what those factors might be, and we were encouraged that this might be a single gene or a single protein phenomenon from our work that we published a couple of years earlier from Jonathan Stoye’s lab working on—a slide made by John Coffin, I believe—
John Coffin: [inaudible 00:04:56]
Michael: —working on this phenotype. [00:05:00] They've been recognized by Frank Lilly, originally, and been worked on by many groups over the years, where different murine leukemia viruses (MLVs) are restricted in growth in different strains of mice. In a nutshell, an N strain of mouse that carries the N alleles of Fv1 is susceptible to N-tropic MLV strain, so the mouse dies of leukemia, if you have one or two copies of the B allele of Fv1, those mice are now resistant to the leukemia and they survive. It's a single gene [00:05:30] protein that can confer very potent resistance to viral infection. This encourages further that perhaps we might be looking at something somewhat similar in the case of HIV.
Now, there were two critical next steps in this work for me. First was to come up with a way of tackling this. We didn't know—Our hypothesis was that the non-permissive cells contain within them genes that were neutralized by Vif, and these were inhibitors of viral infectivity. [00:06:00] Now, there was no human genome sequencing those days, there were no lovely microarrays. So we decided to compare the mRNA expression—the mRNAs are expressed in permissive and non-permissive cells in an attempt to identify these genes by a functional assay. The second key thing, of course, is to identify somebody crazy enough to take this project on. This is when Ann Sheehy here, joined my lab as a postdoctoral fellow. She had boundless energy and enthusiasm for taking on this rather risky project. [00:06:30]
I have to say that many of my mentors and friends thought I was absolutely mad to take on a project like this. There's one person in the audience here today who always told me, he thought this was an excellent project, and I should spend a lot of time on it. That was Ron Desrosiers. I was always very grateful for the support he gave me in the early days of this work.
The strategy was then to use cDNA subtraction to identify cDNA selectively expressed in non-permissive cells, screening them by Northern blotting to see which ones gave the right [00:07:00] expression profile, and then test them in functional assays. Now, the 15th fragment we pulled out is this one here—you can see it had exactly the pattern we were looking for, it's expressed in these cells where vif is required and it's barely expressed in these cells where vif is not required.
Now, of course, this is an absolutely horrible Northern blot. In fact, for some reason, I had been left responsible for washing this filter. I think we almost missed a phenotype, and I was banned from the lab after this effort, and rightly so. [00:07:30] Now, the problem was, the fragments you get from this cDNA subtraction, they're usually 3' UTR. So we had no idea what open reading frame this rather promising fragment was connected to, and we did have other candidates. So we were just sort of biding our time.
About 15 months later, this sequence was deposited in the database, of a gene which—an open reading frame matched our 3'-UTR. (6) [00:08:00] We rapidly cloned this thing out, and then there's a very simple functional assays for looking at activity. Basically, code transfected into permissive cells with proviruses that do or do not lack a vif gene, harvest virus particles and put them on indicator cells, and measure whether you get infection.
That's precisely what we do and did with that gene she got. These are the first data she got, this is actually a scintillation counter printout. (7) You can see that when this clone that we were [00:08:30] calling CM15 at the time, was present in a vif deficient virus. The infectivity dropped way down here. This would be the control, and this was wild type virus, which was barely affected.
I think by this time, Anne had mastered the British skill for understatement. She thought the effect appears significantly more dramatic. Significantly more dramatic? It was below background! It was really obvious, it was a very strong phenotype. Of course, it repeated, and there's just a graphical representation of that. [00:09:00] When vif is absent in producer cells and you have what a gene, then became called APOBEC3G, have that present, you basically lose viral infectivity. That's exactly what we were looking for.
Now, by this time, a lot more sequence with vif was coming available about human genes, and it turns out that APOBEC3G fell in a family of 11 human genes, which are indicated here. (8) Now, two of them have been worked on a fair amount. Prior to that APOBEC1, which is an acronym for apolipoprotein B editing complex polypeptide 1 [00:09:30] which is why this gene family has such a long complicated name, because it was a founder member. That edits apolipoprotein B, mRNA one specific point. A second family member AID, drives antibody by diversification. Now both of these enzymes are cytidine deaminases. These enzymes that remove this amino group from the cytidine ring in polynucleotides, RNA or DNA, converting it to uridine, and therefore changing the coding sequence. [00:10:00]
So the obvious question was, was APOBEC3G affecting the sequence of HIV? Now, at this time, we teamed up with a group in Cambridge led by Michael Neuberger (1953–2013), who had worked on AID for quite a long time. He was one of the experts on it. When I say we, here is Kate Bishop, who is now a postdoc in my lab in London. This is actually a picture taken at Cold Spring Harbor this summer when she was running the Retrovirus Meeting here. Here is Michael, who sadly is no longer with us, [00:10:30] and two of his postdocs Reuben [Harris] and Svend [Petersen-Mahrt].
Michael was not only an incredibly sharp mind and a fantastic collaborator. He was also a historian, and he was also very mischievous. Every time we talked to him or I would talk to him on the phone, he would say, "Oh, we're going to come down from Cambridge, and we're going to work with you, scientists at King's on DNA." [laughter] Sort of reiterating something from about 40, 50 years ago. Anyway, Michael would always do that to us, but he [00:11:00] was a wonderful man to work with.
The experiment was very simple. Basically, do the experiment I showed you earlier but you just transfect an APOBEC3G when you're making your virus particles and recover cDNAs out of target cells, and just sequence them. You can see here that when the virus lacks vif and you put up APOBEC3G in the producer cells, you get a massive number of guanosine to adenosine transition mutations on the positive strand of viral DNA. (9) Now, this, of course is driven by cytidine to uridine [00:11:30] changes on the minus strands. To put together our work and that of many, many groups in the fields, this is our current understanding of how this restriction mechanism works.
Oops, I don't think I'm the first person to do that.
It turns out that four of the APOBEC3 proteins are antiviral, G, F, D, and H. These get trapped in virus particles as they assemble through RNA protein interactions that then get [00:12:00] carried forward into the next cell, and then one of two things happen. If reverse transcription occurs and then you have single-stranded DNA hindering that process, that then becomes a target for the APOBEC3 proteins. They deaminate cytidines to create uridines, and if those DNAs are maintained in cells, and you get second strand synthesis, they then become guanosine to adenosine mutations. This can be up to 10% of the guanosines in the viral sequence, and as you can imagine that is an enormous mutational load. We call it hypermutation, [00:12:30] and that just call sufficient genetic damage to inhibit the virus in terms of infectivity.
The second thing that can happen is, in fact, reverse transcription itself is inhibited and I'll come onto that point a little bit later. This was only discovered because we were studying Vif deficient viruses. What does Vif do? Vif though simply is the viral protein that contracts APOBEC3G. It does this by engaging a ubiquitin ligase complex, as well as the APOBEC3 proteins resulting in polyubiquitination [00:13:00] of the APOBEC proteins and they're targeting to the proteasome for degradation, and therefore their removal and they can't get packaged into particles. The key observation here was from Xianghui Yu at Johns Hopkins in, I think it was 2003 where he pulled out this complex using a biochemical approach, a very important contribution to the field. (10, 11)
The identification for the APOBEC3 proteins also gave us a satisfying explanation for some strange observations that have been made over the years. [00:13:30] The first one from Vinay Pathak and Howard Temin (1934–1994), they had noticed G-to-A hypermutations, occasionally when studying avian retroviruses in tissue culture. (12) And Simon Wain-Hobson had noticed something similar with HIV. The explanation for this hypermutation you would see was the APOBEC3 proteins. (13)
Now, mutagenesis isn't entirely random and, in fact, you can work out. The preferred target sites for these different enzymes, and a lot of people have contributed to this. (14) [00:14:00] Very simply, APOBEC3G prefers guanosine-guanosine, and APOBEC3F, for example, prefers guanosine-adenosine. With that information in your head, then you can then go back and start analyzing HIV sequences during a natural infection and work out which mutations were probably driven by APOBEC proteins. You can strip those out from sequence diversification and workout that, to a degree, APOBEC3 proteins probably contribute, to a certain extent to the sequence diversification as injury, [00:14:30] natural HIV infection which, of course, one of the hallmarks of HIV infection, the massive sequence diversity that occurs. It seems to contribute in some minor way, to on top of the copying errors we talked about earlier in the conference.
Another consequence, all the cancer genome sequencing that's going on these days around the world of the eight different types of mutations that one can get. The conclusion is that one of these types up here is actually driven by [00:15:00] APOBEC3 driven editing. (15) Among this family of proteins, not only do you have proteins that control transposons and infectious elements like retroviruses. The cost of the hosts is that these enzymes also have the potential to mutate the host genome, and that's used to be a real event. APOBEC3B and 3H are probably the enzymes responsible for that.
What do we work on now? We're still very interested in the effect on reverse transcription. (16, 17) [00:15:30] We first thought about this when looking at a load of wild type and engineered editing deficient APOBEC enzymes. The best correlation with the inhibition of infectivity over here, is the lack of cDNA accumulation in target cells.
You all could imagine this happening by several different mechanisms. One could be APOBEC3 proteins could sit on viral RNA and just act as a barrier to the progression of reverse transcriptase, or perhaps you could just modify the activity reverse transcriptase directly. [00:16:00] We're very interested in trying to address these questions. We have recently developed a linker ligation, deep sequencing strategy to map the three prime ends of retroviral cDNAs that are made during infection. (18) The scheme is shown here. And you can do this to maps, but single nucleotide resolution, the 3’ ends of cDNA during infection. If you do this looking at the strong stop DNA, no APOBEC around in this experiment, [00:16:30] you see a particular peak here, which actually is strong stop DNA and you see a certain profile like this. (19) If you start putting APOBEC3 into those particles, APOBEC3G, you see, in fact, these peaks appearing when APOBEC3G is present. We assume these are probably going to be the pore sites because the APOBEC is sitting on the viral RNA and preventing our team moving along. It turns out that's not the case because, of course, we have the sequence. We knew, in fact, that these are [00:17:00] in fact all editing sites for APOBEC3G itself. In fact, the explanation for seeing these peaks is the recognition of edited cDNAs by host cell DNA repair enzymes, the creation of basic sites which then get cleaved by a nuclease, and that is why you see these stops.
In fact, you can manipulate cells so that doesn't happen and you basically see the same profile, whether you have APOBEC3 proteins there or not, which makes us think then that the enzymes are [00:17:30] just gradually, or just diminishing the enzymatic functionality of reverse transcriptase itself, as opposed to inducing specific pore sites.
How might it do this? We know by a variety of interaction essays—this just happens to be coding and precipitation—that APOBEC3G actually will interact with reverse transcriptase. (20) We have a number of assays that support this conclusion. Using mutations like this, which stop that interaction are going to be key for us to try and decipher this in the future. [00:18:00]
What I've told you then about is APOBEC3 proteins here being packaged into nascent virus particles, passed into target cells and both inhibiting reverse transcription and inducing hypermutation. Subsequent to this, there have been a number of proteins identified by people in this room that are potent inhibitors of HIV infection, and often as an antagonist. (21) We have Vif as the antagonist for APOBEC3, we heard about TRIM5 alpha, which actually doesn't have a viral antagonist, [00:18:30] It uses changes in capsid to avoid this protein.
Paul Bieniasz and John Guatelli identified tetherin as an inhibitor of RNA replication that's antagonized by vpu. There's some SAMHD1, which is antagonized by the HIV-2 protein vpx, and most recently the SERINC proteins by nef. In fact, you'll notice that a lot of these inhibitory activities converge on the early parts of the lifecycle, which probably makes sense because, if you're going to prevent infection, you really want to stop this thing happening, which is the integration of proviral DNA. Something we've heard about on the [00:19:00] first night of the conference because once you've got this, you've got a persistent lifelong infection of that cell.
Now, there are a number of trends that pull these different restrictions, what became known as the restriction factors together. A couple of them, I'll just to comment on the ones in bold. In viruses, in their what and their natural hosts, in fact, the restriction factors tend not to be very active or very relevant and that's because of the action of these antagonist proteins such as Vif, Vpu, Nef, et cetera.
The other thing [00:19:30] we realized after was, in fact, they all seem to or most of them seem to be induced by interferon and then this drew us into thinking more about interferon, which in the retrovirus field until relatively recently, it was a fairly neglected area, although quite a few people in this room have mentioned early on in their careers that they worked on interferon and retroviruses, and then moved on to something more interesting. Here is one very important observation published by David Asmuth, a few years ago. (22) These are in HIV infected patients. [00:20:00] They were not on therapy, but they had a stable viral load. The 12-week course of therapeutic interferon gave about a one-and-a-half log drop in viral load in these patients. Type one interferon really can diminish HIV replication in vivo.
In a very nice study here published by Danny Douek’s group a couple of years ago using an SIV rhesus macaque model. (23) If you add an antagonist of type one interferon at the time of viral exposure, those monkeys succumb to disease [00:20:30] much more quickly. Both sets of observations argues that type one interferon probably pretty important for controlling HIV infection. In fact, in culture, David Ho was showing this first I think for HIV in 1985.
It is indeed true, a bit like the Vif story, you can find cells in culture where interferon shows a very strong anti-HIV effect, and you can find sales where it has no effect. Here are three such examples. (24) [00:21:00] We thought we would revisit what we had done before and try and identify the proteins induced by interferon that are responsible for controlling HIV infection in these instances. Now, as I've already explained, we didn't think these are going to be restriction factors, these were going to be novel antiviral genes. Now, of course, we have the genome sequence, you can buy microarrays, it's very easy to do comparative transcriptomics across a whole load of cells, which is what we did.
When we did this, and so did a couple of other groups—Paul Bieniasz [00:21:30] and Chen Liang, both did much the same type of experiment. And this protein here called MX2, or “mixer virus resistance 2” was identified by all three of us about three years ago as a pretty potent inhibitor of HIV infection. (25, 26, 27) You're going to express ectopically in non-expressing cells and they become pretty resistant to infection. Or you can take into cells in the presence of interferon, take out MX2 by adding siRNA, or you can do it by CRISPR these days, and you get a pretty good restoration of infectivity. [00:22:00] This protein is used to block the nuclear import of the viral DNA once it has been made.
As of yet, we don't know of any natural evasion mechanism for this. We think it's proteins like MX2 that are going to be responsible for the effects that we see, for example, on interferon administration in the patients I showed a couple of slides ago. Now it turns out MX2, of course, has a relative in the human genome that is very famous in the virology field. A protein called MX1 was cloned in 1986 [00:22:30] by Otto Haller, Peter Staehli and Charles Weissmann. This is a very potent inhibitor of a number of viruses, most famously influenza virus, which is how it was discovered. (28) I should say the MX1 was the first viral restriction factor ever identified.
Both proteins MX1 and MX2 are closely related to a human protein that’s got nothing to do with viruses or viral inhibition, I should say. dynamin is a protein that assembles around the neck of [00:23:00] invaginating endosomes and constricts them, so they pinch off the potent of the interior of the cell. Models have been derived for how MX1 might inhibit flu. That is that the replication nuclear protein complex gets sort of encircled by these rings of MX1 protein, and that disassembles that replication complex.
The MX1 theory was a pretty good guiding light for us for our work on MX2. Turns out, [00:23:30] even though these proteins are rather similar to each other—in fact, they share 63% sequence identity—they're rather different in their functionality. Here's an alignment of the two proteins in cartoon form. Here's the structure of MX1. Species specificity or viral specificity for MX1 is determined by this region here, loop four, which sits right at the terms of the stem, structural stock part of the protein. For MX2, and HIV, it's this amino-terminal piece here which actually doesn't appear in the structure. It's up at this end. [00:24:00] GTPase function is required for inhibition by MX1, it's not required for MX2. It's a completely different apparent mechanism of action, yet very two very closely related proteins. And we continue to be very interested in precisely how MX2 does inhibit HIV-1 infection.
Now, if we go back to our life cycle slide, MX2 was an early on found as a non-antagonized inhibitor of HIV infection. [00:24:30] More are being identified now. If 10 proteins GTP binding protein five and Schlafen 11, there are papers to support the antiviral role of all of these proteins, presenting a rather complicated constellation then of host proteins. Some of which are antagonized now, some of which are not antagonized, obviously antagonized, all of which can serve to inhibit the replication of HIV-1.
I should say, they're almost estimated for almost 1,000 interferon-stimulated [00:25:00] genes in the human genome. There's a lot of scope for other viral inhibitors out there. This has now become or has become a very active area of research in my lab and in many other labs around the world. We continue to learn very exciting things about human biology along this journey. At that point, I just want to thank all the people that I have worked in my lab or I have collaborators over the years, and the various funders that have supported our work, and thank you for your attention.
Paul Bieniasz (Moderator): Okay. We have time for a couple.
Anna Marie Skalka: What happens if you knockout MX2 in non-dividing cells?
Michael: Actually, we've never done that experiment. Paul has done that one.
Anna: Do you want to answer it?
Paul: MX2 becomes significantly more potent in non-dividing cells.
Mike: Why was that?
Paul: Well, if the model that Mike presented [00:26:00] is correct, that it intercepts during transit through the nuclear pore in a non-dividing cell, that's really the only way that HIV can access chromatin in a dividing cell, less the possibility of infecting during mitosis. Trim5 also has that effect too.
Audience 2: I have a question? I wanted to find out, is there any evidence that MX2 is packaged into virions? If not, how does the cell [00:26:30] realize that the PIC is available, that it needs to be activated?
Michael: MX2 is not packaged into virus particles. It is sitting in the target cell and a little bit like Trim5 that Joe Sodroski talked about this morning, it recognizes viral capsids as they're traveling in that target cell towards the nucleus. What it does for those capsids is not clear, whether it just binds and stops them moving or whether it triggers a disassembly in the [00:27:00] way that Trim5 seems to do for the capsid. We don't know yet. It's a rather tricky protein to work with biochemically. It's an active area of research.
John Coffin: Yes, a comment that's on the importance of APOBEC3 proteins, which I think came home during the most recent human rumor virus scare. The XMRV story, when it was discovered that—it actually has been reported over and over again, [00:27:30] that passage of some tumor cells through mice will sometimes pick up an endogenous virus from the mouse, and re-raising the questions, why don't we get infected with these viruses, because obviously, long surveys have really failed to show it? So when XMRV was put either into cell culture with tumor cells, it often replicated very well. When it's put into culture with fresh isolated PBMCs or put into animals, [00:28:00] it very quickly died out and very quickly died with a substantial hypermutation, strongly suggesting that, in fact, this was probably a or maybe the major factor that has protected us from being infected with all the gammaretroviruses and all these different species were exposed to.
The importance of that really do not—to our lives, I think—cannot be underestimated. That's brought home by the fact that there's a gammaretrovirus that has recently [00:28:30] been introduced into marsupials, in Koalas in Australia and is devastating them, and they don't have APOBEC3.
Michael Malim: Of course, some of your own work, the endogenized sequences often have the hallmarks of APOBEC3 protein editing.
Michael Emerman: Mike, actually, I won't ask you another historical question. The reviewer of your Nature paper that first describe 715, looked up the sequence and realize it was cytidine deaminase. [00:29:00] I can't remember if he pointed it out in his review, at what point did you become aware that it was the cytidine deaminase?
Michael: We knew straight away from the homology. In our paper, we had a sequence alignment with APOBEC1, in fact.
Emerman: I don't think you said it was it.
Michael: You needed to do a functional essay and we didn't have it at the time.
Emerman: [00:29:30] That's what the reviewer asked you to do?
Michael: Yes. In fact, the reviewer, I have to say—maybe one of the reviewers certainly said, "This tells us nothing new." [laughter] Actually, that's just probably not one of my favorite comments I ever had on the paper was when we were trying to—
Emerman: That's not the review I was talking about.
Michael: —was when we were trying to show that you can in fact—In fact, this was many as earlier when I was in Bryan Cullens’ lab, we were trying to show that HIV could truly infect non-dividing cells. [00:30:00] One of our reviewers wisely said, "We were entering an area of retroviral quicksand." Which [laughs] I think also turned out to be true. [chuckles]
Paul: Warner, and then we'll move on.
Warner Greene: This is more of a comment kind of anecdotal, two stories, one I remember when Bryan Cullen came into my office and said, "Warner, I really want to recruit this young postdoc by the name Michael Malim. Flossie Wong-Staal is after him as well. [00:30:30] [laughter] I agreed to call Michael and we started talking and it came out that he was a member of the golf team, and I tell you, this was it. This was it. [laughter] So Mike and I have actually played a number of tournaments together, and I think Flossie, I don't know what history would have been. [laughs] had he gone on to San Diego.
Michael: Well, actually, Warner you are lucky because we have to move our offices soon and I found in the bottom of one of my drawers the picture from the member guests—
Michael: —that we won [00:31:00] together in 1988 or '89, I think, but I don't think it does either of us any favors. [chuckles]
Warner: The other anecdote is a story about APOBEC1. There was this young postdoctoral fellow who came to Gladstone [Institute of Virology & Immunology/UCSF], he was an orthopedic surgeon, failed orthopedic surgeon. He came and he started working on APOBEC1 which they were involved in cardiovascular research. He figured out that it was [00:31:30] an editing enzyme, and they overexpressed it and suddenly these animals started developing—these transgenic mice started developing hepatic cancers.
He became very interested in cell differentiation, he moved back to Kyoto, Japan. Identified five transcription factors that could convert a somatic cell into an induced pluripotent stem cell and won the Nobel Prize, Shinya Yamanaka (山中 伸弥, b. 1962). Shinya, even had his roots in APOBEC biology. [00:32:00]
Paul: Okay, thanks very much, let's move on.
[00:32:05] [END OF AUDIO]
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- Sheehy, Ann M., Nathan C. Gaddis, Jonathan D. Choi, and Michael H. Malim. “Isolation of a Human Gene That Inhibits HIV-1 Infection and Is Suppressed by the Viral Vif Protein.” Nature 418, no. 6898 (August 8, 2002): 646–50. doi:10.1038/nature00939.
- Chen, Kuan-Ming, Elena Harjes, Phillip J. Gross, Amr Fahmy, Yongjian Lu, Keisuke Shindo, Reuben S. Harris, and Hiroshi Matsuo. “Structure of the DNA Deaminase Domain of the HIV-1 Restriction Factor APOBEC3G.” Nature 452, no. 7183 (March 6, 2008): 116–19. doi:10.1038/nature06638.
- Bishop, Kate N., Rebecca K. Holmes, Ann M. Sheehy, Nicholas O. Davidson, Soo-Jin Cho, and Michael H. Malim. “Cytidine Deamination of Retroviral DNA by Diverse APOBEC Proteins.” Current Biology 14, no. 15 (August 10, 2004): 1392–96. doi:10.1016/j.cub.2004.06.057.
- Yu, Xianghui, Yunkai Yu, Bindong Liu, Kun Luo, Wei Kong, Panyong Mao, and Xiao-Fang Yu. “Induction of APOBEC3G Ubiquitination and Degradation by an HIV-1 Vif-Cul5-SCF Complex.” Science 302, no. 5647 (November 7, 2003): 1056–60. doi:10.1126/science.1089591.
- Guo, Yingying, Liyong Dong, Xiaolin Qiu, Yishu Wang, Bailing Zhang, Hongnan Liu, You Yu, Yi Zang, Maojun Yang, and Zhiwei Huang. “Structural Basis for Hijacking CBF-β and CUL5 E3 Ligase Complex by HIV-1 Vif.” Nature 505, no. 7482 (January 2014): 229–33. doi:10.1038/nature12884.
- Pathak, Vinay K., and Howard M. Temin. “Broad Spectrum of in Vivo Forward Mutations, Hypermutations, and Mutational Hotspots in a Retroviral Shuttle Vector after a Single Replication Cycle: Substitutions, Frameshifts, and Hypermutations.” Proceedings of the National Academy of Sciences 87, no. 16 (August 1, 1990): 6019–23. doi:10.1073/pnas.87.16.6019.
- Vartanian, Jean-Pierre, Andreas Meyerhans, Monica Sala, and Simon Wain-Hobson. “G—>A Hypermutation of the Human Immunodeficiency Virus Type 1 Genome: Evidence for DCTP Pool Imbalance during Reverse Transcription.” Proceedings of the National Academy of Sciences 91, no. 8 (April 12, 1994): 3092–96. doi:10.1073/pnas.91.8.3092.
- Kim, Eun-Young, Ramon Lorenzo-Redondo, Susan J. Little, Yoon-Seok Chung, Prabhjeet K. Phalora, Irina Maljkovic Berry, John Archer, et al. “Human APOBEC3 Induced Mutation of Human Immunodeficiency Virus Type-1 Contributes to Adaptation and Evolution in Natural Infection.” PLOS Pathogens 10, no. 7 (July 31, 2014): e1004281. doi:10.1371/journal.ppat.1004281.
- Helleday, Thomas, Saeed Eshtad, and Serena Nik-Zainal. “Mechanisms Underlying Mutational Signatures in Human Cancers.” Nature Reviews Genetics 15, no. 9 (September 2014): 585–98. doi:10.1038/nrg3729.
- Bishop, Kate N., Mohit Verma, Eun-Young Kim, Steven M. Wolinsky, and Michael H. Malim. “APOBEC3G Inhibits Elongation of HIV-1 Reverse Transcripts.” PLOS Pathogens 4, no. 12 (December 5, 2008): e1000231. doi:10.1371/journal.ppat.1000231.
- Holmes, Rebecca K., Fransje A. Koning, Kate N. Bishop, and Michael H. Malim. “APOBEC3F Can Inhibit the Accumulation of HIV-1 Reverse Transcription Products in the Absence of Hypermutation Comparisons with APOBEC3G.” Journal of Biological Chemistry 282, no. 4 (January 26, 2007): 2587–95. doi:10.1074/jbc.M607298200.
- Kwok, Chun Kit, Yiliang Ding, Yin Tang, Sarah M. Assmann, and Philip C. Bevilacqua. “Determination of in Vivo RNA Structure in Low-Abundance Transcripts.” Nature Communications 4, no. 1 (December 16, 2013): 2971. doi:10.1038/ncomms3971.
- Pollpeter, Darja, Maddy Parsons, Andrew E. Sobala, Sashika Coxhead, Rupert D. Lang, Annie M. Bruns, Stelios Papaioannou, et al. “Deep Sequencing of HIV-1 Reverse Transcripts Reveals the Multifaceted Antiviral Functions of APOBEC3G.” Nature Microbiology 3, no. 2 (February 2018): 220–33. doi:10.1038/s41564-017-0063-9.
- Wang, Yufei, Trevor Whittall, Durdana Rahman, Evelien M. Bunnik, Robert Vaughan, Jørgen Schøller, Lesley A. Bergmeier, et al. “The Role of Innate APOBEC3G and Adaptive AID Immune Responses in HLA-HIV/SIV Immunized SHIV Infected Macaques.” PLOS ONE 7, no. 4 (April 13, 2012): e34433. doi:10.1371/journal.pone.0034433.
- Doyle, Tomas, Caroline Goujon, and Michael H. Malim. “HIV-1 and Interferons: Who’s Interfering with Whom?” Nature Reviews Microbiology 13, no. 7 (July 2015): 403–13. doi:10.1038/nrmicro3449.
- Asmuth, David M., Robert L. Murphy, Susan L. Rosenkranz, Juan J. L. Lertora, Shyam Kottilil, Yoninah Cramer, Ellen S. Chan, et al. “Safety, Tolerability, and Mechanisms of Antiretroviral Activity of Pegylated Interferon Alfa-2a in HIV-1- Monoinfected Participants: A Phase II Clinical Trial.” The Journal of Infectious Diseases 201, no. 11 (June 1, 2010): 1686–96. doi:10.1086/652420.
- Sandler, Netanya G., Steven E. Bosinger, Jacob D. Estes, Richard T. R. Zhu, Gregory K. Tharp, Eli Boritz, Doron Levin, et al. “Type I Interferon Responses in Rhesus Macaques Prevent SIV Infection and Slow Disease Progression.” Nature 511, no. 7511 (July 2014): 601–5. doi:10.1038/nature13554.
- Goujon, Caroline, and Michael H. Malim. “Characterization of the Alpha Interferon-Induced Postentry Block to HIV-1 Infection in Primary Human Macrophages and T Cells.” Journal of Virology 84, no. 18 (September 15, 2010): 9254–66. doi:10.1128/JVI.00854-10.
- Goujon, Caroline, Olivier Moncorgé, Hélène Bauby, Tomas Doyle, Christopher C. Ward, Torsten Schaller, Stéphane Hué, Wendy S. Barclay, Reiner Schulz, and Michael H. Malim. “Human MX2 Is an Interferon-Induced Post-Entry Inhibitor of HIV-1 Infection.” Nature502, no. 7472 (October 2013): 559–62. doi:10.1038/nature12542.
- Kane, Melissa, Shalini S. Yadav, Julia Bitzegeio, Sebla B. Kutluay, Trinity Zang, Sam J. Wilson, John W. Schoggins, et al. “MX2 Is an Interferon-Induced Inhibitor of HIV-1 Infection.” Nature 502, no. 7472 (October 2013): 563–66. doi:10.1038/nature12653.
- Liu, Zhenlong, Qinghua Pan, Shilei Ding, Jin Qian, Fengwen Xu, Jinming Zhou, Shan Cen, Fei Guo, and Chen Liang. “The Interferon-Inducible MxB Protein Inhibits HIV-1 Infection.” Cell Host & Microbe 14, no. 4 (October 16, 2013): 398–410. doi:10.1016/j.chom.2013.08.015.
- Staeheli, Peter, Otto Haller, W. Boll, J. Lindenmann, and Charles Weissmann. “Mx Protein: Constitutive Expression in 3T3 Cells Transformed with Cloned Mx CDNA Confers Selective Resistance to Influenza Virus.” Cell 44, no. 1 (January 17, 1986): 147–58. doi:10.1016/0092-8674(86)90493-9.
- 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
- 4.1 Ronald Desrosiers — The Origin of SIVmac: Non-human Primate Models for HIV
- 5.0 Anna Marie Skalka — Introduction, Session 5
- 5.1 Flossie Wong-Staal — Discovery of Human Retroviral Transactivators
- 5.2 Joseph Sodroski — Primate Host-Specific Selection of Immunodeficiency Virus Gag and Env Proteins
- 5.6 Michael Emerman — Host-virus Co-evolution
- 6.3 Bruce Walker — Role of T Cells in Controlling HIV Infection
- 8.2 David Ho — Unraveling of HIV Dynamics In Vivo
- African green monkeys, vervet monkeys (Chlorocebus)
- Annual meeting on retroviruses, CSHL
- antibody, immunoglobulin (Ig)
- Asmuth, David
- Bishop, Kate
- blood — banks, donors, plasma, screening, transfusions, clotting factors (factor VIII), PBMCs
- capsid, capsid protein (p24)
- cDNA clones, cDNA library
- cell fusion
- Cold Spring Harbor Laboratory (CSHL)
- control — experimental control, control group, blinded experiment
- Cullen, Bryan R. (b. 1951)
- Douek, Daniel C.
- Duke University, Duke University School of Medicine
- education and early career
- Fisher, Amanda G.
- Fv1 restriction factor
- Guatelli, John
- Harris, Reuben S.
- Haseltine, William A. (b. 1944)
- History and sociology of science, medicine, and health care
- Human Genome Project (HGP, 1990–2003)
- iconoclasm in science
- Imperial College London
- in vitro vs. in vivo
- Johns Hopkins University, Johns Hopkins University School of Medicine
- leukemia and lymphoma
- Liang, Chen
- macaque, rhesus macaque
- Martin, Malcolm A.
- models (model systems, model organisms, modeling)
- molecular cloning
- murine leukemia virus (MLV)
- Nature (journal)
- Neuberger, Michael (1953–2013)
- Northern blot
- Oxford University
- Pathak, Vinay K.
- peer review
- Petersen-Mahrt, Svend
- reading frame, open reading frame
- restriction factor
- reverse transcriptase
- scientific competition and collaboration
- scintillation counter
- sensitivity and specificity; false positive, false negative; biological specificity
- SERINC protein family
- Session 5: Molecular Biology of the Extraordinary Virus
- Session 9: Public Event
- Sheehy, Ann M.
- simian immunodeficiency virus (SIV)
- simultaneous discovery (multiple discovery)
- Staeheli, Peter
- Stoye, Jonathan P. (b. 1952)
- Strebel, Klaus
- structural biology
- Temin, Howard M. (1934–1994)
- three prime untranslated region (3'-UTR)
- transfection, transduction, viral vector
- TRIM5α (TRIM5alpha)
- UC San Diego
- UCSF (University of California San Francisco)
- University of Cambridge
- University of Pennsylvania (Penn) and Perelman School of Medicine
- Wain-Hobson, Simon
- Weissmann, Charles (b. 1931)
- XMRV xenotropic murine leukemia virus–related virus
- Yamanaka, Shinya (山中 伸弥, b. 1962)
- Yu, Xianghui
Found 3 search result(s) for Malim.
... how vif can disable a host defense mechanism. I think Mike Malim is going to present that. Now, interestingly, the essential genes tat and rev actually were ...
Apr 27, 2021
... been born out by the first one of these interactions to be discovered, which what Mike Malim talked about, which was vif, and then APOBEC. I gave a talk about the idea ...
Apr 27, 2021
... that's expressed on the human cell and not on the mouse cell, or alternatively, as similar to what Michael Malim was just saying, it could be some restriction factor in the mouse cell. That's where ...
Apr 27, 2021
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