Mystery Rays from Outer Space

Meddling with things mankind is not meant to understand. Also, pictures of my kids

May 28th, 2008

A little learning

Kopp et al 1995, proteasomeOne of the problems with genomics research is that the people who interpret it may not know much about the genes they identify. For example:

… single nucleotide polymorphisms (SNPs) in two genes critical for T-cell function are associated with susceptibility to MDD:1 PSMB4 (proteasome 4 subunit), important for antigen processing …2

Kopp et al 1995, HN3/PSMB4
PSMB4 location in proteasome3

OK, first of all, the proteasome is important in antigen processing, but antigen processing is probably about the least important of its myriad tasks. Suggesting that the function of the proteasome is antigen processing is like claiming the the function of my car is to hold coffee, because it happens to have cup-holders.4

Second, PSMB4 per se has never been implicated in antigen processing.5 Not only is it not one of the interferon-inducible trio of proteasome subunits that have been implicated in antigen processing, PSMB4 is not even catalytic.6

This looks like someone had a vague memory of seeing something in a textbook years ago, and didn’t try to look at the literature at all. Or who wanted to squeeze data into a preconceived theory.


  1. MDD: Major depressive disorder[]
  2. Wong ML, Dong C, Maestre-Mesa J, Licinio J.  Polymorphisms in inflammation-related genes are associated with susceptibility to major depression and antidepressant response. Mol Psychiatry. 2008 May 27. [Epub ahead of print] doi:10.1038/mp.2008.59 []
  3. Kopp F, Kristensen P, Hendil KB, Johnsen A, Sobek A, Dahlmann B. The human proteasome subunit HsN3 is located in the inner rings of the complex dimer. J Mol Biol. 1995 Apr 28;248:264-72 doi:10.1016/S0022-2836(95)80049-2 []
  4. Also, in my case, about 2000 little plastic dinosaurs, tucked into every cranny and hidden under the booster seats in the back.  I’m not sure what their function is either[]
  5. As far as I know; which is reasonably far[]
  6. Though it may be involved in proteolysis anyway.  But the point remains — not shown to have a role in antigen processing[]
May 28th, 2008

Alum, take 2: A better answer

Yu et al, Fig 6
Inflammasomes (From Yu et al, 2005)1

We’ve known for quite a while now how adjuvants work. Adjuvants (the components of vaccines that cause an immune response to start up, but that are not themselves the target of the immune response) trigger the parts of the innate immune system that normally identify microbial patterns, so that the immune system becomes aware that there’s a dangerous situation on its hands. (I have a much longer explanation here.)

It was a little annoying, though, that the most important adjuvant — alum, the adjuvant most commonly used for human vaccines — didn’t fit into this explanation. We didn’t know what innate triggers alum tickled to drive immune responses.

A month or two ago, I talked about a paper2 that claimed to answer that long-standing question. Their answer is that alum works through damaging tissue; damaged tissue releases a danger signal, uric acid, and according to Kool and the Gang2 that’s how alum drives immune responses. It’s an interesting suggestion, but I didn’t buy it:

I’m not entirely convinced that this is the whole, or even the main, story. … simple experience says that while vaccines sting, you don’t expect any kind of large-scale necrosis in your injected arm afterward – no more than you’d get from a modest bruise, which isn’t enough to trigger the kind of adjuvant effects we see with alum.

A paper that’s just become available in advance online status3 backs up my skepticism.

This is from Richard Flavell’s group at Yale. They determined that alum activity, at physiological doses, requires an intracellular receptor, Nalp3, that’s a member of the NLR family. NLRs (“Nod-like receptors”) are conceptual parallels to TLRs (“Toll-like receptors”); TLRs and NLRs are receptors for danger signals, and Nalp3 in particular is a receptor for uric acid, among other things. 4

Strictly speaking, uric acid itself does not act as a danger signal. Uric acid is a normal component of extracellular tissues, and if it was inflammatory we’d be in perpetual agony. When dying cells release their own stores of uric acid, though, the surrounding fluid becomes overloaded, and uric acid precipitates out as monosodium urate (MSU) crystals. It’s these MSU crystals that are actually inflammatory. Flavell’s insight was that MSU crystals might be conceptually siimilar to alum — another insoluble, particulate adjuvant — and so the two might act through the same pathway.

Sure enough, knockout mice without Nalp3 (or without other components of the Nalp3 reconition particle) failed to respond to alum (or to uric acid), whereas knockouts for a different NLR member did just fine. The knockouts responded normally when a different adjuvant was used.

Thus, by eliminating signalling through the Nalp3 inflammasome, we have eliminated one critical pathway used by alum to initiate humoral and cellular immunity. In doing so, aluminium hydroxide adjuvants ‘hijack’ an innate immune pathway that is exquisitely sensitive to cellular damage, perhaps as a result of the similarity to MSU in its physical structure.

Eisenbarth et al 2008 Fig 4The effect is pretty striking, actually (for example, the figure to the right).

The previous paper I talked about (Kool et al)2 also pinned alum into the uric acid pathway, but reached the conclusion that alum works through uric acid, rather than parallel to it, by causing tissue damage. Flavell’s group agree that this can happen, but disagree that it’s the normal mode of action:

In vitro, alum induced cell death at very high doses … in WT macrophages and in macrophages deficient in Nalp3 and Caspase-1 (Fig. 3b); however, the induction of IL-1beta by alum did not depend on the presence of MSU because the addition of uricase, which degrades MSU crystals and prevents the induction of IL-1beta (ref. 10), had no effect on IL-1beta production in response to LPS and alum (Fig. 3c).

I’m altogether happier with this explanation.

One interesting question that leaps to my mind — now we know the genes involved in alum recognition — is whether natural variants in these genes exist (I’m sure they do) and whether such variants correlate with vaccine responses in humans. Could we predict whether someone only needs a single dose of vaccine to be protected compared to her cousin who needs three doses? Are there people who lack components of this altogether — like the various TLR3 mutants I talked about earlier — and what happens to their vaccine response?


  1. Yu JW, Wu J, Zhang Z, Datta P, Ibrahimi I, Taniguchi S, Sagara J, Fernandes-Alnemri T, Alnemri ES (2006) Cryopyrin and pyrin activate caspase-1, but not NF-kappaB, via ASC oligomerization. Cell Death Differ 13:236–249. doi:10.1038/sj.cdd.4401734[]
  2. Kool, M., Soullie, T., van Nimwegen, M., Willart, M.A., Muskens, F., Jung, S., Hoogsteden, H.C., Hammad, H., Lambrecht, B.N. (2008). Alum adjuvant boosts adaptive immunity by inducing uric acid and activating inflammatory dendritic cells. Journal of Experimental Medicine DOI: 10.1084/jem.20071087[][][]
  3. Eisenbarth, S.C., Colegio, O.R., O’Connor, W., Sutterwala, F.S., Flavell, R.A. (2008). Crucial role for the Nalp3 inflammasome in the immunostimulatory properties of aluminium adjuvants. Nature DOI: 10.1038/nature06939 []
  4. Martinon F, Petrilli V, Mayor A, Tardivel A, Tschopp J (2006) Gout-associated uric acid crystals activate the NALP3 inflammasome. Nature 440:237-241. doi:10.1038/nature06939[]
May 25th, 2008

More (but really less) viral microevolution

Dengue virus (JVI cover)Last week I talked about evolution of HIV during transmission, and I was going to talk further about evolution of Dengue virus among schoolchildren1 as an interesting contrast to HIV.

The authors measured Dengue virus sequences over time in particular school districts in an endemic region, and I  entertained myself with an analogy between school districts for Dengue, and individuals for HIV, as pools in which virus circulated and evolved, and from which  viruses flung forth tentacles in attempts to spread. Dengue behaves very differently than HIV — the latter undergoes continuous, extensive evolution in situ, whereas it turned out that in the case of Dengue virus, microevolution within the school district is not very extensive — and I thought it might be interesting to ask why they are so different.

But on further contemplation I decided that (as is often the case with facile analogies) the situations are really not all that similar, and I don’t know that either case informs the other in any particularly useful way.

The critical difference is that in the case of Dengue sequence variation is dominated by virus migration into and out of the school districts:

… we observed little evolutionary change in those viral isolates sampled over multiple time points within individual schools, indicating a low rate of mutation fixation. These results suggest that frequent viral migration into Kamphaeng Phet, coupled with population (school) subdivision, shapes the genetic diversity of DENV on a local scale, more so than in situ evolution within school catchment areas.

Dengue virus (False colour)That’s not to say that the comparison is completely wrong; there may be a unit (whether within an individual, or within a certain geographically or socially-restricted unit somewhere) in which Dengue microevolution is an important contributer to persistence or transmission between units. But this paper doesn’t seem to have caught that unit, so I don’t think there’s much to really dig into.

In any case, there’s a paper, just become available in its online version, that’s much more interesting, and that strongly supports a speculation I made just about a month ago; so I’ll talk about that  in a day or two instead.


  1. Jarman RG, Holmes EC, Rodpradit P, Klungthong C, Gibbons RV, Nisalak A, Rothman AL, Libraty DH, Ennis FA, Mammen MPJ et al. (2008) Microevolution of Dengue viruses circulating among primary school children in Kamphaeng Phet, Thailand. J Virol 82:5494-5500. doi:10.1128/JVI.02728-07[]
May 21st, 2008

Microevolution and bottlenecks: HIV transmission

HIV (Wellcome Images)“All politics is local” may be a cliche; but “All evolution is local” is at least equally true, and is a more interesting concept to geeks like me. A mutated virus may spread through a population, but it starts somewhere. What are the bottlenecks, what are the resources that evolution can draw on, what are the checks or drivers of transmission and spread?

It’s only relatively recently, though, that the techniques to properly measure microevolution of viruses have become generally available; genomic sequencing of reasonably large chunks of virus has become fast and cheap enough that very small changes in virus sequence can be used to track evolution over short times and distance. I talked about using this to track the foot and mouth disease outbreak in England in 2007. Two recent studies look at microevolution to analyze bottlenecks and transmission, in quite different contexts: Dengue virus circulation in schools, and HIV transmission between individuals. I’ll talk about the dengue study some other time; here I only have room for the Keele et al paper.1

I’ve talked a fair bit (like here and here) about the evolution in situ that HIV undergoes in each of its hosts, evolving rapidly in response to local conditions such as immune responses. Much of the variation in the infected individual is selected, of course; selected in response to local conditions — those local conditions being the genetics of the host, and to a large extent the host’s immune system. The immune system puts tremendous pressure on the virus, and the only way it can escape from the prison is to cripple itself. HIV immune escape variants are usually relatively defective viruses, because the mutations that allow them to become invisible to the immune system, damage the virus’s ability to replicate and spread.

HIV assembling in a macrophage
HIV infecting a macrophage2

Immune systems are idiosyncratic; yours is different than mine. When HIV is transmitted from one person to another the virus moves from one selection immune landscape to a very different one. The mutations that saved it in the first person are now probably no longer protective, yet the damage that those mutations were doing is still very much present – a double whammy. Fortunately for HIV (less so for humanity) it is still able to mutate its way back to a functional virus. If you examine HIV in one individual and then in the next step in the transmission chain, the new host’s virus will probably have started to revert back to the platonic essence of HIV; less, of course, the mutations that the new host’s immune system imposes on it.

A question is: What does the virus have to work with in this process? We speak of HIV as a quasi-species, traveling around as a cloud of related but different viruses. Within that cloud is variation that can be immediately selected. But is that true in transmission? How many viruses actually take that gigantic leap from one host to the next?

This is important for a couple of reasons. The big one is vaccination. One of the huge obstacles to HIV vaccination is variation; not only within a population, but within an individual. Let’s say you are vaccinated and protected against the most common HIV variant. If you are infected only with a handful of viruses, you will probably shut them down. But if you’re infected with a cloud of many different viruses, somewhere in that cloud will be a resistant virus; the chance of protection have gone way down. Which of those is actually what happens?

Keele et al 2008 Fig 2That’s the question that Keele1 (and a cast of thousands, or at any rate another 36 authors; particle phsyics authorship on a biology paper) asked, examining thousands of virus samples (just one gene, not the whole genome; but based on single virus genomes, not pooled genomes from the virus cloud) from over 100 patients shortly after they were newly infected with HIV. They used a mathematical model (which I am for now going to accept on faith; with two grants due in the next two weeks, I don’t have time to sit down and work through the math) to consider three different possibilities:

  1. A cloud of viruses is transmitted;
  2. A limited number of viruses is transmitted out of the cloud;
  3. A cloud of viruses is transmitted, but is rapidly thinned down to become a limited number of viruses, due to selection within the new host.

They concluded that in fact the second possibility was true: Only a very small number of viruses manage to establish a foothold in the hostile new terrain:

we found that 78 (76%) had evidence of infection by a single virus or virus-infected cell and that 24 others (24%) had evidence of infection by at least two to five viruses. Aside from early selection of CTL escape variants found in several subjects, there was no suggestion of virus adaptation to a more replicative variant or bottlenecking in virus diversity preceding peak viremia. … we interpret the findings of low multiplicity infection and limited viral evolution preceding peak viremia to suggest a crucial but finite window of potential vulnerability of HIV-1 to vaccine-elicited immune responses.1

(My emphasis)

They also noted particular characteristics of the successful viruses, though I think their study, not being specifically designed for this, wasn’t able to come up with any surprises. But of course this opens the door to this further question: What’s special about these tiny few viruses that are successful transmitters, compared to the thousands or millions of other variants circulating in the original host? Are they just lucky little viruses, or are these the only ones that have some unique qualification for spread? And if so, can we take advantage of that quality to block spread?


  1. Keele BF, Giorgi EE, Salazar-Gonzalez JF, Decker JM, Pham KT, Salazar MG, Sun C, Grayson T, Wang S, Li H et al. (2008) Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc Natl Acad Sci U S A doi:10.1073/pnas.0802203105[][][]
  2. Gross, L., 2006. Reconfirming the Traditional Model of HIV Particle Assembly. PLoS Biology, 4(12), p.e445 EP []
May 18th, 2008

Autoimmunity and CD1 (Part II)

Last week I talked some general issues about autoimmunity, and gave a brief background on NKT cells. Today I’ll talk about the paper that spawned that discussion.1

A common general model for autoimmune goes something like this:

  • If you have a genetic predisposition toward autoimmunity2
  • And you are exposed to a microbial antigen,
  • Sphingomonas

  • That is somewhat similar to one of your body’s own antigens
  • And the exposure involves inflammation, which sends a “Danger!” signal to the immune system,
  • Then immune cells that are normally tolerant to the self antigen
  • Become reactive toward the microbial antigen
  • And cross-react with the self antigen. This low-level self-reactive inflammation
  • Causes cell death, releasing more antigen in the the presence of cell-death “Danger” signals.
  • Causing a runaway feedback loop that results in outright autoimmune disease

But as I said, it’s been very difficult to track through a reaction from beginning to end, to support or refute this model.

Matter et al., Fig 3 (Inflamed bile duct)
Matter et al., Fig 3 (Inflamed bile duct)

Primary biliary cirrhosis (PBC) is an autoimmune disease3 of the liver characterized by inflammation of the bile ducts (here is the American Liver Foundation’s PBC information page). The immunity seems to be mainly targeted at mitochondrial antigens, which raises the question of why the liver is specifically involved — mitochondria are found in just about every cell type.

NKT cells recognize CD1, which binds to lipid-type antigens typical of bacterial cell walls. Bendalac’s group found that they could cause a PBC-like disease in mice by infecting them with a particular bacterium4 that is normally considered to be a fairly innocuous commensal. They tested this bacterium because it was previously shown to trigger antibodies that cross-react with the mitochondrial antigens that are targets in PBC. (Remember that mitochondria are historically extremely symbiotic bacteria, so the cross-reactivity doesn’t come completely out of the blue.)

Antibodies are produced by B cells. However, the disease could be blocked by preventing NKT cells from getting activated (by infecting mice lacking the NKT target, CD1). The rationale for doing this experiment was that innate immune responses to this particular bacterium are, a little unusually, normally driven by NKT cells.

Novosphingobium aromaticivoransThe autoimmune-type disease lasted in these mice long after they had eliminated the bacteria — months, compared to a week or two to eliminate the actual infection. What’s more, even though NKT cells were essential to get the disease going, once it had started up, the disease could be transferred to new mice by swapping across classical T cells only (i.e. T cells but no NKT cells) — even into mice that had never seen the bacteria and didn’t even have CD1, which were doubly protected against having the disease start on its own. In other words, NKT cells start the disease, but don’t keep it going.

So what seems to be happening is that the NKT cells recognize the bacteria and produce massive inflammation. Because NKT cells tend to home to the liver5, they are able to overcome tolerance of cross-reactive cells in the liver, making liver antigens more at risk. The cross-reactive T and B cells, enraged by the constant roar of inflammation the NKT cells produce, attack the cross-reactive self antigens, damaging the cells and causing a constant inflammatory trigger. At this point the disease has become self-perpetuating, and you don’t need the NKT cells any more (and indeed, they quiet down about this time, as the bacteria are eliminated).

These findings establish the missing connection between the microbial innate immune trigger and chronic effector T and B lymphocyte attack of small bile ducts observed in PBC. 6

This is probably not a universal effect in detail — NKT cells are likely not important in the majority of autoimmune diseases — but it does give support to the general concepts that have been floating around for a while now.


  1. Mattner, J., Savage, P., Leung, P., Oertelt, S., Wang, V., Trivedi, O., Scanlon, S., Pendem, K., Teyton, L., Hart, J. (2008). Liver Autoimmunity Triggered by Microbial Activation of Natural Killer T Cells. Cell Host & Microbe, 3(5), 304-315. DOI: 10.1016/j.chom.2008.03.009[]
  2. Usually the mechanism is unknown[]
  3. Probably. There us still some uncertainty, but that is the best bet[]
  4. Novosphingobium aromaticivorans[]
  5. For reasons that are not, as far as I know, understood[]
  6. Invariant Natural Killer T Cells Trigger Adaptive Lymphocytes to Churn Up Bile. Sebastian Joyce and Luc Van Kaer. Cell Host & Microbe (15 May 2008) 3:275-277[]
May 15th, 2008

On parasite/host interactions

I don’t know why I read the ScienceDaily newsfeed, because it drives me crazy every single day.  I had naively thought that whoever massages the press releases they receive would have, maybe, a teeny tiny clue about what’s gone on in the field before, but they seem to have the historic awareness of tree squirrels. Today’s gem:

It’s a paradox that has confounded evolutionary biologists since Charles Darwin published On the Origin of Species in 1859: Since parasites depend on their hosts for survival, why do they harm them? … The study, published in the early online edition of the journal Proceedings of the National Academy of Sciences, provides the first empirical evidence in a natural system of what’s called the trade-off hypothesis.

It’s not a “paradox” at all, and while it may “baffle” the marketing department that wrote the press release ScienceDaily regurgitated, it certainly hasn’t baffled evolutionary biologists for a long time.  I’ve talked about this exact subject here:

… if there’s a link between increased transmission and increased virulence, then the balance will not favour the pathogen becoming benign.

Here:

I’ve previously talked about the common misconception that viruses evolve toward benignity. This is usually phrased something like, “Natural selection favours viruses with low pathogenicity/virulence (so they don’t eradicate their hosts)“, or “Viral pathogenesis is an abnormal situation of no value to the virus”. This claim is clearly wrong –clearly both through common sense, and through observation.

And here:

I’ve observed before that the common belief that viruses evolve toward avirulence is not particularly true. It’s more accurate to say that viruses evolve toward improved transmission. Some viruses are better transmitted if they let their host survive longer, but other viruses have to be virulent in order to spread. The former may evolve toward reduced (though not necessarily loss of) virulence, but the latter would “want” to maintain stable virulence.

May 14th, 2008

Autoimmunity and CD1 (Part I)

Dr. Kilmer's Swamp Root Kidney Liver & Bladder CureWe walk a fine line between death due to immune deficiency, smothered under the weight of pathogens and parasites, and death by hyperimmunity, eaten alive by our own defenses. It’s amazing that our immune system can be tuned so precisely as to recognize anything foreign, yet ignore the vast antigenic universe of our own normal self.

Of course, sometimes the immune system fails, in both directions. We often hear about deaths from pathogens, and autoimmune diseases in general are pretty common. There are many ways by which (it’s believed) the immune system can become self-reactive, but a very common observation is that there are both genetic and environmental predisposing causes to autoimmunity. That is, you may have the genetic makeup to be autoimmune, but until you’re exposed to some environmental trigger, autoimmunity never develops. So, for example, if your identical twin has an autoimmune disease, you are much more likely than someone in the general population to develop the disease; but you still have a good to excellent chance of never getting the disease.

Liver blood vesselsIn many cases the neither the environmental triggers nor the genetic factors are well understood. The most likely environmental trigger, though, is some kind of microbe. In some cases, this may be because of “molecular mimicry” — the microbe has an antigen that looks like self antigen; the self antigen is normally ignored, because the immune system needs some kind of “danger” signal before it becomes activated; the microbial antigen is seen in the context of microbial “danger” signals; an immune response forms against the microbial antigen; the immune response cross-reacts with the self antigen; self cells are damaged by this immune response; the dead cells release more danger signals along with self antigen; and a positive feedback loop drives a full-fledged autoimmune disease.

That’s the model, but there aren’t many, if any, diseases where the whole process has been tracked through step by step; in fact, I think that there has been so much difficulty getting clear molecular connections between microbes and autoimmunity that there’s a robust search for other mechanisms. However, in the latest issue of Cell Host and Microbe, Albert Bendelac’s group shows a series of links between bacterial infection and the autoimmune disease human primary biliary cirrhosis (PBC).1 (There’s also a helpful, if rather dry, commentary2 by Sebastian Joyce and Luc van Kaer in the same issue.) Rather than trying to cover everything today I’m going to give background here, and then talk about the specific findings in a few days.

CD1 - top view with ligandOne interesting thing about Bendelac’s paper is that they link CD1 to the disease, through NKT cells. CD1 is an MHC class I family member; I talked about it back here, and that’s its mug shot to the left here (click for a larger version). CD1, like many members of the MHC class I family, has a “groove” in its “top” side. MHC class I proper binds peptides in that groove, but CD1 has a much more hydrophobic groove that binds to greasy things like lipids, glycolipids, and lipopeptides. These kinds of molecules are typically found in some kinds of bacteria — especially mycobacteria, like tuberculosis and leprosy, but also other kinds of bacteria such as the commensal microbe Sphingomonas.

MHC class I molecules, with their peptides, are recognized by cytotoxic T lymphocytes (CTL),3 but CD1 molecules and their lipids are recognized by a specialized subset of T cells, “natural killer-like” T cells (NKT cells). The function of this CD1/NKT system really isn’t all that clear. The early guesses that this was a branch of the immune system specialized for dealing with mycobacteria has been weakened as NKT cells have been linked to resistance to various viruses, and also as various viruses have been shown to block CD1 — suggesting that CD1 and NKT cells would otherwise eliminate them.

OK, enough for now. In my next post I’ll talk more about the disease itself, and then try to spell out the process by which, according to Bendelac, NKT are central to the autoimmune reaction; as well as how this abnormal reaction suggests some of the normal functions of NKT and CD1.


  1. Mattner J, Savage PB, Leung P, Oertelt SS, Wang V, Trivedi O, Scanlon ST, Pendem K, Teyton L, Hart J et al. (2008) Liver Autoimmunity Triggered by Microbial Activation of Natural Killer T Cells. Cell Host & Microbe 3:304-315.[]
  2. Joyce S, Van K, Luc (2008) Invariant Natural Killer T Cells Trigger Adaptive Lymphocytes to Churn Up Bile. Cell Host & Microbe 3:275-277.[]
  3. And natural killer cells, but let’s not go into that now[]
May 11th, 2008

A therapeutic catalytic antibody?

Catalytic antibodyI’m not so much an antibody guy, but of course I’ve heard about catalytic antibodies. Catalytic antibodies bind, with the very high affinity that’s typical of many antibodies, to transition state molecules, stabilizing the transition state and facilitating the chemical reaction. They’ve been around for quite a while (I think the first, or at least first widely-announced, catalytic antibody1 was described in the mid-1980s) and a fair number of them have been created.

But as far as I know, catalytic antibodies remain a curiosity — a fascinating curiosity, but one without a lot of practical application. Although they can be custom-made and can have great specificity, as enzymes they tend to be really crappy (as you might expect), acting thousands or millions of times slower than “genuine” enzymes. Again, I’m no expert, but it seems that in spite of decades of promise, there hasn’t been much payoff; which is a shame, because the concept is so cool they deserve to make it big.2

Recently, though, there was a paper3 offering a catalytic antibody that actually was therapeutic in a real live animal model. Is this the one where promise actually follows through to reality?

Helicobacter pyloriThe antibody was raised against a virulence factor, urease, of Helicobacter pylori, the ulcer-causing bacterium. (Urease helps neutralize the stomach acid, so it helps H. pylori colonize stomachs.) The antibody degraded urease reasonably well; and more remarkably, the light chain alone of the antibody was also able to degrade H. pylori urease. I don’t know how common this is for catalytic antibodies,4 but it strikes as potentially useful, since the light chain can be more readily synthesized and is probably more stable on its own.

The interesting part was that they treated mice with this — I think the first time catalytic antibodies have been used in vivo. They infected the mice with H. pylori, and then treated them with either the catalytic light chain in buffer, or with buffer alone (they should really have used a control light chain in buffer, though — in general this paper doesn’t strike me as terribly well-controlled when is comes to the animal work, but part of that may be the poor English throughout). The treated mice had about a third as many bacteria in their stomachs as did control mice, suggesting that the antibody actually did some good. Presumably it degraded urease in vivo as it does in vitro, and by inceasing stomach acidity helped reduce the bacterial survival.

This is still far, far from any kind of useful treatment, I think, but it’s a step forward.


  1. Pollack SJ, Jacobs JW, Schultz PG (1986) Selective chemical catalysis by an antibody. Science 234:1570-1573.[]
  2. If I’m wrong, by the way, and catalytic antibodies have achieved a toehold somewhere in medicine or industry, please let me know. As I say, I don’t follow this field all that closely.[]
  3. Hifumi, E., Morihara, F., Hatiuchi, K., Okuda, T., Nishizono, A., Uda, T. (2007). Catalytic Features and Eradication Ability of Antibody Light-chain UA15-L against Helicobacter pylori. Journal of Biological Chemistry, 283(2), 899-907. DOI: 10.1074/jbc.M705674200[]
  4. It’s not unique, because the authors say they had the same thing for a previous catalytic antibody they made[]
May 10th, 2008

On HIV variation

The amount of HIV diversity within a single infected individual can exceed the variability generated over the course of a global influenza epidemic, the latter of which results in the need for a new vaccine each year.

–Walker BD, Burton DR (2008) Toward an AIDS vaccine. Science 320:760-764.

(See my previous posts here and here for more explanation.)

May 7th, 2008

More HERVs

HERV buddingThe other day I was talking about immune recognition of human endogenous retroviruses (HERVs) in tumors. (HERVs are the husks of ancient retroviruses, now trapped in our genomes. Some of them still express various proteins, either under normal conditions or when stimulated, as in tumors.) One of the reasons this is an interesting finding, is that HERVs may offer a relatively constant antigen, even though the tumors themselves may be highly variable.

There are other, rather obvious, scenarios in which we would like to have a constant antigen in the face of an antigenically-variable disease. For example, HERVs have been proposed to be useful vaccine targets in HIV infection.

One of the many obstacles to overcome in developing a vaccine against HIV is the virus’s rapid mutagenesis. Because of its error-prone replication, HIV can readily escape a lot of immune recognition. Especially when cytotoxic T lymphocytes (CTL) recognize a limited number of antigenic targets, all the virus needs to do to escape immune control is mutate a single amino acid. Usually once the virus does this and escapes immune control, new CTL arise and once again shut down the virus, but only to have new escape variants arise and replicate. Over the multi-year course of an HIV infection, there may be dozens or hundreds of major HIV variants, each escaping temporarily from CTL and destroying T cells during their limited period of freedom.

There are several strategies aimed at reducing the effectiveness of immune escape: targeting multiple HIV antigens, so that the virus would have to simultaneously find many mutations at once; targeting regions in the virus that are so essential that they can’t tolerate mutation; and so on. But wouldn’t it be nice if there was an antigen that wouldn’t change?

HIV and HERVs are distant cousins, both retroviruses, so it seems reasonable that HIV infection might turn on sleeping HERVs. In fact, for nearly 10 years there have been intermittent studies suggesting this might be the case; first based on antibody responses in HIV patients1, and recently with more specific evidence of reactivation of HERVs both in patients2 and in the lab, in infected cells.3

Garrison et al 2008 Fig 6Last fall Douglas Nixon’s group took this to the next step.4 Although the antibody responses1 had suggested that HERVs were immunogenic when turned on by HIV, antibodies aren’t believed to be terrible important in control of HIV; rather, CTL are thought to be critical.5 Nixon’s group showed that in HIV-infected people, there were often functional CTL responses to HERVs; what’s more, the higher the anti-HERV response, the lower the HIV plasma load, implying that the anti-HERV CTL might actually be controlling HIV. (See the figure to the left; click for a larger version.)

As endogenous retroviral sequences are fixed in the human genome, they provide a stable target, and HERV-specific T cells could recognize a cell infected by any HIV-1 viral variant. HERV-specific immunity is an important new avenue for investigation in HIV-1 pathogenesis and vaccine design.

Let’s go back to a paper6 I mentioned last year, where a group looked at genomic variation linked to disease progression in HIV. They found three genomic regions that were linked to viral set-point; one is an RNA polymerase, one is in the MHC region and affects levels of the MHC class I gene HLA-C, and the third … well, the third is a HERV, called HCP5.

The authors pointed out that HCP5 might not be the actual factor involved, because it might be riding along with HLA-B*5701, an MHC class I allele that’s associated with HIV resistance (and I noted that natural killer ligands MICA and MICB are also close by). Still, they clearly like the idea that HCP5 is itself directly involved. They suggested that it might act by an antisense mechanism or something, but I think it might be very interesting to look at CTL responses to HCP5 proteins.


  1. Stevens RW, Baltch AL, Smith RP, McCreedy BJ, Michelsen PB, Bopp LH, Urnovitz HB (1999) Antibody to human endogenous retrovirus peptide in urine of human immunodeficiency virus type 1-positive patients. Clin Diagn Lab Immunol 6:783-786.[][]
  2. Contreras-Galindo R, Kaplan MH, Markovitz DM, Lorenzo E, Yamamura Y (2006) Detection of HERV-K(HML-2) viral RNA in plasma of HIV type 1-infected individuals. AIDS Res Hum Retroviruses 22:979-984.[]
  3. Contreras-Galindo R, Lopez P, Velez R, Yamamura Y (2007) HIV-1 infection increases the expression of human endogenous retroviruses type K (HERV-K) in vitro. AIDS Res Hum Retroviruses 23:116-122.[]
  4. Garrison, K.E., Jones, R.B., Meiklejohn, D.A., Anwar, N., Ndhlovu, L.C., Chapman, J.M., Erickson, A.L., Agrawal, A., Spotts, G., Hecht, F.M., Rakoff-Nahoum, S., Lenz, J., Ostrowski, M.A., Nixon, D.F. (2007). T Cell Responses to Human Endogenous Retroviruses in HIV-1 Infection. PLoS Pathogens, 3(11), e165. DOI: 10.1371/journal.ppat.0030165[]
  5. Because of the way CTL recognize their targets, by the way, it doesn’t matter if the HERVs produce defective proteins — even a truncated protein that is unstable and rapidly destroyed might be a good CTL target.[]
  6. Fellay, J., Shianna, K. V., Ge, D., Colombo, S., Ledergerber, B., Weale, M., et al. (2007).A whole-genome association study of major determinants for host control of HIV-1. Science, 317(5840), 944-947.[]