Mystery Rays from Outer Space

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

September 7th, 2010

Assassination or accident?

I have as much respect for viruses’ ability to manipulate their host as the next guy, and I’m probably more of a fan of viral immune evasion than that next guy. But I still do think that coincidences do happen.

A paper from John Trowsdale and colleagues1 shows that Kaposi’s Sarcoma Herpesvirus (KSHV) destroys HFE, and they suggest that this is “a molecular mechanism targeted by KSHV to achieve a positive iron balance.” Without dissing their observations (which are perfectly convincing) I’m not entirely convinced by their conclusion. Still, it’s an interesting suggestion, and I’m keen to see some kind of followup to it.

The reason I’m not convinced is that this has the look of a spillover effect to me. We already know that KSHV attacks MHC class I molecules via its K3 and K5 molecules, and that it does so by targeting the cell-surface pool to lysosomes. This is a very familiar pattern; most, if not all, herpesviruses block MHC class I molecules. Although it’s been hard to formally prove “why” herpesviruses do this,2 the general assumption is that this allows the virus to at least partially avoid recognition by T cells, and this lets the virus survive better — perhaps because it builds a larger population very early, or perhaps because it is able to last longer late, or whatever.

At any rate, there’s a fairly simple and logical reason why it would make sense for KSHV to block MHC class I molecules, and as I say they do, in fact, do this. Now, why would they attack HFE? HFE is an iron-binding protein that’s involved in the regulation of iron metabolism. Why would KSHV be interested in iron metabolism?

Quite a few pathogens are actually very concerned about iron metabolism, of course. Bacteria generally need iron for their metabolism,3 and pathogenic bacteria have evolved ways of grabbing iron away from their hosts (while their hosts have evolved way of holding on tighter and tighter to that iron). But in general viruses, as opposed to bacteria, don’t have specific needs for iron. Trowsdale’s group makes the argument — and offers some experimental evidence — that KSHV does in fact want iron. “KSHV presumably down-regulates HFE to affect iron homeostasis,” they say, and “These results indicated an iron requirement for lytic KSHV and with the virus targeting HFE to satisfy this demand.” However, I don’t think they really show this directly; they show that there are changes in iron receptors in the presence of KSHV, but as far as I can see they don’t show that the presence or absence of iron actually affects the virus in any way.

HFE complex HLA-A2 complex
HFE heavy chain (red) complexed with beta-2 microblogulin (blue) HLA-A2 (classical MHC class I) heavy chain (red) complexed with beta-2 microblogulin (blue) and a peptide (green)

So let’s say KSHV doesn’t really care about iron per se. Why is the virus attacking this iron receptor, then? To me, the simpler solution is that it’s just a side effect of the virus attack on MHC class I, because HFE is in fact an MHC class I molecule.4 Not all MHC class I molecules are involved in immunity, and HFE is the classic counterexample, an MHC class I molecule that has a clear non-immune role. 5

Even though HFE has a different role, it has a very similar structure to the classical MHC class I molecules — see the images to the right (click for larger versions), and for more comparisons see my post from a couple of years ago, “MHC Molecules: The Sitcom“.  It doesn’t have the peptide bound in the top groove (green in the HLA-A2 complex here) that classical MHC class I molecules use to provide specific signals to T cells, but it’s very similar. It’s plausible — at least to me — that the virus doesn’t care in the least about iron metabolism, but is just attacking everything on the cell surface that looks like an MHC class I molecule, and HFE is getting caught in the covering fire.

Interestingly, though, this isn’t the first time this has been proposed.  A few years ago a paper from Drakesmith et al proposed pretty much the same model for HIV, via the HIV immune evasion molecule nef.  Nef downregulates a large number of immune-related molecules, and also downregulates HFE. Drakesmith et al, like Trowsdale’s group, argue that this is “deliberate”, and that the modified iron metabolism directly benefits HIV;6 but I don’t know if that’s been followed up (Trowsdale’s paper, surprisingly, doesn’t cite Drakesmith et al).

I’m open to the idea that viruses do “want” to tweak iron metabolism, because that would be pretty cool, but so far I’m leaning to notion that HFE is just an accidental victim of the viral war on immunity.


  1. Rhodes DA, Boyle LH, Boname JM, Lehner PJ, & Trowsdale J (2010). Ubiquitination of lysine-331 by Kaposi’s sarcoma-associated herpesvirus protein K5 targets HFE for lysosomal degradation. Proceedings of the National Academy of Sciences of the United States of America PMID: 20805500[]
  2. I put “why” in quotes because obviously it’s not planned. But it’s easier than saying, “why herpesviruses have evolved this ability” or “what selective advantage this ability confers to the herpesviruses”.[]
  3. I say “generally” because I’m not a bacteriologist, and no doubt there’s some bizarre oddball bug that doesn’t need iron to get along. But I don’t know any of them. As far as I know bacteria all need iron[]
  4. It’s a class Ib molecule, a non-classical MHC class I molecule, but it is MHC class I.[]
  5. It’s worth noting that HFE might — just might — have an immune role, too. There are T cells that recognize HFE. It’s not clear, at least to me, what these T cells do, and whether they have a real function or if it’s just a case –another case? — of accidental spillover.
    Rohrlich PS, Fazilleau N, Ginhoux F, Firat H, Michel F, Cochet M, Laham N, Roth MP, Pascolo S, Nato F, Coppin H, Charneau P, Danos O, Acuto O, Ehrlich R, Kanellopoulos J, & Lemonnier FA (2005). Direct recognition by alphabeta cytolytic T cells of Hfe, a MHC class Ib molecule without antigen-presenting function. Proceedings of the National Academy of Sciences of the United States of America, 102 (36), 12855-60 PMID: 16123136[]
  6. Drakesmith H, Chen N, Ledermann H, Screaton G, Townsend A, & Xu XN (2005). HIV-1 Nef down-regulates the hemochromatosis protein HFE, manipulating cellular iron homeostasis. Proceedings of the National Academy of Sciences of the United States of America, 102 (31), 11017-22 PMID: 16043695[]
May 4th, 2010

Does immune evasion allow rapid HIV progression?

How not to be seenI was getting a little concerned and distressed by the lack of evidence for any function of viral MHC class I immune evasion. It’s kind of a relief to see articles demonstrating function coming out.

MHC class I is the target for cytotoxic T lymphocytes (CTL), which are generally believed to be pretty important in controlling viral infection. So when some viruses were shown to block MHC class I in cultured cells, it seemed pretty obvious that this would be a big benefit for the virus. You’d expect these viruses to be exceptionally resistant to CTL, for example.

But when people actually looked in animals (as opposed to in tissue culture), the ability to block MHC class I didn’t seem to do all that much. I’ve summarized some of those experiments here and here. For example, the MHC class I immune evasion genes in adenoviruses and in mouse cytomegalovirus (MCMV) didn’t show much effect on the actual infection at all.1 Mouse herpesvirus 68 (MHV68) had shown an effect, but not at the time point that you might expect — not early after infection, when CTL are kicking in and clearing virus, but rather later on, during the latent phase.2

We all believed there must be a function, because viruses don’t hang on to genes for millions of years unless those genes are important,3 but I was starting to wonder if perhaps we were looking in the wrong places — whether any immune effects might be spillover from some other function, say. But, as I say, we’re starting to get confirmation that these things really are doing more or less what we’d expected all along.

A little while ago, Klaus Fruh and Louise Pickert showed a significant effect of MHC class I immune evasion in rhesus cytomegalovirus: without that ability new viruses couldn’t superinfect hosts that already carry the virus. 4 (I talked about it here.) It’s quite possible — though of course not certain until it’s actually tested — that this is also true for human cytomegaloviruses (which are very closely related to the rhesus version) and for mouse CMV (which are less closely related but in the same family). So now we have functional data for MHC class I immune evasion for representatives of two broad groups of viruses, the betaherpesviruses (the cytomegaloviruses) and the gammaherpesviruses (the MHV68 story).

Now there’s another paper5 showing a function for the MHC class I immune evasion ability of HIV (actually for SIV, but again it’s probably true for the closely-related HIV).

HIV has a gene, nef, that can block MHC class I expression. This has been shown in cultured cells, but understanding its relevance in actual infections has been difficult:

Although these data suggest that Nef-mediated immune evasion could play an important role in AIDS pathogenesis, there has been little direct evidence linking disease progression with MHC-I downregulation in vivo. 5

Obviously you can’t make a nef-less HIV and just throw it into people to see what happens. Even doing the experiment in monkeys with SIV is complicated by the fact that nef is very polyfunctional — as well as downregulating MHC class I, it also targets a number of other molecules.

But you can take advantage of natural variation, both in the virus and the host.  Nef isn’t equally effective on all MHC class I types, for one thing. As well, nef can develop mutations within the host.  It turns out that rapid disease progression correlates with the extent of MHC class I downregulation, whereas effects on other genes affected by nef (CD3 and CD4) didn’t correlate:

The extent of MHC-I downregulation on SIV-infected cells varied among animals …  the level of MHC-I downregulation on SIV-infected cells was significantly greater in the rapid progressor animals than in normal progressors.  … high levels of MHC-I downregulation on SIV-infected cells are associated with uncontrolled virus replication and a lack of strong SIV-specific immune responses.5

This is strictly a correlation study, so we can’t confidently say that MHC downregulation causes disease progression. Still, it’s an interesting finding, and perhaps one that can be followed up in human studies.


  1. Gold MC, Munks MW, Wagner M, McMahon CW, Kelly A, Kavanagh DG, Slifka MK, Koszinowski UH, Raulet DH, & Hill AB (2004). Murine cytomegalovirus interference with antigen presentation has little effect on the size or the effector memory phenotype of the CD8 T cell response. Journal of immunology (Baltimore, Md. : 1950), 172 (11), 6944-53 PMID: 15153514
    Only slightly qualified by
    Lu, X., Pinto, A., Kelly, A., Cho, K., & Hill, A. (2006). Murine Cytomegalovirus Interference with Antigen Presentation Contributes to the Inability of CD8 T Cells To Control Virus in the Salivary Gland Journal of Virology, 80 (8), 4200-4202 DOI: 10.1128/JVI.80.8.4200-4202.2006[]
  2. Stevenson, P., May, J., Smith, X., Marques, S., Adler, H., Koszinowski, U., Simas, J., & Efstathiou, S. (2002). K3-mediated evasion of CD8+ T cells aids amplification of a latent ?-herpesvirus Nature Immunology DOI: 10.1038/ni818[]
  3. I will admit there’s a certain circular quality to this argument.  ”The gene must be important, because viruses don’t carry unimportant genes.  We know that, because this gene that they’ve hung on to must be important.”[]
  4. Hansen, S., Powers, C., Richards, R., Ventura, A., Ford, J., Siess, D., Axthelm, M., Nelson, J., Jarvis, M., Picker, L., & Fruh, K. (2010). Evasion of CD8+ T Cells Is Critical for Superinfection by Cytomegalovirus Science, 328 (5974), 102-106 DOI: 10.1126/science.1185350[]
  5. Friedrich, T., Piaskowski, S., Leon, E., Furlott, J., Maness, N., Weisgrau, K., Mac Nair, C., Weiler, A., Loffredo, J., Reynolds, M., Williams, K., Klimentidis, Y., Wilson, N., Allison, D., & Rakasz, E. (2010). High Viremia Is Associated with High Levels of In Vivo Major Histocompatibility Complex Class I Downregulation in Rhesus Macaques Infected with Simian Immunodeficiency Virus SIVmac239 Journal of Virology, 84 (10), 5443-5447 DOI: 10.1128/JVI.02452-09[][][]
April 10th, 2010

Immune databases and hypotheses

The folks associated with the IEDB (Immune Epitope Database) have published a very nice and useful guide to all the serious contenders in the immune database field.  1 If you have a particular need, this is an excellent starting point for choosing the appropriate starting point.  (It’s an open access article, too.)

They’ve obviously looked in a lot more depth than I have, but they make a few comments that my more limited assessment strongly supports:

… our survey highlights clear shortcomings in the predictive tools available. Namely, MHC class II and B cell epitope predictive tools merit improvement, both in terms of predictive performance and, for MHC class II, in terms of coverage of species and alleles currently available. 1

They comment that most (80%) of citations of the databases are attributable to “practical applications”, which I take to mean direct use of the prediction tools (identification of epitopes in new flu strains, for example), construction of new tools (e.g. better prediction of epitopes), and maybe papers that review the databases (which is rather circular, I think).

Hearn et al 2009 FIgure 8
FIGURE 8. Aminopeptidases influence amino acid frequency N-terminal of naturally presented MHC I epitopes. Regions N-terminal to naturally processed MHC I epitopes, or selected randomly from protein pre- cursors, were identified as described in Materials and Methods. A, Probability of divergence occuring randomly (Chi2 test) vs position relative to epitope start site. B, Observed amino acid frequencies at position 1 (P1) relative to epitope start vs no divergence from back- ground (45-degree line). The amino acids that diverge +/-2 SDs from background frequency are indicated.2

The other 20% of citations are, I guess, using the databases to generate and test hypotheses.   This seems high, to me.  I don’t think I’ve seen very much basic science in immunology that builds on this sort of resource.  I think we’re reaching the point where these databases are usable to test and develop new hypotheses, though, and I hope to see more of this in the near future.

One example is our recent paper,2  where I used the IEDB to ask what influence ER aminopeptidases have on MHC class I epitopes (see the Figure to the left). (If you care, we concluded that aminopeptidases were probably most important for trimming N-terminal extensions of up to three residues, and that there was a global preference for a half-dozen amino acids and a bias against valine and, of course, proline — proline is resistant to aminopeptidase trimming in general, so that finding supported the approach.)

We weren’t the first to use this general approach (Schatz et al3 came up with the same idea independently and published before we did) but we used the IEDB, instead of the SYFPEITHI database, and were able to identify many more epitopes.   (My last run at the database coincided with the database being revised and half the search tools I needed stopped working, which was annoying, but the manager [Randi Vita] was very helpful and we managed to grind through the queries, albeit in slow motion compared to earlier runs.)


  1. Salimi, N., Fleri, W., Peters, B., & Sette, A. (2010). Design and utilization of epitope-based databases and predictive tools Immunogenetics, 62 (4), 185-196 DOI: 10.1007/s00251-010-0435-2[][]
  2. Hearn, A., York, I., & Rock, K. (2009). The Specificity of Trimming of MHC Class I-Presented Peptides in the Endoplasmic Reticulum The Journal of Immunology, 183 (9), 5526-5536 DOI: 10.4049/jimmunol.0803663[][]
  3. Schatz MM, Peters B, Akkad N, Ullrich N, Martinez AN, Carroll O, Bulik S, Rammensee HG, van Endert P, Holzhütter HG, Tenzer S, & Schild H (2008). Characterizing the N-terminal processing motif of MHC class I ligands. Journal of immunology (Baltimore, Md. : 1950), 180 (5), 3210-7 PMID: 18292545[]
January 22nd, 2010

A flood of DRiPs

"Untitled (Green Silver)” - Jackson Pollock
“Untitled (Green Silver)” – Jackson Pollock

In the past few weeks not only did I post a short update on the DRiPs hypothesis here, but coincidentally a bunch of papers on DRiPs have also been published. I’ll probably cover some of these in more detail at some point, but here are some of the recent papers and my brief comments.

Just as a reminder: the DRiPs (“Defective ribosomal products”) hypothesis proposes that most of the peptides presented to cytotoxic T lymphocytes don’t come from the actual proteins that we normally measure — rather, the immunologically relevant peptides come from deformed and defective proteins that are mis-read and misfolded during their translation. (More explanation of DRiPs here and here; more explanation of how T cells recognize cells and where peptides come in, here.)

Jon Yewdell’s insight,1 which is still somewhat controversial, was that defective proteins may actually be very common. Instead of being rare and abnormal events, he argued, protein production is a highly error-prone business, and a large fraction of newly synthesized proteins are broken. These defective products are very rapidly recycled into peptides and amino acids, and because of this rapid recycling they are the major source of peptides for T cell recognition.

On his original publication I had no problem with the underlying concept, but wasn’t overwhelmed by the data, and felt that there were too many counterexamples; since then he, and others, have put forward more and more examples, and I think it’s also fair to say that Jon has softened a little on the original hypothesis.2 I’m more or less convinced that DRiPs are one important source of peptides, though I remain dubious that they are the only, or (and here I get very uncertain) even the major source.

Anyway, in the past few weeks, we’ve seen these papers:

  • The Synthesis of Truncated Polypeptides for Immune Surveillance and Viral Evasion3

This is from Nilabh Shastri, and it’s not a big conceptual departure from some of his previous work. He’s argued for quite a while that aberrant proteins are major sources of T cell targets (see my posts here and here, for examples). Here he extends the argument to the EBNA1 protein from Epstein-Barr virus. This is a remarkably interesting protein for many reasons, one of which is that there’s reason to believe that DRiPs must be the only real source of T cell targets from EBNA1. Here, Shastri shows that in fact DRiPs (in the forms of truncated synthesis products) are in fact targets for T cells (“Thus, translation of viral mRNAs as truncated polypeptides is important for determining the antigenicity of virus proteins“). (I don’t know if it’s fair to generalize to all viral mRNAs from this very unusual protein, though.)  Very intriguingly, he also shows that DRiPs seem to be specifically blocked by EBNA1 mRNA!

Regulating production of DRiPs at the level of mRNA translation may serve as an immune evasion strategy for latent viruses. …  It is tempting to speculate that episome maintenance proteins, found in herpesviruses of various species, might have evolved to inhibit pMHC I presentation by interfering with production of DRiPs.

Is this a new viral immune evasion mechanism? And if so, how widespread is it? I know Nilabh (or someone from his lab) reads this blog occasionally, and I’d be interested in hearing their ideas on this — is it pure speculation, or do they have reason to extend the observation?

  • Viral adaptation to immune selection pressure by HLA class I–restricted CTL responses targeting epitopes in HIV frameshift sequences4
HIV-1 frameshift inducing element
HIV-1 frameshift inducing element

These authors looked at proteins produced by reading frame shifts from HIV.  Although HIV does a lot of frame-shifting “deliberately”, here we’re looking at frame-shifts that are (probably) not “real”.  That is, while it’s possible that some of these proteins have a biological function, for the most part they’re probably nonsense proteins, the product of incorrect selection of reading frames by the ribosome, and therefore you’d expect them to be recognized as improper proteins by the quality-control system and rapidly destroyed. In that sense they fit into the “DRiPs” concept. This fits neatly with Shastri’s previous work on frame-shifting, as well as providing modest support of the DRiPs concept.

The interesting thing here is that this paper offers evidence for large-scale immunological importance of peptides from frame-shifted proteins.  Shastri has previously shown convincing evidence that peptides derived from frame-shifted proteins can be recognized by T cells, but I always wondered if that was just a test-tube novelty. In this paper, though, Berger et al. argue that these frame-shifted potential targets show evidence of evolutionary selection, suggesting that they are recognized often enough to be a significant factor in the viral life-cycle.

  • CD8 T cell response and evolutionary pressure to HIV-1 cryptic epitopes derived from antisense transcription. 5

And this is a very similar paper, showing the same thing for antisense-derived peptides. Like the frame-shifted proteins discussed above, these antisense proteins would probably be nonsense and rapidly degraded — defective ribosomal products, in other words — and again, there’s some evidence that these are under immunological selection, suggesting that this recognition is a real-world phenomenon.

These findings indicate that the HIV-1 genome might encode and deploy a large potential repertoire of unconventional epitopes to enhance vaccine-induced antiviral immunity.5

  • The antiviral factor APOBEC3G improves CTL recognition of cultured HIV-infected T cells. 6

This is a particularly cool paper.7 We know that APOBEC3G — a host protein that evolved, apparently, to provide protection against infection with retroviruses such as HIV — acts by driving hypermutation of infecting retroviral genomes. HIV resists this effect through its protein vif, which in turn drives rapid degradation of several APOBECs.

But in spite of this vif-mediated protection, it’s probably true that APOBECs still have some effect on HIV, especially very early in an infection before vif can take them out; so there’s a background of mutation in HIV driven by APOBECs. This paper shows that APOBEC-driven mutation improves T cell recognition of HIV-infected cells, and the effect is probably because the mutations force HIV to make even more defective proteins, so that there are more T cell targets. This was done in rather an artificial system (mainly by either eliminating vif altogether, or by cranking up the levels of APOBEC3G artificially), so it’s not clear how important it would be in a natural infection.

I also wonder if this argues against the notion that DRiPs are normally a big factor, because if so the background of DRiP-derived peptides should be quite high and increasing it might not be a big factor; but that’s a quantitative issue that’s hard to deal with. Still, an interesting take on antiviral effects.

  • Defective Ribosomal Products Are the Major Source of Antigenic Peptides Endogenously Generated from Influenza A Virus Neuraminidase 8
"Drips" (Inger Taylor)
“Drips” (Inger Taylor)

This is the paper that most explicitly tests DRiPs, which is not surprising, since it comes from Jon Yewdell himself.9 The paper starts with quite a fair summary of the hypothesis’s status, including some of the problems with previous experiments:

In all of these studies, we used recombinant vaccinia viruses (VVs) to express SIINFEKL-containing source Ags. It is possible that we grossly overestimated the contribution of DRiPs to Ag processing in these studies due to the use of VV to express non-VV genes. We recently showed that differences in viral translation mechanisms can greatly increase the fraction of DRiPs; expression of influenza A virus (IAV) nuclear protein by an Alphavirus vector resulted in the defective translation of >50% of nuclear protein recovered from cells. VV expression is known to modify the Ag processing pathway of some inserted viral gene products compared with their natural infection context. Further, the fusion of multiple genes to create chimeric proteins can greatly decrease the fidelity of protein synthesis or protein folding …8

In an attempt to get around some of these problems, they tried to come up with a more natural system.  What they built is more natural, but still is fairly artificial (as they acknowledge); still, their findings did add more support to the basic idea. (As a sign that Jon has softened his position some in the past decade, their comment “Although DRiPs are clearly a major source of antigenic peptides, it is important to recognize that peptides are also generated from natural protein turnover” is one that I think all but the most hardened anti-DRiPers would agree with; it’s coming down to a question of quantitation, of what “major” actually means, rather than absolutes.)

I still suspect that there are cases where DRiPs are critical, and cases where they’re not particularly important, and I don’t have a good sense for how many instances of each there are. My gut feeling is about half and half, but it’s not something I’d defend with my life.


  1. Yewdell, J. W., Aton, L. C., and Benink, J. R. (1996). Defective ribosomal products (DRiPs): A major source of antigenic peptides for MHC class I molecules? J. Immunol. 157, 1823-1826[]
  2. Which has made it a bit of a moving target when it comes to disproving it, unfortunately[]
  3. Cardinaud, S., Starck, S., Chandra, P., & Shastri, N. (2010). The Synthesis of Truncated Polypeptides for Immune Surveillance and Viral Evasion PLoS ONE, 5 (1) DOI: 10.1371/journal.pone.0008692[]
  4. Berger, C., Carlson, J., Brumme, C., Hartman, K., Brumme, Z., Henry, L., Rosato, P., Piechocka-Trocha, A., Brockman, M., Harrigan, P., Heckerman, D., Kaufmann, D., & Brander, C. (2010). Viral adaptation to immune selection pressure by HLA class I-restricted CTL responses targeting epitopes in HIV frameshift sequences Journal of Experimental Medicine, 207 (1), 61-75 DOI: 10.1084/jem.20091808[]
  5. Bansal, A., Carlson, J., Yan, J., Akinsiku, O., Schaefer, M., Sabbaj, S., Bet, A., Levy, D., Heath, S., Tang, J., Kaslow, R., Walker, B., Ndung’u, T., Goulder, P., Heckerman, D., Hunter, E., & Goepfert, P. (2010). CD8 T cell response and evolutionary pressure to HIV-1 cryptic epitopes derived from antisense transcription Journal of Experimental Medicine, 207 (1), 51-59 DOI: 10.1084/jem.20092060[][]
  6. Casartelli, N., Guivel-Benhassine, F., Bouziat, R., Brandler, S., Schwartz, O., & Moris, A. (2009). The antiviral factor APOBEC3G improves CTL recognition of cultured HIV-infected T cells Journal of Experimental Medicine, 207 (1), 39-49 DOI: 10.1084/jem.20091933[]
  7. I’m presenting this one on Friday in the Immunology Journal Club I run here.[]
  8. Dolan, B., Li, L., Takeda, K., Bennink, J., & Yewdell, J. (2009). Defective Ribosomal Products Are the Major Source of Antigenic Peptides Endogenously Generated from Influenza A Virus Neuraminidase The Journal of Immunology, 184 (3), 1419-1424 DOI: 10.4049/jimmunol.0901907[][]
  9. Interestingly, it looks as if Jon has turned his attention back to influenza viruses in the past year — he cut his teeth on influenza, quite a number of years back, but it hasn’t been his main focus for a while. I guess H1N1 gave him the excuse he needed to move back that way.[]
July 22nd, 2009

MHC that’s not in the MHC

Tammar Wallaby
Tammer Wallaby

Everyone knows that the MHC is in the MHC, right? Well, it’s not necessarily so.

That’s not as tautological as it sounds. MHC (major histocompatibility complex) can refer to either the protein complex, or to the genomic region. In most species the genes encoding MHC proteins are clustered together into a distinct region of the genome that usually contains a bunch of genes that are functionally, and in some cases structurally, linked. For example, the human MHC genomic region contains not only many MHC class I genes, but also the TAP genes that are required for their function (outline of function here); MHC class II genes, and a number of genes required for their function; some proteasome subunits that are also involved in the antiviral MHC function; and so on. There’s a crude map here, and a somewhat more detailed one here; in humans and many other species the MHC genomic region is densely packed with genes, many of which are immunologically important.

Although the details are different the same concept applies to many vertebrates — chickens 1, Xenopus (frogs),2 and sharks,3 for example, have only one classical MHC class I gene, but it’s recognizably in the MHC genomic region, tightly linked to TAP and not quite as tightly linked to MHC class II genes.

Why are these functionally-related genes clustered together? There are probably a bunch of reasons, and the reasons may actually be different for different species. A recent paper,4 showing a partial exception to the rule, makes some interesting suggestions. Siddle et al5 have looked at wallaby MHC genes and find that their classical MHC class I genes are actually scattered throughout the genome, and are not in the MHC region.

First of all, what’s the advantage of having a single MHC class I gene tightly linked to TAP (probably the primordial organization)? TAP transports peptides to the MHC (again, cartoons of MHC class I function here), and the MHC then presents the peptides to T cells for antiviral surveillance. That means that TAP needs to handle the same kinds6 of peptides that the MHC class I does. By linking the genes for TAP and the MHC class I, the two can evolve in tandem — if a particular MHC class I gene likes to bind peptides ending with, say, arginine, then it can co-evolve along with a TAP that likes to transport peptides ending in arg. MHC class I genes are extremely variable, and in non-mammalian species, TAP genes are also relatively variable, 7 arguing for this kind of co-evolution.

The problem with this organization is that it only really allows one MHC class I specificity. If the TAP has a certain, strong, specificity (ending with Arg, say), and you had several different MHC class I proteins each with different peptide preferences (one that wants peptides ending with Arg, but another that wants peptides ending in tyrosine), then some of them wouldn’t match the TAP peptides and would go wanting.

Chickens (Altamira)(By the way, this makes a start at explaining a paper that puzzled me some time ago [post is here]. The chicken B21 MHC class I allele was said to have very weak peptide preferences — allowing “promiscuous peptide binding”. But if TAP has strong peptide preferences, then the MHC is only going to bind to a limited subset of peptides, no matter how promiscuous the MHC is itself. That doesn’t explain everything, but it makes a start. I should mention, though, that a different group looking at B21 did, in fact, identify peptide binding preferences,8 suggesting that binding isn’t actually promiscuous; but now I wonder if they were detecting TAP preferences rather than MHC.)

Although it’s not a hundred percent clear why MHC class I is so diverse,9 according to the most plausible explanations the advantages of diversity are going to be increased if you have several different MHC class I genes, with different peptide-binding properties. If you can hoick the MHC away from TAP, then, you’d allow the MHC to start diversifying independent of TAP. You’d probably need TAP to now be fairly peptide-promiscuous (which it is, in most mammals), and shift the peptide specificity over to the MHC class I molecules themselves.

Humans, mice, and most mammals that have been looked at do this (separate MHC class I from TAP, and have multiple MHC class I alleles) by sliding the MHC class I genes over to the side, remaining within the MHC genomic region but becoming far enough separated from TAP that the genes can evolve more or less independently. Wallabies apparently have done the same thing functionally, but instead of sliding over and keeping the genes in the MHC genomic region, they’re scattered throughout the rest of the genome, apparently via retrotranspon-mediated transposition.

The classical class I have moved away from antigen processing genes in eutherian mammals and the wallaby independently, but both lineages appear to have benefited from this loss of linkage by increasing the number of classical genes, perhaps enabling response to a wider range of pathogens.4

Incidentally, it occurs to me that there is an extra cost to this increased diversity. By un-linking TAP specificity from MHC class I peptide preferences, mammals force TAP to be highly promiscuous, and to transport a wide range of peptides — unlike in chickens, TAP no longer “knows” what MHC allele it’s dealing with and has to offer every possible peptide sequence that any of the thousands of MHC class I alleles could bind. That means that there must be a vast amount of wasted peptides transported into the endoplasmic reticulum; in contrast, I would expect chickens, for example, to predominately only transport peptides that can bind to their MHC class I. If you suspect, as I do, that peptides are intrinsically toxic at high doses, then mammals must have developed (or enhanced) some mechanisms for destroying the extra peptides, that non-mammalian vertebrates don’t have to worry about. I have a guess as to what the mechanism might be, but I’m not sure exactly how to test it right now.


  1. Kaufman J, Milne S, Gobel TW, Walker BA, Jacob JP, Auffray C, Zoorob R, Beck S: The chicken B locus is a minimal essential major histocompatibility complex.Nature 1999, 401:923-925. []
  2. Nonaka M, Namikawa C, Kato Y, Sasaki M, Salter-Cid L, Flajnik MF: Major histocompatibility complex gene mapping in the amphibian Xenopus implies a primordial organization.Proc Natl Acad Sci U S A 1997, 94:5789-5791. []
  3. Ohta, Y., McKinney, E.C., Criscitiello, M.F., and Flajnik, M.F. 2002. Proteasome, TAP, and class I genes in the nurse shark Ginglymostoma cirratum: Evidence for a stable class I region and MHC haplotype lineages. J. Immunol. 168:771-781.[]
  4. Siddle, H., Deakin, J., Coggill, P., Hart, E., Cheng, Y., Wong, E., Harrow, J., Beck, S., & Belov, K. (2009). MHC-linked and un-linked class I genes in the wallaby BMC Genomics, 10 (1) DOI: 10.1186/1471-2164-10-310[][]
  5. The same Siddle, I believe, who I recently cited for work on the Tasmanian Devil genome a couple of times[]
  6. That is, the same general amino acid sequences[]
  7. Ohta Y, Powis SJ, Lohr RL, Nonaka M, Pasquier LD, Flajnik MF. Two highly divergent ancient allelic lineages of the transporter associated with antigen processing (TAP) gene in Xenopus: further evidence for co-evolution among MHC class I region genes. Eur J Immunol. 2003 Nov;33(11):3017-27.[]
  8. Sherman MA, Goto RM, Moore RE, Hunt HD, Lee TD, Miller MM (2008) Mass spectral data for 64 eluted peptides and structural modeling define peptide binding preferences for class I alleles in two chicken MHC-B haplotypes associated with opposite responses to Marek’s disease. Immunogenetics 60:527–541.[]
  9. MHC diversity: see here and its linked articles, also here and here and linked articles therein[]
March 26th, 2009

HIV escape, one-on-one

Houdini escape - FleischmanIt’s well known that HIV mutates rapidly in infected patients in order to escape from the immune system. The mutations in HIV track with the peptides that bind to MHC class I in any particular patient. When the virus is transmitted to a new patient, though, those mutations don’t help it much, because MHC is so variable between individuals that the new infected person will very likely have a different MHC class I pattern. (In fact, the mutations the virus developed in the first patient, are likely to be actively harmful to the virus.) The virus has to start all over again and discover a new path toward immune escape. Over a long enough time, the virus may be able to slowly accumulate mutations that allow it to escape from the worst of the MHC class I alleles (see here for a possible example), but it’s very difficult, simply because MHC is so diverse.

But MHC class I itself is only the final stage of a longish pathway of antigen presentation — the route by which peptides are produced, modified, transferred into the right location, bind to the right proteins, all that stuff. (If it’s slipped your memory a little, I made a summary page for MHC class I antigen presentation here.) Within that pathway, at least in humans, it’s only the MHC class I heavy chain itself that’s wildly diverse; the other steps are pretty similar between any two individuals. So why doesn’t the virus mutate to avoid one of these monomorphic steps, and then not have to worry about re-mutating all over again after the next transmission?

Putting that less teleologically, why don’t mutations in HIV, that allow it to escape from the monomorphic steps in antigen presentation, persist in each new individual and accumulate within the population? Those mutations should be just as beneficial to the virus in the new infected person as in the original infectee.

Rob de Boer’s group  asked this question recently,1 and found that

… within hosts, proteasome and TAP escape mutations occur frequently. However, on the population level these escapes do not accumulate1

TAP structure - Tampe
TAP structure2

(My emphasis) And the reason is the same reason other immune escape mutations don’t easily accumulate in the population: MHC is too diverse. If I follow the argument correctly, because the other components of the system are monomorphic, they have a very broad specificity for peptides, whereas MHC itself has a fine specificity. The virus can’t mutate every possible sequence in its genome that would interact with, say, TAP, because there would be thousands of them. If a mutation that prevents TAP binding does arise in one host, it’s selected because it prevents recognition of a particular MHC class I-binding peptide, and when it moves into a new host that peptide is no longer relevant for immune escape, so it’s not selected any more.

That means that, even taking the whole antigen presentation pathway into account:

The total number of predicted epitope precursors and CTL epitopes in a large population data set of HIV-1 clade B sequences is not decreasing over time. 1

I am a little cautious about accepting this paper completely, because it’s heavily based on database analysis without a lot of testing; we don’t actually know whether the escape mutations they identify for TAP actually do escape TAP, for example. They make a number of arguments, in passing, for the accuracy of the epitope prediction programs out there; I am slowly backing in to some acceptance of the notion that the predictive programs are getting pretty good, which wasn’t my position a couple of years ago, but I still am not convinced they’re as good as they say here.

But the conclusion is fairly simple and straightforward, and it leads to an interesting suggestion:

… we speculate that only one of the steps in the antigen presentation pathway has to be polymorphic to prevent pathogens from adapting to any step in the pathway. The mechanism functions best when the polymorphy occurs at the most specific step in the pathway, as that increases the fraction of epitope precursors that is not under selection pressure. While in humans it is the MHC class I molecules that are highly polymorphic and specific, other solutions do appear to exist. The TAP molecules of rats are more specific than the human TAP, and have a limited functional polymorphism, and the TAP and MHC genes of chickens are equally polymorphic on the nucleotide level 1

Chicken MHC is an interesting case, and is very strongly linked to resistance to some pathogens. But the reason for the tight linkage to resistance isn’t really known; there’s no obvious reason at the level of the MHC. It might be interesting to look at TAP as part of the resistance, as well.  I have some chicken stuff in the lab, and I should see if we can test that.


  1. Schmid, B., Kesmir, C., & de Boer, R. (2008). The Specificity and Polymorphism of the MHC Class I Prevents the Global Adaptation of HIV-1 to the Monomorphic Proteasome and TAP PLoS ONE, 3 (10) DOI: 10.1371/journal.pone.0003525[][][][]
  2. Structural arrangement of the transmission interface in the antigen ABC transport complex TAP.
    Oancea G, O’Mara ML, Bennett WF, Tieleman DP, Abele R, Tampé R.
    Proc Natl Acad Sci U S A. 2009 Mar 18  doi: 10.1073/pnas.0811260106[]
March 9th, 2009

The next step in the HIV arms race?

Frog & Toad (Arnold Lobel)Any time a species meets some kind of barrier, there’s going to be selection to overcome that barrier.  In the case of pathogens, one major barrier they have to hurdle is their hosts’ immune systems.  What’s more, this isn’t a simple, static barrier.  Immune systems change on a day-to-day basis; and immune systems also change on a population basis, as the individuals in the host population are in turn selected by the pathogen.

Last week I talked about an example where a population — frogs in the UK, in this case — are apparently being selected by a pathogen.   The relatively recent introduction of frog virus 3 into the UK has caused large-scale die-offs of frogs there, and Teacher et al.1 have just shown evidence that the survivors have been selected for a particular MHC class I type.

MHC class I is often associated with resistance to viruses, because it’s responsible for recognition by antiviral T cells.  What probably happens is that viruses sweep through a population, infecting (and imposing a selective pressure on) most members of the population.  A few individuals that happens to have some particular MHC class I type are relatively resistant to the virus, and have a selective advantage; that MHC allele becomes more frequent in the population; and the population as a whole becomes relatively resistant to the virus.  Of course, this now presents a new barrier to the original virus, and there’s selective pressure on it; virus mutants that are resistant to that particular MHC type do better; the virus sweeps through the new population; and a new minority with a different MHC type has a new selective advantage.

This is the most popular model (“frequency-dependent selection”), but it’s been hard to definitively show examples of it because things are happening on a evolutionary timescale. Even with the very rapid (as evolution goes) change in the UK frogs’ MHC, we don’t have all the pieces.  We see that frogs in the UK have a different set of MHC alleles than those frogs that haven’t been exposed to FV3, but we don’t have the population frequencies of these alleles over the time since the virus was introduced.  And we don’t have examples of  the virus accommodating itself to the new MHC; we’d see that as virus sequences changing over time.

Last week I ended the frog story by saying:

Some people may wonder if this frog virus story has any real relevance to humans. Well, apart from the pure scientific interest of tracking a potential frequency-dependent selection event in real time, one of the clearest links between an MHC class I allele and resistance to a viral infection is in humans, where the MHC class I alleles HLA-B27 and HLA-B57 are linked to resistance to HIV and HCV. Is it possible for HIV to adapt at the population level, so that the dominant strains of HIV in the world are no longer contained by HLA-B57? More generally, if we succeed in developing a T cell-based vaccine against HIV, it will probably have strong allele-dependent effects — will HIV adapt to this vaccine?

SeesawAstute readers2 may have guessed that I wasn’t just guessing wildly, and indeed I had already seen the paper from Kawashima et al.,3 on exactly this topic.

Even though HIV is generally incredibly good at ripping through human immune responses without being controlled, there are some people who are long-term non-progressors (LTNP); they’re infected with HIV, yet they manage to control the virus pretty well, without antiviral treatment, for long periods. Many of these people, it turns out, have a particular subset of MHC class I types; they’re much more likely than the general population to have the HLA-B51, HLA-B57, or HLA-B27 MHC class I alleles.

HIV normally mutates very rapidly within infected individuals, so that as an antiviral immune response arises the virus may be temporarily controlled, but the new mutations that arise escape from the immune control and continue to replicate.  It seems that this immune escape is less likely to happen when the individual has one of the LTNP-associated alleles, and that’s probably because the immune target associated with HLA-B51 (etc) is essential for the virus’s survival.  When HIV mutates the immune target, the virus can’t replicate properly.  The only way HIV can escape immune control by people with these MHC alleles is to make multiple mutations at the same time, compensating for the escape mutation with several other changes.  These multiple mutations are exponentially less probable than single mutations, so the virus is essentially controlled, for a long time.

Humans are today a very large, highly mixed population, and it would take a vast plague, even worse than HIV, to rapidly cause frequency changes that we could measure in the brief period since HIV become common.4  But that hasn’t always been true; humans historically have included relatively small and isolated populations subject to intense disease selection, and we believe we see the outcome of that today in that different human populations  have different frequencies of HLA-B51, B57, and B27 — the equivalent of frogs in the UK vs. elsewhere.

What’s happening to HIV in those areas where HLA-B51 is common?  The prediction is that viruses that have managed to make the mutations that give resistance to HLA-B51 should have a selective advantage in those areas that isn’t seen elsewhere.  That’s precisely what Kawashima et al. saw.

… the frequency of these epitope variants (n = 14) was consistently correlated with the prevalence of the restricting HLA allele in the different cohorts (together, P < 0.0001), demonstrating strong evidence of HIV adaptation to HLA at a population level.  3

HLA-B51 + HIV peptide
HLA-B51 complexed with an immunodominant HIV peptide

Immune escape isn’t the only selective pressure on HIV.  There’s the ability to spread from one individual to another, for example, which isn’t necessarily linked to immune escape.  In principle, some of the other selective factors may counteract immune escape selection.  And in general, some (though not all) of the mutations that allow a virus to escape immune control by on individual are harmful to the virus. That means that some of the escape sequences will quickly revert back to the generic HIV sequence. If HLA-B51 is rare in the population, the virus will constantly be reverting back to generic sequences and the HLA-B51-resistant strain will not particularly accumulate.  But if HLA-B51 is common, even these reverting sequences will build up in the population.

As anticipated, non-reverting variants such as I135X accumulate at the population level, but even rapidly reverting mutations such as T242N can accumulate, if the selection rate exceeds the reversion rate 3

Perhaps as a result, formerly-protective MHC alleles are no longer protective in some areas:

Data here suggest that, whereas 25 years ago HLA-B*51 was protective in Japan, this is no longer the case. The apparent increase in I135X5 frequency in Japan over this time supports the notion that HLA-B*51 protection against HIV disease progression hinges on availability of the HLA-B*51-restricted TAFTIPSI6  response. However, whether this is the case remains unknown. 3

Any effective anti-HIV vaccine will probably rely on antiviral T cells, and will therefore rely on MHC class I presentation.  What this paper suggests is that HIV is likely to be a moving target.  Even if an effective vaccine is developed, it is possible that the virus will gradually evolve resistance to the vaccine.

Thus, the data presented here, showing evidence that the virus is adapting to CD8+ T-cell responses, … highlight the dynamic nature of the challenge for an HIV vaccine. … The induction of broad Gag-specific CD8+ T-cell responses may be a successful vaccine strategy, but such a vaccine will be most effective if tailored to the viral sequences prevailing, and thus may need to be modified periodically to keep pace with the evolving virus.  3

Since we still don’t have any vaccine that protects against HIV at all, this is pretty much a hypothetical worry.  Still, it’s something to think about for the future.


  1. Amber G. F. Teacher, Trenton W. J. Garner, Richard A. Nichols (2009). Evidence for Directional Selection at a Novel Major Histocompatibility Class I Marker in Wild Common Frogs (Rana temporaria) Exposed to a Viral Pathogen (Ranavirus) PLoS ONE, 4 (2) DOI: 10.1371/journal.pone.0004616[]
  2. The only kind I have, I’m sure[]
  3. Yuka Kawashima, Katja Pfafferott, John Frater, Philippa Matthews, Rebecca Payne, Marylyn Addo, Hiroyuki Gatanaga, Mamoru Fujiwara, Atsuko Hachiya, Hirokazu Koizumi, Nozomi Kuse, Shinichi Oka, Anna Duda, Andrew Prendergast, Hayley Crawford, Alasdair Leslie, Zabrina Brumme, Chanson Brumme, Todd Allen, Christian Brander, Richard Kaslow, James Tang, Eric Hunter, Susan Allen, Joseph Mulenga, Songee Branch, Tim Roach, Mina John, Simon Mallal, Anthony Ogwu, Roger Shapiro, Julia G. Prado, Sarah Fidler, Jonathan Weber, Oliver G. Pybus, Paul Klenerman, Thumbi Ndung’u, Rodney Phillips, David Heckerman, P. Richard Harrigan, Bruce D. Walker, Masafumi Takiguchi, Philip Goulder (2009). Adaptation of HIV-1 to human leukocyte antigen class I Nature DOI: 10.1038/nature07746[][][][][]
  4. Someone who knows about evolution could probably attach some numbers to this.[]
  5. I135X is the HIV sequence that’s escaped HLA-B51 control[]
  6. TAFTIPSI is the original HIV sequence that’s controlled by HLA-B51[]
March 2nd, 2009

Evolution snapshot: Frogs vs. virus

Altamira Ushigaeru '94
Ushigaeru (Bullfrog) – Takeda Hideo, 1994

Pathogens and their hosts tend to co-evolve — not necessarily to a peaceful co-existence, though. Often it’s an arms race: Individuals that are resistant to the pathogen leave more offspring, and resistance spreads through the population; then pathogens that can infect the formerly-resistant hosts are selected and spread; and a new subset of the hosts begin to do better and their genes spread through the population.

(Of course, the other possibility is that the host or the pathogen will develop resistance too slowly, and one or the other will go extinct, at least locally.)

This back-and-forth seesawing is, of course, a multi-generation thing, and so it’s hard to watch it happening in real time. We’re more likely to see snapshots in time, where either the pathogen or the host has temporarily got the upper hand. In some cases we may be able to watch parts of it happen in motion.  I’ve mentioned some examples earlier — Marek’s Disease in chickens, myxomavirus in Australian rabbits here and here — but even there we’re talking about many decades of evolution.

In the late 1980s, frogs in the UK began to die by the tens of thousands. It turned out that a new virus had entered the UK, a member of the ranavirus family. Ranaviruses are relatively recently-recognized pathogens, and there’s a lot of evidence that they’re being spread by human activities, though I don’t know that the specific UK ranavirus has been shown to have entered that way. Ranavirus-associated die-offs have recently been identified in North America, too, though so far it’s not at the same level as in the UK — though it’s likely just a matter of time. (Ranaviruses are not, by the way, the major cause for the world-wide die-off of amphibians in general, which may be more directly caused by a fungal infection.)

The class I major histocompatibility complex (MHC class I) is heavily involved in resistance to viruses. MHC class I arose about 450 million years ago (Ah, how well I remember it) in the shark lineage, and it’s present in all vertebrates, though in many combinations and variations. The MHC region of the genome is also incredibly diverse (that is, individuals in a species are likely to have a different MHC sequence from other individuals); it’s by far the most variable region of the vertebrate genome, with some 1000 alleles identified in humans.

Frog would a-wooing go
Arents Cigarette Cards (1932-1934)

In general it’s agreed that the underlying reason for MHC diversity is that the diversity helps with resistance to pathogens. The details of how pathogen resistance drives that diversity are debated, and I’ve talked about those reasons before (see here and its linked articles, also here and here and linked articles therein). But pretty much all the models agree that if a particular MHC allele is associated with increased resistance to a common pathogen, that allele should become more common in the population.

It’s pretty hard to actually measure that in a real population, pathogens being uncooperative and populations being moving targets and all. So when we see, for example, that humans in malaria-prone regions are more likely to have one particular MHC class I allele that might give some protection against malaria,1 we can’t really be certain that the particular allele in that area has increased over time, or that malaria resistance has driven the hypothetical increase. Changes in MHC allele frequency might be driven by natural selection, but it would take a pretty terrible plague to cause easily detected changes over a short time.

The UK ranavirus epidemic may be one such plague. Teacher et al2 have looked at the MHC region of wild Common Frogs (Rana temporaria), and compared the alleles in a population of frogs in the thick of the ranavirus epidemic, to one not exposed. The ranavirus-selected frogs are much more likely to have a particular group of MHC class I alleles, suggesting that these frogs have been selected for resistance to the virus.

Rana temporaria
Rana temporaria

This is only a suggestion at the moment, because for one thing there was no evidence that the frogs with the putative resistant allele were, in fact, more resistant to ranavirus. That should be a doable experiment, though. It’s a starting point for further work, and for further snapshots to see how the frog and virus populations co-evolve, because one particularly interesting question is how the virus is adapting to this newly-abundant population of resistant frogs.3

One popular model for MHC diversity is frequency-dependent selection — a rare MHC allele happens to confer resistance to an important pathogen, individuals with that allele are selected, the allele becomes common, and then the pathogen adapts in turns — mutates so that the allele no longer confers protection — and a new rare allele is selected instead. I don’t know of any clear examples where each step in this model has been shown, probably because we can only see the snapshots, not the moving picture. Here’s an opportunity to see the whole story.

We’re at a point where we almost have the technology to track the whole ranavirus genome over time. You may remember the foot-and-mouth disease outbreak a couple years ago, where researchers were able to sequence whole genomes from the FMD virus as it spread among farms, mutating as it went — we aren’t quite at the point where we can do that with ranavirus (it’s a member of the iridovirus family, which have much, much larger genomes than the FMD virus) but we’re close; storing virus snapshots captured over time will pay off in a few years.

Some people may wonder if this frog virus story has any real relevance to humans. Well, apart from the pure scientific interest of tracking a potential frequency-dependent selection event in real time, one of the clearest links between an MHC class I allele and resistance to a viral infection is in humans, where the MHC class I alleles HLA-B27 and HLA-B57 are linked to resistance to HIV and HCV. Is it possible for HIV to adapt at the population level, so that the dominant strains of HIV in the world are no longer contained by HLA-B57? More generally, if we succeed in developing a T cell-based vaccine against HIV, it will probably have strong allele-dependent effects — will HIV adapt to this vaccine? I’ll talk more about that next week.


  1. Hill AVS, Allsopp CEM, Kwiatkowski D, Anstey NM, Twumasi P, et al. (1991) Common West African HLA antigens are associated with protection from severe malaria. Nature 352: 595-600.[]
  2. Amber G. F. Teacher, Trenton W. J. Garner, Richard A. Nichols (2009). Evidence for Directional Selection at a Novel Major Histocompatibility Class I Marker in Wild Common Frogs (Rana temporaria) Exposed to a Viral Pathogen (Ranavirus) PLoS ONE, 4 (2) DOI: 10.1371/journal.pone.0004616[]
  3. Assuming, of course, that this MHC allele does confer resistance[]
October 6th, 2008

Sex, stats, and sweat

Sweaty t shirtIt’s been suggested for a long time that mice select mates by smelling MHC types, perhaps in the urine. MHC is by far the most variable region in vertebrate genomes, so this would offer a way for mice to avoid inbreeding: The more related the mice, the more likely they are to be similar at the MHC, so selecting a different MHC will help avoid inbreeding.

Partly as an argument by analogy, and partly through some rather poor-quality experiments, it’s also been argued that humans select mates the same way — that differences in MHC type make a partner more desirable. These are the notorious sweaty T shirt experiments that most people seem to have at least vaguely heard of.

I started off very skeptical about the human claims, because the quality of the experiments has, as I say, tended to be poor. There have been small numbers of people, indifference to alternative explanations, and a lot of post hoc hand-waving. (If the preferences turned out to be reversed, why, it was because the female was near her period, or something like that.) I think that most people who have actually looked at the data have had similar reservations, but that hasn’t stopped the concept from becoming pretty well known.

MHC & mate choice I became even more skeptical about the human experiments as I learned more about the mouse data. The evidence for MHC as a mechanism for avoiding inbreeding turned out to be relatively weak, or at least inconsistent (see here for my first discussion); and recently a paper that I found fairly convincing (discussed here) suggested that MHC is not in fact used by mice in this way at all — rather, a much more plausible, highly variable family of molecules called “major urinary proteins” (MUPs) are the source of the anti-inbreeding odor in mouse urine.

Much of the interest in human MHC and sex has been driven by the mouse observation, so I think that if mice don’t use MHC to select mates, then likely humans don’t, either. Still, it remains possible, even probable, that difference species use different methods to select mates. And since humans don’t even have variable MUPs (as far as I know) MHC remains in the chase.

A recent paper1 tries to look at this in a more objective manner, using genome-wide data on couples. Unfortunately the numbers are still quite small (just 30 couples each from a European-American subset, and an African subset) and the results remain slightly ambiguous. Their conclusion was that

African spouses show no significant pattern of similarity/dissimilarity across the MHC region … We discuss several explanations for these observations, including demographic effects. On the other hand, the sampled European American couples are significantly more MHC-dissimilar than random pairs of individuals … This study thus supports the hypothesis that the MHC influences mate choice in some human populations.

So, heads we win, tails you lose, because even though their hypothesis was invalidated overall, some post-hoc wiggling (“demographic effects”) lets them dismiss the data they don’t like.

I’m still pretty skeptical about any real effect from MHC on mate choice. I’m willing to be convinced otherwise, but it’s going to take a larger and more rigorous study than this one to make me interested.


  1. Raphaëlle Chaix, Chen Cao, Peter Donnelly, Molly Przeworski (2008). Is Mate Choice in Humans MHC-Dependent? PLoS Genetics, 4 (9) DOI: 10.1371/journal.pgen.1000184[]
July 14th, 2008

Unconventional antiviral immunity

Mouse polyomavirus
Mouse polyomavirus

When we talk about anti-viral T cells, we’re usually talking about cytotoxic T lymphocytes (CTL) that recognize a peptide in association with class I major histocompatibility complexes (MHC class I). MHC class I is extremely polymorphic; there are many hundreds of different MHC class I alleles.

At any rate, that’s true for the classical MHC class I genes. But as well as classical MHC class I, there are also (you’ll never guess) non-classical MHC class I genes. Lots of them. For the most part we don’t really know quite what they do. Typically they’re not very polymorphic, compared to classical class I alleles. Since the major hypotheses explaining which there are so many classical MHC class I alleles involve protection against pathogens, this might hint that non-classical MHC class I don’t behave like classicals — either they don’t protect against pathogens at all, or they do so in a very different way.

Both of these possibilities are true for various non-classicals. For example, some of the non-classical MHC class I genes act as ligands for natural killer (NK) cells, which do recognize pathogens but do so in a very different manner than do CTL. Other non-classicals seem to have little to do with pathogen recognition — there are iron-binding molecules, neuronal molecules, and so on.

But a paper from Aron Lukacher’s lab1 suggests that at least some non-classical MHC class I genes can act much like the classical genes, which has interesting implications for anti-viral vaccines.

There are mice that have no classical MHC class I genes at all. (Hidde Ploegh’s lab generated them, by crossing mice lacking the H-2K MHC class I gene with those lacking the H-2D MHC class I gene. Since these genes are side by side, the frequency of crossing-over is very low, and Ploegh got the mice by pure brute force, examining thousands of mice to find the single mouse that had crossed over appropriately to generate a double knockout. I have always felt a mixture of admiration and sympathy for the post-doc assigned that project.) These mice actually do reasonably well as far as controlling viruses — the immune system is highly redundant, and there are many antiviral systems in play – so it wasn’t a huge surprise to find that the classical MHC class I-less mice could control infection with polyomavirus quite well.

What was a surprise was that eliminating CD8 T cells also eliminated polyomavirus control. 2 If there’s no classical MHC class I, what could the CD8 T cells be recognizing? The answer turned out to be, non-classical MHC class I. 3 WIth a bit more mapping, it seems that the CD8 T cells were recognizing a non-classical MHC class I gene called “Q9″ (catchy, eh?).

Qa-2 non-classical MHC class IQ9 is a member of the Qa-2 family, which I have always believed were involved in natural killer cell recognition,4 although in retrospect I see that there’s evidence that CD8 T cells can recognize them.5  That’s a picture of Qa-2 off to the right (click for a larger version), and there are more images of it in my previous post comparing the different types of MHC.

What’s more, the CD8 cells recognize a really pretty conventional epitope. Classical MHC class I alleles present peptides that are around 9 amino acids long, while various non-classical proteins present anything from glycolipids to nothing at all. The Q9 complex turned out to present a rather boring 9-amino acid peptide6 that, to my eye, could have been cheerfully presented by any of a hundred classical MHC class I complexes.

So basically, this is a very conventional-looking anti-viral response, but directed against an unconventional MHC. There are occasional hints in the literature that this might be more than a one-off,7  though it’s not clear how common it is.  (This unconventional response might normally be drowned out by the conventional response, so that it’s hard to see unless you look in the MHC class I knockout mice.)

Why is this interesting (apart from the obvious point that anything remotely to do with MHC is intrinsically interesting, of course)? As I said, classical MHC is highly polymorphic, while non-classical MHC is not. There are only a handful of Q9 alleles known. If you made an antiviral vaccine with a peptide that binds to Q9, it should work in most mice, whereas if you make a similar vaccine directed to classical MHC class I, you’d need to tailor the vaccine to each individual mouse strain. Humans don’t have Q9 (the non-classical MHC are much less conserved between species than are the highly conserved classicals), but they do seem to have analogous proteins that are non-polymorphic and that may be able to work in antiviral contexts.

There’s a couple of other interesting things about this (Q9 binds to a wide range of peptides,8 for example, which reminds me of an existential question I had that was prompted by chicken MHC; and Lukacher makes the interesting suggestions that polyomavirus and Q9 might be the product of specific co-evolution), but I have a pair of intrepid little boys who camped out in our back yard for the first time last night, and they are proudly hiking the five feet to the house to tell me all about it now.


  1. Swanson, P.A., Pack, C.D., Hadley, A., Wang, C., Stroynowski, I., Jensen, P.E., Lukacher, A.E. (2008). An MHC class Ib-restricted CD8 T cell response confers antiviral immunity. Journal of Experimental Medicine, 205(7), 1647-1657. DOI: 10.1084/jem.20080570[]
  2. At any rate, the virus titre went up something like 50-fold.[]
  3. A clue came from their previous finding the mice lacking β2-microglobulin were highly susceptible to polyomavirus infection. Many, though not all, non-classical MHC class I proteins need β2-m to form a normal structure.[]
  4. The nonclassical major histocompatibility complex molecule Qa-2 protects tumor cells from NK cell- and lymphokine-activated killer cell-mediated cytolysis. Chiang EY, Henson M, Stroynowski I. J Immunol. 2002 Mar 1;168(5):2200-11. []
  5. Chiang, E.Y., and I. Stroynowski. 2005. Protective immunity against disparate tumors is mediated by a nonpolymorphic MHC class I molecule. J. Immunol. 174:5367-5374.
    and
    Correction of defects responsible for impaired Qa-2 class Ib MHC expression on melanoma cells protects mice from tumor growth. Chiang EY, Henson M, Stroynowski I. J Immunol. 2003 May 1;170(9):4515-23. []
  6. HALNVVHDW[]
  7. For example, Braaten, D.C., J.S. McClellan, I. Messaoudi, S.A. Tibbetts, K.B. McClellan, J. Nikolich-Zugich, and H.W. Virgin. 2006. Effective control of chronic {gamma}-herpesvirus infection by unconventional MHC Class Ia-independent CD8 T cells. PLoS Pathog. 2:e37.[]
  8. Promiscuous antigen presentation by the nonclassical MHC Ib Qa-2 is enabled by a shallow, hydrophobic groove and self-stabilized peptide conformation.  He X, Tabaczewski P, Ho J, Stroynowski I, Garcia KC.  Structure. 2001 Dec;9(12):1213-24.[]