Mystery Rays from Outer Space

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

November 3rd, 2010

Shield or target? A downside of immune evasion

T cells & herpes simplex
T cells (green) and herpesvirus-infected cells (red)
(from Akiko Iwasaki)

We know that lots of viruses, especially herpesviruses, block antigen presentation. The assumption has been that they are thereby preventing T cells from recognizing infected cells, though long-term readers of this blog1 will know that I’ve been puzzled about the details of this for quite a while.

A recent paper2 raises yet another complication for this pathway: In humans3 there are T cells that specifically recognize cells in which antigen presentation is blocked:

Our data indicate that the human CD8+ T cell pool comprises a diverse reactivity to target cells with impairments in the intracellular processing pathway2

If so, you might wonder why the viruses would bother blocking antigen presentation. They might avoid recognition by T cells specific for the viral proteins, but at the cost of being recognized and eliminated by the T cells that recognize antigen-presentation-defective cells.

As always, I don’t have an answer. I do have the unhelpful observation that viruses are incredibly subtle and efficient, and given that herpesviruses have apparently maintained the ability to block antigen presentation for some 400 million years it’s presumably useful to them. I’ll also add the even more unhelpful observation that immune systems are also incredibly subtle and efficient and have also persisted for 450 million years.

How Not to be Seen

However, there may be a clue in the techniques that Lampen et al used to turn up this subset of T cells: They used multiple rounds of stimulation, which is going to expand these cells massively. We don’t know how abundant they are inside a normal human – perhaps they are so rare that they don’t have a chance to impinge on herpesvirus infection early enough.

The catch with that, though, is that tumors also frequently get rid of antigen presentation via mutation; in fact, eliminating antigen presentation seems to be one of the most common forms of mutations in cancers, suggesting that it’s an important part of their ability to survive and expand in the face of immune attack. Tumors are immunologically present much longer than viruses ((Although herpesviruses set up a lifelong infection, most of that is generally in a non-immunogenic, latent form). So why doesn’t this long-term tumor presence lead to amplification of these antigen-presentation-deficient-specific T cells that would eliminate the tumor?

My guess here is that this is where TRegs come in. As I said in a recent post, TRegs are very commonly, if not universally, associated with tumors, and prevent immune attack on the tumor. I wonder if the tumors mutate to avoid T cell recognition early in their development, before they are able to trigger the TReg response; that allows them to grow large enough and long enough that by the time the presentation-defect-destroyers kick in, the tumors have their TReg defenders set up.  (I admit that this doesn’t account for the correlation between a tumor’s loss of antigen presentation, and poor prognosis, but I leave this as an exercise for the reader.)

And, of course, where either of these defense systems for the proto-tumor fails, we normally would simply not see any tumor at all. Perhaps this is happening all the time inside us — proto-tumors are being eliminated by T cells, some are mutating their antigen presentation pathway and lasting a little longer and are then eliminated by a different subset of T cells, and we never know it.


  1. If any[]
  2. Lampen, M., Verweij, M., Querido, B., van der Burg, S., Wiertz, E., & van Hall, T. (2010). CD8+ T Cell Responses against TAP-Inhibited Cells Are Readily Detected in the Human Population The Journal of Immunology DOI: 10.4049/jimmunol.1001774[][]
  3. As has been previously shown in mice[]
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 9th, 2010

Immune evasion versus superinfection

HCMV from J Virol
Human cytomegalovirus-infected cell

A number of viruses, especially herpesviruses, block the MHC class I antigen presentation system. It’s been widely assumed that this is for the obvious reason and that it allows the virus to avoid T cell recognition and elimination. But there’s been an awkward lack of experimental support for that assumption, to the point that I’ve begun to question it (and, more productively, to develop experimental systems with which to test it).   (See the list of posts below for some of my earlier comment on the subject.)

Now, at last, Klaus Fruh offers actual evidence that this assumption may be correct. 1

This deserves a long post, which it’s not going to get today.2 Briefly, Klaus’s group used a herpesvirus of monkeys (rhesus cytomegalovirus; rhCMV) to test this. This is closely related to the human herpesvirus human cytomegalovirus, which is a ubiquitous virus; the vast majority of humans have it, are infected with it as toddlers, remain infected with it throughout their lives, and don’t suffer any problems with it. It’s a rare cause of a mono-like disease, and it’s a concern in immune-suppressed people (especially transplant recipients), but mainly it seems to be a pretty innocuous hitchhiker.

Previous posts on MHC class I immune evasion

Immune evasion does work
Herpesvirus immune evasion: An emerging theme?

Immune evasion: Who needs it?

Viral T cell evasion in vivo: The vanishing evidence

Immune evasion: What is it good for?

The CMV family of herpesviruses carry a particularly impressive arsenal of anti-MHC class I immune evasion genes. (MHC class I is the target that antiviral T cells, also known as cytotoxic T lymphocytes or CTL, recognize. There’s an outline of the process that permits that recognition here.) Whereas herpesviruses like herpes simplex, or chicken-pox virus, and so on, seem to use only one gene to block MHC class I, CMVs seem to use three or four. This would suggest that this sort of immune evasion is really important for these viruses, but when Ann Hill actually tested that notion in mice3 removing these immune evasion genes had only a very small impact.

Fruh’s group has now done something similar using his rhesus model, and looked at an unusual characteristic of CMVs: They are able to repeatedly superinfect the same host. That is, someone4 can be infected with CMV, can have an apparently effective immune response to CMV, and yet can be infected by a new CMV virus. This is pretty unusual, of course. You’d expect that there would be a vaccine-type effect, in which the natural infection would drive a protective immune response. As far as I know, you don’t often see this sort of superinfection even with other herpesviruses, which is why, for example, the chicken-pox vaccine works.

Virus-Cell Interaction; Joerg Schroeer; Art of Science
“Human cytomegalovirus infected human endothelial cells”
by Joerg Schroeer

They made a pretty drastic mutant of the RhCMV to eliminate all four of the MHC class I immune evasion genes (taking out another half-dozen genes as collateral damage, but they checked that these weren’t confounding the story). This mutant virus, in spite of having completely lost its ability to block MHC class I, was perfectly able to infect monkeys and to set up a long-term infection — just like Ann Hill’s findings with mouse CMV. What the mutant virus was not able to do was superinfection.

Together, our results suggested that RhCMV was unable to superinfect in the absence of the homologs of US2, US3, US6, and US11 because the virus was no longer able to avoid elimination by CTL. 5

But when the pre-infected monkeys had their CTL temporarily eliminated, then the mutant viruses were able to superinfect. What’s more, after the virus got in and set up its new infection, CTL couldn’t clear them, even though the viruses still had no ability to evade MHC class I:

Our data imply that T cell evasion is not required for establishment of primary CMV infection or once the sites of persistence (e.g., kidney and salivary gland epithelial cells) have been occupied, but rather it is essential to enable CMV to reach these sites of persistence from the peripheral site of inoculation in the CMV-immune host. 5

This is really cool stuff. It offers an explanation for why Hill’s group didn’t see an effect for MHC class I immune evasion in their mouse CMV model — they didn’t specifically look at superinfection, though they looked at many other aspects of infection. (Does mouse CMV superinfect as robustly as human?)  It also offers an explanation for why experimental CMV vaccines have been ineffective — the immune evasion functions allow the virus to temporarily evade the immune response.

As I say, I don’t think superinfection is so common in other families of herpesviruses, so this may not be a universal explanation for MHC class I immune evasion by herpesviruses; but then, it’s been the CMV system that’s been most puzzling, anyway, so we may not need to go so far to look for answers after all.


  1. 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[]
  2. I’m still chilling with my kids on their spring break, not to mention a dozen other distractions[]
  3. Gold, M. C., Munks, M. W., Wagner, M., McMahon, C. W., Kelly, A., Kavanagh, D. G., Slifka, M. K., Koszinowski, U. H., Raulet, D. H., and Hill, A. B. (2004). Murine cytomegalovirus interference with antigen presentation has little effect on the size or the effector memory phenotype of the CD8 T cell response. J Immunol 172, 6944-6953.

    Pinto, A. K., and Hill, A. B. (2005). Viral interference with antigen presentation to CD8+ T cells: lessons from cytomegalovirus. Viral Immunol 18, 434-444.

    Lu, X., Pinto, A. K., Kelly, A. M., Cho, K. S., and Hill, A. B. (2006). Murine cytomegalovirus interference with antigen presentation contributes to the inability of CD8 T cells to control virus in the salivary gland. J Virol 80, 4200-4202.[]

  4. Or some monkey[]
  5. 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[][]
January 6th, 2010

How could vaccinia virus block T helpers?

Smallpox pustules (R. Carswell, 1831)
Smallpox pustules
(R. Carswell, 1831)

In contrast to the many viruses that block antigen presentation by MHC class I, only a handful appear to block presentation by MHC class II.  I don’t understand why any would try to block MHC class II in the first place, but another example of it has just been published.

A little background: Major histocompatibility complexes (MHC) are recognized by T cells. T cells come in several flavors, the best-understood of which are CD4 (T Helper) and CD8 (cytotoxic T lymphocyte; CTL) lymphocytes. CD8 T cells are fairly specialized to deal with cells infected with viruses;1 they recognize MHC class I. CD4 T cells are at the top of the adaptive immune response; they coordinate subsequent responses, by calling in other cell types, driving antibody or CTL responses, and so on.

MHC class I is on the surface of most cells, as you’d expect, because most cells can be infected with viruses. MHC class I is, among other things, a way of directing the CTL attack to the appropriate, virus-infected, cell, and so they deal, fairly strictly, with what’s going on inside their own particular cell. They don’t take up proteins from outside the cell, because then the cell might get killed when it’s actually a neighbor that’s infected. 2

MHC class II, on the other hand, is a general alarm call that signals “Something’s invading the body, somewhere”. MHC class II is only on a limited number of cells, but those cells do take up protein from outside themselves and show it to CD4 T cells. Presentation on MHC class II does not mean that the particular cell is infected.

So it’s quite logical that viruses would be interested in blocking MHC class I, and as I say there are now many examples of viruses that do so. It’s also logical for viruses to want to block MHC class II, since doing so would reduce all the immune responses against them — antibodies, T cells, whatever.

But how would that work? Again: The cells that do MHC class II antigen presentation are not necessarily infected cells. If a virus is going to block MHC class II, it would have to go out of its way infect the MHC class II-presenting cells (known as professional antigen-presenting cells; APC). Not only that, it would probably have to infect a lot of them, to make a real impact on the overall CD4 T cell response, because even a few unaffected APC will drive a fairly significant immune response, making the suppressed ones irrelevant.

So even though viruses might “want” to block MHC class II, there are practical problems that make it hard to do. Nevertheless, there are a couple of viruses who have genes that can block MHC class II. Human cytomegalovirus is the clearest example, I think,3 and several groups have shown that vaccinia virus blocks MHC class II presentation in infected cells.4 Now a paper in Virology5 argues that the vaccinia gene catchily called “A35″ is responsible for this block. Since close relatives of A35 are present in many other poxviruses, MHC class II blockade may be widespread in this family.

A35 colocalizes with RhoB in endosomes
Colocalization between A35 and RhoB in endosomes5

The data are reasonably convincing, though there are some complications. 6 But I’m still puzzled by how this is supposed to work. Vaccinia virus, and poxviruses in general, aren’t renowned for infecting dendritic cells and macrophages, which are the cell types they’d have to efficiently target if MHC class II blockade was to help them.

Removing A35 from vaccinia makes it much less virulent in mice:

A mutant A35 deletion virus (A35?) replicated normally in several tissue culture cell lines, but was highly attenuated (100–1000 fold) in the intranasal and intraperitoneal mouse challenge models7

And apparently this is associated with a reduced immune response to the virus:

Thus far our animal model data are consistent with this hypothesis, showing a reduction in both VV specific antibody and splenic T lymphocyte responses. 8

Which is consistent with a blockade of MHC class II, true, but if you have reduced viral replication for any reason you’d also expect reduced immune responses, because there would be less viral antigen to drive the response. That is, even though A35 blocks MHC class II, and A35 increases virulence, I’m not convinced that A35 increases virulence because it blocks MHC class II. Viral proteins are notoriously multifunctional, and I wonder if the MHC class II blockade is just one function of A35; or perhaps even if it’s just a side-effect of the “real” virulence function.

I’m open to the notion that A35 (and other viral proteins) are true MHC class II blockers, and that this is functionally important, but I’d like to see more data before I put it in the bank.


  1. Also, intracellular bacteria, intracellular parasites, and tumor cells[]
  2. There are exceptions to this rule, including an important phenomenon called “cross-priming” or “cross-presentation”, but that’s not relevant to this discussion now.[]
  3. For example, Johnson DC, Hegde NR. Inhibition of the MHC class II antigen presentation pathway by human cytomegalovirus. Curr Top Microbiol Immunol. 2002;269:101-15.[]
  4. For example, Li, P., Wang, N., Zhou, D., Yee, C.S., Chang, C.H., Brutkiewicz, R.R., Blum, J.S., 2005. Disruption of MHC class II-restricted antigen presentation by Vaccinia virus. J. Immunol. 175 (10), 6481–6488.[]
  5. Rehm, K., Connor, R., Jones, G., Yimbu, K., & Roper, R. (2009). Vaccinia virus A35R inhibits MHC class II antigen presentation Virology DOI: 10.1016/j.virol.2009.11.008[][]
  6. For example, it looks as if there may be other genes, besides A35, that also contribute to MHC class II blockade.[]
  7. Roper, R.L., 2006. Characterization of the Vaccinia virus A35R protein and its role in virulence. J. Virol. 80 (1), 306–313.[]
  8. Rehm, K.E., Jones, G.J.B., Tripp, A.A., Metcalf, M.W., and Roper, R.L., in press. The Poxvirus A35 Protein is an Immunoregulator. J. Virol.[]
November 4th, 2009

Tumor TRegs are more focused than I expected

TRegs infiltrate a tumor
TRegs infiltrate into a tumor

One of the reasons the immune system doesn’t destroy tumors is the presence of regulatory T cells (TRegs) that actively shut down the anti-tumor response.  For once, there’s a little bit of encouraging news on that front.

TRegs are normal parts of the immune system.  They actively prevent other T cells (and so on) from attacking their target. 1  What’s more, TRegs are antigen-specific.  That is, they recognize a specific target, just as do other T cells, but instead of responding by, say, destroying the cells (like  cytotoxic T lymphocyte) or by releasing interferon (like a T helper cell) a TReg’s response to antigen is to prevent other T cells from doing anything in response to that antigen.  In other words, TRegs cause an antigen-specific inhibition of the conventional immune response. 2

Back to tumors.  We know that immune responses don’t routinely eliminate tumors by the time they’re detectable.  There is some evidence that lots of very small, proto-tumors, are in fact destroyed by the immune system very early on, before they’re clinically detectable, but those tumors that survive that attack seem to be pretty resistant to immune control.  At least part of that resistance is because TRegs get co-opted into the tumor’s control (see here, and references therein, for more on that).

So if TRegs are antigen-specific, and TRegs control immune responses to the tumor, what are the tumor antigens that are driving the TRegs?

I would have assumed that TRegs are looking at many, many tumor antigens, including both normal self antigens3 as well as classical tumor antigens.4  But a recent paper5 suggests, to my surprise, that this assumption is wrong.  Instead, “Tregs in tumor patients were highly specific for a distinct set of only a few tumor antigens“. 5 What’s more, eliminating TRegs cranked up the functional immune response, but only to those antigens TRegs recognized — as you’d expect, if the suppression is indeed antigen specific.

This is interesting for several reasons.  If TRegs can be specific for tumor antigens, then at least in theory ((In practice, we don’t quite have the tools yet, I think) it should be possible to turn off these TRegs while leaving the bulk of TRegs intact (and therefore not precipitating violent autoimmunity).  It also suggests that if the TRegs are only suppressing a subset of effector T cells, there’s something else preventing most effector T cells from, well, effecting.  Maybe those are antigen non-specific TRegs, or maybe there’s something else we need to know about.

I’d like to see this sort of study replicated, and a little more fine-tuning on identifying the TReg’s targets (the readout was intentionally fairly coarse here, in order to identify as many as possible).  Still, it’s an unexpected, and potentially very useful, observation.


  1. It’s still not quite clear how they do this[]
  2. There are also antigen-nonspecific TRegs, but we will ignore them for now.  They’re not as effective as the antigen-specific sort, anyway.[]
  3. Because TRegs, unlike most immune cells, can be stimulated by normal self antigens[]
  4. That is, antigens that are mutated, or dysregulated, and that therefore act as standard targets for immune cells[]
  5. Bonertz, A., Weitz, J., Pietsch, D., Rahbari, N., Schlude, C., Ge, Y., Juenger, S., Vlodavsky, I., Khazaie, K., Jaeger, D., Reissfelder, C., Antolovic, D., Aigner, M., Koch, M., & Beckhove, P. (2009). Antigen-specific Tregs control T cell responses against a limited repertoire of tumor antigens in patients with colorectal carcinoma Journal of Clinical Investigation DOI: 10.1172/JCI39608[][]
October 28th, 2009

On designing malaria vaccines

Our deepening knowledge of the immune evasion mechanisms of malaria is revealing the parasite’s ability to orchestrate the human immune response. … It would thus seem futile to test novel antigens or vaccine platforms without first incorporating features designed to circumvent parasite immune evasion strategies. … The prominent feature of a successful vaccine targeting chronic infectious agents such as malaria may therefore not be the antigens it includes, but rather the strategy used to free the immune system from its shackles.

Casares, S., & Richie, T. (2009). Immune evasion by malaria parasites: a challenge for vaccine development Current Opinion in Immunology, 21 (3), 321-330 DOI: 10.1016/j.coi.2009.05.015

September 17th, 2009

Stealth influenza

"Avoid influenza, gargle daily"
“How to avoid influenza: Gargle Daily”

Every virus that infects a vertebrate, has to be able to deal with the vertebrate immune system. The virus’s ancestors that infected vertebrates must have been able to deal with the vertebrate immune system. Those viruses that couldn’t handle an immune response are extinct.

Some of the ways viruses handle immunity, we don’t think of as really “specific”. Rapid replication, for example, has benefits for the virus that extend past just beating the immune system to the punch. But just about every virus, even the smallest ones, also have some form of specific immune evasion gene — some way of blocking, dodging, diverting, or confusing the immune system.

In spite of this nearly universal presence, we don’t really have a good grasp of precisely what viral immune evasion genes do, as far as supporting viral pathogenesis. (For that matter, it’s only for a handful of viruses that we really have much understanding of the pathogenesis in general.) Some viruses have a huge number of genes that are clearly immune evasion genes, others apparently only have one or two. Sometimes you can knock out an immune evasion gene and virtually destroy the virus’s ability to infect; sometimes the knockout only has a modest effect; sometimes there’s no effect at all, or it may even make the virus more, rather than less, virulent.

Viruses are so different from each other1 that there are probably few if any general rules for immune evasion. Still, we’re not even at a point yet where we have non-general rules, so the more we learn the more likely we are to see patterns.

Physicians thank influenza (1803)
Physicians expressing their thanks to influenza.
Coloured etching attributed to Temple West, 1803.

Influenza, of course, has its own set of immune evasion genes. The most important one is the NS1 gene.2 NS1 blocks the interferon pathway, and to the extent that we can generalize, it seems that blocking interferon is one of the most critical things any virus can do. Almost every virus has some way of meddling with the interferon pathways, whether by preventing interferon from being triggered or inducing resistance to the effects of interferon. It’s been known for quite a while that NS1 does this — prevents interferon from being turned on — for influenza viruses, and it’s also been known that NS1 is very, very important to the virus. Mutant influenza viruses without NS1 are much, much less virulent than wild-type virus, and even targeting NS1 after an infection has started can help treat influenza.

(A flip side of this is that influenza viruses with a particularly effective NS1 may be more virulent. The 1918 pandemic influenza, which had a very high mortality rate,3 seems to have a particularly effective NS1 that can block interferon in several ways, and it’s been shown that swapping just the NS1 from the 1918 virus can make otherwise mild flu viruses more virulent. See my previous post about that.)

But there’s a bit of a paradox here. We know that NS1, the interferon blocker, is important to influenza virus. But we also know that interferon is very important in controlling influenza virus infections. For example, mice that can’t respond to interferons are much more susceptible to infection with avian influenza.4 So if NS1 works by blocking interferon, why does interferon still protect?

For that matter, one of the major explanations for why some influenza viruses (like avian flu and the 1918 flu) are so virulent, is the “cytokine storm” hypothesis.  (I talked about cytokine storms here and here.)  According to this concept, these viruses are especially lethal because they induce a huge release of cytokines, such as interferon. Yet at the same time the argument is made that these viruses are the ones with especially effective interferon blockers. If they’re really good at blocking interferon, then why do people die of having too much interferon?

It turns out that part of the answer may be timing. A recent paper from Thomas Moran’s group5 shows that in the very earliest stages of influenza virus infection, interferons are not being produced; then, a couple of days in, there’s a sudden big bang of cytokines. Knocking NS1 out of the virus changed this; interferons were produced from the beginning of the infection, and the virus was shut down. They call this phenomenon “stealth replication”:

Our data demonstrate that the initiation of lung inflammation does not begin until almost 2 full days after infection, when virus replication reaches its apex. The migration of lung DCs to lymph nodes and the subsequent priming of naive T cells are similarly subject to this delay. We demonstrate that the delay in the generation of immediate lung inflammation is mediated by the influenza NS1 protein. We propose that the virally encoded NS1 protein establishes a time-limited “stealth phase” during which the replicating influenza virus remains undetected, thus preventing the immediate initiation of innate and adaptive immunity. 5

They point out that in normal human influenza virus infection, symptoms take a couple of days to kick in, which fits because most of the “flu-like symptoms” we talk about are generic effects of cytokines. They also point out that a lot of virus transmission occurs before symptoms — i.e. in the first couple days of infection.

Thus, a stealth phase may also occur in humans and probably functions to maximize the probability of transmission before cytokines such as type I IFNs hamper the normal replicative cycle of influenza virus.5

This also helps make sense of the cytokine storm concept, I think. If avian or 1918 NS1 is especially good at preventing cytokines, then there might be a slightly longer stealth period, during which time the virus can replicate more. Then, when the immune system suddenly does become aware of an infection, there’s a huge amount of virus present, and the cytokine response would be correspondingly huge.

We might even be able to generalize to other viruses:

The stealth phase concept is not only applicable to influenza virus but can probably be extended to virtually all “real” human viral pathogens that have been shown to have an asymptomatic incubation time. For example, measles and varicella zoster viruses have a substantially prolonged evasion period that can last up to 2 wk. During this asymptomatic phase, these viruses also transmit to other susceptible hosts. Research aimed at interfering with the stealth phase may lead to the development of novel modulators as preventive treatments that target this early immune evasion mechanism. 5

I want to point to a previous post I made here, too, about herpes simplex virus. HSV has a wide range of immune evasion molecules, and we don’t have much understanding of what these things do in a natural infection.Frank Carbone’s group  did experiments with mouse infection that showed that HSV has a very narrow window (less than 24 hours) during which it can move from its original site of infection, in the skin, to neurons where it sets up a life-long infection. If the immune response can control HSV in this window, the virus can’t get into neurons and its life cycle is cut short. I speculated at the time that this might help explain immune evasion by HSV — it wouldn’t have to be super efficient, just keep things under control during that brief, early window. Seems quite similar to the influenza situation: Timing is critical, and perhaps immune evasion is one reason why.


  1. “Virus” isn’t a natural division; it groups together things with very different, and completely unconnected, evolutionary histories[]
  2. “NS” stands for “Non-structural”, meaning that the protein isn’t part of the virion that floats around and infects new cells — rather, the NS1 protein is produced anew in each cell after infection.[]
  3. As influenza infections go — not close to something like smallpox or ebola, but some 20 times higher than normal seasonal flu[]
  4. Szretter, K., Gangappa, S., Belser, J., Zeng, H., Chen, H., Matsuoka, Y., Sambhara, S., Swayne, D., Tumpey, T., & Katz, J. (2009). Early Control of H5N1 Influenza Virus Replication by the Type I Interferon Response in Mice Journal of Virology, 83 (11), 5825-5834 DOI: 10.1128/JVI.02144-08[]
  5. Moltedo, B., Lopez, C., Pazos, M., Becker, M., Hermesh, T., & Moran, T. (2009). Cutting Edge: Stealth Influenza Virus Replication Precedes the Initiation of Adaptive Immunity The Journal of Immunology, 183 (6), 3569-3573 DOI: 10.4049/jimmunol.0900091[][][][]
July 2nd, 2009

Simple, obvious, and wrong answers

Macrophage and mycobacterium
Macrophage phagocytosing mycobacteria

Sometimes the simple, obvious answer is right, and sometimes it’s completely backwards.

Tuberculosis was a terrifying, ubiquitous killer in the 19th century, but is relatively rare today (at least, in developed countries). The reason for the drop in Tb deaths isn’t entirely clear; it started with social factors probably including accidental or deliberate isolation of Tb patients, antibiotic treatment also knocked the disease back, and in some areas the vaccine (known as BCG) made a difference as well.

BCG is one of the oldest vaccines still in wide use; it was developed in the 1920s when a strain of Mycobacterium bovis (tuberculosis of cattle, contagious to humans) spontaneously lost virulence in culture. This avirulent strain of the bacterium was sent around the world and cultured independently, resulting in many distinct vaccine strains in different places and times. These strains are not only distinct genetically, but also phenotypically — they look different in culture, or grow differently, or whatever.

Over time, the vaccine has changed functionally, as well. Very early on the vaccine abruptly became even less virulent. More gradually, it seems that BCG has also become less effective; it’s no longer is able to protect against pulmonary Tb (although it’s still protective against other forms of the disease). Why is this?

At first glance this seems unsurprising. The bacterium has been grown in culture — outside of any animal host — for nearly 100 years. It’s had no selection to maintain its ability to grow in animals, or to avoid their immune responses, so of course it’s going to lose its ability to grow in animals.

But a recent paper1 suggests that exactly the opposite happened. Whether randomly, or because of some unexpected type of selection, the BCG strain has actually amplified an immune evasion function. This modern variant of the vaccine strain isn’t simply passively failing to induce an immune response; it’s actively suppressing the immune response.

Specifically, the authors argue that normal (wild, virulent) Mycobacterium secretes antioxidants as an immune evasion mechanism; that modern BCG also secretes lots of antioxidants; and that this is related to genomic duplications in some BCG strains:

Some BCG daughter strains exhibit genomic duplication of sigH, trxC (thioredoxin), trxB2 (thioredoxin reductase), whiB1, whiB7, and lpdA (Rv3303c) as well as increased expression of genes encoding other antioxidants including SodA, thiol peroxidase, alkylhydroperoxidases C and D, and other members of the whiB family of thioredoxin-like protein disulfide reductases.1

Further reading
Tb family trees
Conspicuous consumption
Life & Death, pre-vaccination

MycobacteriaIn other words, the long-term culture of BCG has yielded variants that are less immunogenic, because they are more actively suppressing the immune response. If their reasoning is correct, then reducing the antioxidant secretion from BCG should increase its immunogenicity. They took a BCG strain and deleted the duplicated antioxidant gene sigH (as well as the overexpressed SodA), and sure enough, the deleted version was more immunogenic and more protective in mice. “By reducing antioxidant activity and secretion in BCG to yield 3dBCG, we unmasked immune responses during vaccination with 3dBCG that were suppressed by the parent BCG vaccine.1

As a possible explanation, they note that their deletion variant also grows more slowly in culture than the “wild-type” BCG, and especially under certain culture conditions, and that this has led, coincidentally, to the reduced immunogenicity:

The practice of growing BCG aerobically with detergents to prevent clumping may have increased oxidant stress to cell wall structures and selected for increased antioxidant production. Then with each transfer the bacilli making more antioxidants represented a slightly greater proportion of the culture until they became dominant. In vivo, these mutations caused the vaccine to become less potent in activating host immunity. In effect, we believe that as BCG evolved it yielded daughter strains with an increased capacity for suppressing host immune responses. 1

If this turns out to be generally true, then there’s a relatively straightforward handle for converting BCG back into a more effective, and safer, vaccine; whereas if the reduced immunogenicity was because of over-attenuation, it’s not so simple — you’d be trying to make a vaccine more virulent, which is a tricky tightrope to walk.

Incidentally, I frequently complain about the terrible, terrible quality of press releases about scientific advances  (and therefore the terrible quality of much “science reporting”, which is basically regurgitating the terrible press releases) so I want to give props to the person at Vanderbilt University Medical Center who put together the release for this paper — it’s a clear, simple, interesting, and as far as I can tell accurate account of the finding, background, and observation.  It can be done well — I wish it was done this well more often.


  1. Sadagopal, S., Braunstein, M., Hager, C., Wei, J., Daniel, A., Bochan, M., Crozier, I., Smith, N., Gates, H., Barnett, L., Van Kaer, L., Price, J., Blackwell, T., Kalams, S., & Kernodle, D. (2009). Reducing the Activity and Secretion of Microbial Antioxidants Enhances the Immunogenicity of BCG PLoS ONE, 4 (5) DOI: 10.1371/journal.pone.0005531[][][][]
June 2nd, 2009

“Mus homunculus” in the lab?

Researchers have used the mouse extensively as a model organism to study the pathogenesis of human infections and found that it imperfectly recapitulates many aspects of infectious disease as seen in patients. 1

Mickey mouse evolution
Humanizing a mouse

That strikes a chord with me because I just sent off a grant application explaining that mice are not suitable models for viral immune evasion.  However, my application may show a failure of imagination (or courage), because what Coers et al.1 are driving toward is humanizing mice to make them better models for human disease, whereas I am merely proposing a different animal model.

What causes species specificity in pathogens?  That is, why is it that many pathogens infect humans very nicely, but don’t infect mice to any extent?  (And, of course, conversely, why do other pathogens cause disease in mice and not in humans.)

Chlamydia trachomatis in human cells
Chlamydia trachomatis in human cells

In some cases, a viral pathogen may simply be unable to get into the appropriate cell in the wrong species. An example is poliovirus, which normally doesn’t infect mice at all. But if you make a transgenic mouse2 that expresses the (human) poliovirus receptor3, then the virus infects mice, and causes disease in them, perfectly well.   In this case, the receptor is the critical determinant of species specificity.  As a natural example of the same concept, SARS virus at least partly adapted to infecting humans by modifying its receptor-binding protein4 to improve interaction with the human version of the protein.

But there are also lots of cases where the virus can get into cells from the other species, yet doesn’t manage to replicate well or cause disease.  I’ve talked about mouse cytomegalovirus (MCMV) and its inability to infect humans here; it turned out that MCMV can’t infect human cells well because its normal ability to disarm the programmed cell death (apoptosis) pathways only works against the mouse versions of the pathway.  There are similar stories with HIV and its primate-infecting cousins; these viruses are limited to infecting hosts in which they (the viruses) can eliminate the APOBEC retrovirus-destroying proteins.  And the poxvirus myxomavirus is at least partly restricted to infecting rabbits because it can only inactivate the interferon pathway in rabbit cells. 5

Mouse manYou may notice two things about these examples: First, the non-receptor examples are generally immune evasion stories.  That is, these viruses are often apparently restricted to infecting a limited number of species because their immune evasion arsenal is limited to those species; take away their immune evasion by putting them in the wrong species, and they’re enfeebled.  Second, these examples are viruses.  The reason for that is just that I’m used to dealing with the crisp, clean mountain air of virology, and I don’t usually descend into the fetid swamps of bacteriology.6

But it turns out that at least in some cases the principles seem to be the same.  The Coers et al. paper1 I cited at the top here makes some very familiar points: The receptor half of the story (“Colonization often relies on species-specific interactions of microbial ligands with host cell receptors“) applies to some bacterial pathogens (“Transgenic mice expressing human E-caherin in the small intestine, on the other hand, are susceptible to oral infections with L. monocytogenes and develop enteropathogenicity and systemic infections“).  And the immune evasion half also applies to some bacterial pathogens (“Additionally, host restriction may be caused by the failure of pathogens to deter immune assaults in the non-typical host“).

Even the nature of the immune evasion targets is familiar. Interferon pathways are frequent targets of bacterial immune evasion, as they are of viral immune evasion.  The details are different, in that the instances Coers et al. describe target a different branch of the interferon induction pathway, but the pattern is the same:

… the mouse-adapted strain Chlamydia muridarum, but not its close relative C. trachomatis, can specifically evade IRG-mediated7 host resistance … The divergent counterimmune mechanisms employed by the human pathogen C. trachomatis and the mouse-adapted pathogen C. muridarum clearly reflect the differences in the IFN? responses of their respective hosts. 1

They finally discuss the possibilities of “Mus homunculus”, humanized mice, tailored to each pathogen, that would make more authentic models of infectious disease.  “Though the creation of humanized mouse models for infectious disease will require substantial effort and resources, the long-term benefits of these new models would undoubtedly be enormous.1


  1. Coers, J., Starnbach, M., & Howard, J. (2009). Modeling Infectious Disease in Mice: Co-Adaptation and the Role of Host-Specific IFN? Responses PLoS Pathogens, 5 (5) DOI: 10.1371/journal.ppat.1000333[][][][][]
  2. Hi, Vincent![]
  3. Transgenic mice expressing a human poliovirus receptor: A new model for poliomyelitis.
    Ruibao Rena, Frank Costantinib, Edward J. Gorgaczc, James J. Leeb and Vincent R. Racanielloa
    Cell 63:353-362 (1990) []
  4. Li W, Zhang C, Sui J, Kuhn JH, Moore MJ, et al. (April 20, 2005) Receptor and viral determinants of SARS-coronavirus adaptation to human ACE2. EMBO J 24.:1634-43.
    Sheahan T, Rockx B, Donaldson E, Sims A, Pickles R, et al. (March 2008) Mechanisms of zoonotic severe acute respiratory syndrome coronavirus host range expansion in human airway epithelium. J Virol 82.:2274-85.[]
  5. Wang F , Ma Y , Barrett JW , Gao X , Loh J , Barton E , Virgin HW , McFadden G (2004) Disruption of Erk-dependent type I interferon induction breaks the myxoma virus species barrier. Nat Immunol 5: 1266-1274[]
  6. In other words, I don’t know much about bacteriology.[]
  7. IRG is part of an interferon-induction pathway[]