Mystery Rays from Outer Space

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

November 29th, 2007

“Darwin’s Surprise” in the New Yorker

Eustace TilleyThe New Yorker has an article on endogenous retroviruses that leaves me with mixed emotions. I’ve subscribed to the New Yorker for 20-odd years now, even hanging on through the lean Tina Brown years, because I love the quality of the non-fiction articles. (And the cartoons.) Their non-fiction is usually well-written and well-researched and usually does a terrific job of bringing across the importance and the interest of a field, whether it’s virology, steel production, or stocking grocery shelves. And in general, I think this article (“Darwin’s Surprise” by Michael Specter) does that as well. There was little in the article that was new to me, but I think that people unfamiliar with the field will have no trouble understanding it.

But here are some quotes from the first page, that made me slap down the magazine and mutter to myself.

Viruses reproduce rapidly and often with violent results, yet they are so rudimentary that many scientists don’t even consider them to be alive.

Because they no longer seem to serve a purpose or cause harm, these remnants have often been referred to as “junk DNA.”

And later on:

… the earliest available information about the history and the course of human diseases, like smallpox and typhus, came from mummies no more than four thousand years old. Evolution cannot be measured in a time span that short.

Those lines are at best lazy, and at worst bullshit.

The whole “viruses aren’t alive” crap isn’t an argument of scientists — in the 20 years I’ve been a virologist, I have never heard a scientist ask the question. Public school teachers, maybe high school biology teachers, maybe philosophers (I don’t know, I’m guessing) might ask the question, but scientists don’t. That’s because it has nothing to do with science. It’s a semantics question. People new to biology think it tells them something profound about What Life Is. It tells you nothing about life; it tells you about “life”, the word. The word “alive” dates back some 800 years. Of course it isn’t suited to explaining viruses. The word “virus” comes from the Latin for “Poison”; that tells us nothing interesting about virus lifestyles.

The whole “junk DNA” has been thrashed out a dozen times (see Genomicron for a good start). The bottom line? If you search Pubmed for the phrase “junk DNA” you will find a total of 80 articles (compare to, say, 985 articles for “endogenous retrovirus”); and a large fraction of those 80 articles only use the phrase to explain what a poor term it is. Scientists don’t use the term “junk DNA’. Lazy journalists use it so they can sneer at scientists (who don’t use it) for using it.

And of course, evolution can easily be measured in four thousand years. For a virus? Eighty years (the history of HIV), 1 or 8 years (West Nile Virus) 2 is plenty.

Aside from those points that bumped my Pet Peeve Bone, the article is a good one. But those just rubbed me the wrong way.

(Having written this, I see that Carl Zimmer at The Loom has beaten me to it.)


  1. Korber, B., Muldoon, M., Theiler, J., Gao, F., Gupta, R., Lapedes, A., Hahn, B. H., Wolinsky, S., and Bhattacharya, T. (2000). Timing the ancestor of the HIV-1 pandemic strains. Science 288, 1789-1796. []
  2. Brault, A. C., Huang, C. Y., Langevin, S. A., Kinney, R. M., Bowen, R. A., Ramey, W. N., Panella, N. A., Holmes, E. C., Powers, A. M., and Miller, B. R. (2007). A single positively selected West Nile viral mutation confers increased virogenesis in American crows. Nat Genet 39, 1162-1166. []
November 29th, 2007

Cancer equilibrium, part II

Colorectal cancer
Blood vessels in a colorectal cancer

As I said in my last post , by the time we can detect a tumor — by the time it’s macroscopic — it’s already been through a long period of selection by the immune system. We see only the survivors of that selection, the cancers that have developed resistance to immune destruction. What happens to the other tumors, that have not yet escaped?

Some of them are eliminated by the immune system. Rarely, if ever, do we observe this; it happens when there are a handful of pre-cancerous cells, a microscopic cluster of a few cells that have made a few steps toward outright carcinogenicity but are not detectable by almost any means we have available today. But if the “long period of selection” is accurate, then there is a third category; as well as those tumors that have escaped control by the immune system and those that are eliminated with it, there must be a set of tumors that are in equilibrium with the immune system.

These equilibrium tumors, again, probably consist only of a handful of cells. The immune system recognizes them and destroys them, but because of some genetic or epigenetic changes in the tumor1 the fledgling tumor is not destroyed; neither can it grow out to be detectable, until at some point it develops further changes that allow it to escape immune control altogether. It’s quite likely that most of the tumors that we eventually see, spend most of their lifespan in the equilibrium stage.

That’s the theory, anyway. As I mentioned last post, there’s more solid evidence for the “Elimination” and “Escape” stages, but there is some circumstantial evidence for “Equilibrium”. Now, a very recent paper by Robert Schreiber’s group looks at the equilibrium stage directly.

Catherine M. Koebel, William Vermi, Jeremy B. Swann, Nadeen Zerafa, Scott J. Rodig, Lloyd J. Old, Mark J. Smyth, Robert D. Schreiber (2007). Adaptive immunity maintains occult cancer in an equilibrium state Nature, 450 (7171), 903-907 DOI: 10.1038/nature06309

The problem with testing the theory is (among other things) that the tumors in equilibrium are, pretty much by definition, undetectable. If they were detectable, we’d say they had escaped. What’s more, another part of the “equilibrium” definition is that it’s a long-term interaction. So not only must you detect the undetectable, you must do this over a long period.

Blogging on Peer-Reviewed ResearchKoebell et al overcame this, at the cost of making the system more artificial, by treating mice with a low dose of a carcinogen. Some mice developed tumors, but eventually after a couple of hundred days new tumors stopped appearing. Many mice were still tumor-free. 2 The question then is this: Are those mice truly tumor-free, or so they actually have tiny, undetectable tumors that are in equilibrium with their immune systems?

Koebell et al, Figure 1 To test this, Koebell et al now shut down the immune systems of the tumor-free mice. Sure enough, tumors abruptly started to grow out in previously clean mice (the red traces in the figure to the right).

This (along with some further controls I won’t go in to) argues that the mice were harboring tumors in equilibrium with the immune system. Knowing this, could these proto-tumors be detected?

In fact, the sites of carcinogen injection often did have tiny, but non-progressing, lumps, a few millimeters around. I would guess that such tiny firm lumps would usually be dismissed as scar tissue from the injection, and so indeed some proved to be; but some of them turned out to look like cancerous cells. And these cells formed progressive tumors in immune-deficient mice — but not mice with an immune system; even though normal immune systems had not been able to eliminate them previously.

The paradox that stable masses from our MCA-treated immunocompetent mice often contained transformed cells but did not increase in size in vivo suggested that net tumour cell expansion was being immunologically restrained.

Is this equilibrium stage a dead end for the tumor? Do unsuccessful tumors get shunted into this stage and either smolder indefinitely, or eventually get eliminated? At least in this model — and very likely in naturally-occurring cancer, though that remains to be proven — equilibrium seems to be a true intermediate stage that can lead to outright tumor growth. Although most of the spontaneous, detectable tumors appeared early on after carcinogen treatment, and after 200 days or so it usually took immune suppression for the tumors to grow out, in a few mice even after several hundred days tumors spontaneously appeared. And these tumors, that spontaneously left the equilibrium stage in normal mice — these tumors were not rejected by normal mice, unlike (many of) the cells from the equilibrium-stage tumors. 3

We show that equilibrium is indeed a component of cancer immunoediting because tumour cells in equilibrium are highly immunogenic (unedited), whereas those spontaneously exiting equilibrium that become growing tumours have attenuated immunogenicity (edited)-results that place this process temporally between elimination and escape.

This has lots of interesting implications. Are tumors in equilibrium potential targets for cancer prevention — say, cranking up immune responses to shift the balance toward elimination? Do tumors in equilibrium have some kind of molecular signature that will make their detection feasible in natural situations? Precisely what changes allow the tumors to progress from equilibrium to escape — and can those changes be targeted, to give the immune system a hand?


  1. Or perhaps because of pure luck and location[]
  2. Actually, many had “small stable masses” where they had been injected with the carcinogen, so they weren’t quite tumor free — see below — but they had no progressive tumors.[]
  3. I notice that although wild-type mice usually rejected the cells from the stable equilibrium tumors, a significant minority actually did go on to form tumors. It’s not clear to me from the figure whether these were progressive tumors or tumors in equilibrium — but in either case, either in the rejection or in the take, something changed in the balance when the equilibrium tumor cells were transplanted into new hosts, even genetically identical ones. I am very interested in what that change in balance is.[]
November 26th, 2007

The three “E”s of cancer immunity

Three Es of cancer immunity A couple of weeks ago I talked briefly about immunity to tumors, saying that “this is actually a long-running controversy that has gone back and forth over the years. There’s too much history to treat all in one post, and indeed there’s circumstantial evidence arguing that in fact immune systems are not major players in cancer resistance. … However, the pendulum swing at the moment has it that the immune system does represent a major barrier to cancer progression.

A few days after I wrote that, a paper came out (so far just online) that helps support one of the models for immunity in cancer prevention:

Koebel, C. M., Vermi, W., Swann, J. B., Zerafa, N., Rodig, S. J., Old, L. J., Smyth, M. J., and Schreiber, R. D. (2007). Adaptive immunity maintains occult cancer in an equilibrium state. Nature doi:10.1038/nature06309

Last time I avoided talking about much of the history of this question, but for this paper a little background is necessary — anyway, it’s interesting in itself. Rather than try to explain the back-story and the new paper all in one go I’ll split them up into separate posts. Today I’ll run through some of the history, and later this week I’ll talk about the new paper itself.

The notion that tumors can be controlled by the immune system is an old one, dating back to Paul Ehrlich’s proposal in the early 20th century.1 However, there really weren’t any tools, such as immune-deficient animals, to test the hypothesis until the second half of the century. In the 1950s, as the understanding of immunity became a little clearer, people (especially Sir Macfarlane Burnet and Lewis Thomas) revisited and refined the idea:2

It is by no means inconceivable that small accumulations of tumour cells may develop and because of their possession of new antigenic potentialities provoke an effective immunological reaction with regression of the tumour and no clinical hint of its existence.

Blogging on Peer-Reviewed ResearchHowever, once some tools did become available, experiments didn’t support this “immunosurveillance” concept. At the time, the best model of immunodeficiency was the nude mouse — a spontaneous mutation that results in athymic mice, that (mostly!) lack T cells. These mice are quite immunodeficient, but they do not, it turns out, develop more tumors than do wild-type mice.3

We now believe that nude mice (and especially the mouse strain Rygaard and Povlsen used, which are unusually susceptible to tumors) are not a great model for this question; for one thing, they still do have some T cells, especially as they get older (which is when tumors are most likely to be an issue, of course). Nevertheless, the studies were the best that could be done at the time, and  the results were fairly definitively negative.  In the 1980s and early 1990s, it was at best controversial whether immunosurveillance was a reality, or if the immune system had any effect at all on tumor development. Hanahan and Weinberg’s massively influential 2000 paper4 on the events required for tumorigenesis didn’t even mention the immune system as a problem for the developing tumor.5

Spontaneous tumors in RAG-/- mice But in mid 1990s and early 2000s the pendulum began to swing back. Some of the most important work came from Robert Schreiber’s lab, showing that immunodeficient animals actually are more susceptible to tumors. This started with relatively artificial systems,6 but led to the critical observation that immunodeficient mice — RAG knockout mice, which lack T cells almost completely, a more complete effect than in nude mice — are more prone to spontaneous tumors as they age7 (see the figure at right for an example).

Another critical finding, that I personally found very exciting at the time,8 showed that tumors that form in immunodeficient mice are much more immunogenic than those that form in wild-type mice. Normally, if you transplant a tumor from one wild-type mouse to another, the tumor is likely to “take”, and continue to grow: It is not rejected by the immune system.  If you transplant from a wild-type to an immunodeficient mouse, again it takes.  But if you transplant a tumor from an immnodeficient RAG knockout mouse to a wild-type mouse, this tumor will be rapidly rejected (and the rejection is immune-mediated).9 This strongly suggests that tumors normally develop ways to avoid immunity.  When there’s no immune system to deal with, tumors don’t have to develop immune evasion mechanisms, and then when these immune-naive tumors are suddenly transplanted to normal mice and exposed to the immune system in all its fury, the tumors have no way of coping with immune attack.

Meanwhile, work from many groups, probably especially Soldano Ferrone, Nick Restifo , and Steven Rosenberg‘s, 10 was showing how frequently and drastically tumors mutate in order to develop resistance to the immune system, which argues that the immune system must be a major selective force during tumor growth. These findings started well before the more direct demonstrations I’ve mentioned, but at first it seemed that this sort of tumor immune evasion was unusual. As more and more cases were described, though, it has gradually come clear that immune evasion is — if not universal — the rule rather than the exception.

Hanahan & Weinberg tumor progression By now, as a result of these sorts of experiments, it’s become pretty much accepted that the immune system is a huge barrier to tumor growth; a seventh hurdle to add to the six that Hanahan and Weinberg described. The understanding is that the interaction between tumors and immunity takes three forms — the three “E”s of cancer immunity: “Elimination”, “equilibrium”, and “escape”.

“Escape” is what we usually see with cancer, because “elimination” mostly occurs before the tumors are clinically detectable. As I said in my earlier post, “by the time we can detect a cancer, it’s already been selected to be immune resistant. The cancers that were susceptible to the immune system were killed off when they were just a little cluster of cells, long before there was anything we could identify.

“Equilibrium” is an intermediate stage between elimination and escape. The tumor has mutated enough, or grows fast enough, or is hidden well enough, that the immune system can’t eliminate it altogether; but at the same time, it hasn’t mutated enough to completely escape immune control. The system is in dynamic equilibrium; the tumor can’t expand, because it’s being killed off as fast as it grows (or its growth is restrained); but the immune system can’t quite kill off the last few cells.

This “equilibrium” stage has been hard to demonstrate in an experimental system, but there have been some strong circumstantial arguments for it. The most famous example may be tumor regrowth after a kidney transplant; the donor had been successfully treated 16 years before the transplant and was believed to be tumor-free, but in the recipient the tumor — now no longer checked by the donor’s immune system — grew out within a couple of year. The tumor and the donor’s immune system had presumably been in equilibrium for 16 years.11

The Koebel et al paper shows evidence for the equilibrium stage in an experimental system. I’ll talk about it later this week.

You may be wondering, by the way, if I knew all these references and dates off the top of my head. The answer is that of course I did. However, last week I just had a general outline of the story. The difference is that this week, I’m covering tumor immunity for the grad immunology class I teach, so I’ve been doing some reading.12 I got the story straightened out, and the original references, from a couple of excellent reviews from Robert Shreider’s group:
Dunn, G. P., Old, L. J., and Schreiber, R. D. (2004). The three Es of cancer immunoediting. Annu Rev Immunol 22, 329-360.

Dunn, G. P., Bruce, A. T., Ikeda, H., Old, L. J., and Schreiber, R. D. (2002). Cancer immunoediting: from immunosurveillance to tumor escape. Nat Immunol 3, 991-998.


  1. Ehrlich P. 1909. Ueber den jetzigen Stand der Karzinomforschung. Ned. Tijdschr. Geneeskd. 5 (Part 1): 273-90[]
  2. Burnet, F.M. Cancer-a biological approach. Brit. Med. J. 1, 841-847 (1957).[]
  3. Rygaard, J., and Povlsen, C. O. (1974). The mouse mutant nude does not develop spontaneous tumours. An argument against immunological surveillance. Acta Pathol Microbiol Scand [B] Microbiol Immunol 82, 99-106.[]
  4. Over 4000 citations and counting![]
  5. Hanahan, D., and Weinberg, R. A. (2000). The hallmarks of cancer. Cell 100, 57-70. []
  6. For example: Kaplan, D. H., Shankaran, V., Dighe, A. S., Stockert, E., Aguet, M., Old, L. J., and Schreiber, R. D. (1998). Demonstration of an interferon gamma-dependent tumor surveillance system in immunocompetent mice. Proc Natl Acad Sci U S A 95, 7556-7561. And Smyth, M. J., Thia, K. Y., Street, S. E., MacGregor, D., Godfrey, D. I., and Trapani, J. A. (2000). Perforin-mediated cytotoxicity is critical for surveillance of spontaneous lymphoma. J Exp Med 192, 755-760. []
  7. Shankaran, V., Ikeda, H., Bruce, A. T., White, J. M., Swanson, P. E., Old, L. J., and Schreiber, R. D. (2001). IFNgamma and lymphocytes prevent primary tumour development and shape tumour immunogenicity. Nature 410, 1107-1111. []
  8. Note to self: Blog about this one some time! Very cool classic paper[]
  9. Shankaran, V., Ikeda, H., Bruce, A. T., White, J. M., Swanson, P. E., Old, L. J., and Schreiber, R. D. (2001). IFNgamma and lymphocytes prevent primary tumour development and shape tumour immunogenicity. Nature 410, 1107-1111.[]
  10. This is just off the top of my head and I’m probably forgetting some. Sorry![]
  11. MacKie, R. M., Reid, R., and Junor, B. (2003). Fatal melanoma transferred in a donated kidney 16 years after melanoma surgery. N Engl J Med 348, 567-568.[]
  12. And the Koebel et al. paper came out at a really fortuitous time.[]
November 23rd, 2007

Niches and bone marrow transplants

thymocytesStuffed with duck as I am (we don’t do turkey for Thanksgiving in our house) I’m not up to a long post, but I thought a paper in the latest issue of Science was pretty cool. The paper is
Czechowicz, A., Kraft, D., Weissman, I. L., and Bhattacharya, D. (2007). Efficient Transplantation via Antibody-Based Clearance of Hematopoietic Stem Cell Niches. Science 318, 1296-1299. 1

Very briefly, they show that one of the obstacles to bone marrow grafts — even in the absence of host-versus-graft immunity — is that there are a limited number of niches for hematopoietic (bone marrow) stem cells. The native stem cells occupy those niches, so injecting in a donor’s stem cells is very inefficient; only a tiny number can find a home and supply new, desirable progeny. If I’m interpreting the data right, there seem to be only a few hundred open slots, out of maybe 25000 total slots, available for donor stem cells.

Blogging on Peer-Reviewed ResearchThey came up with a protocol that transiently and specifically eliminated host stem cells — opening up niches — before the graft, and the results were pretty dramatic. Without treatment, the chimerism rates (indicating efficiency of donor engraftment) was around 3%; with treatment, it was 90%. If this works in humans as it does in mice, it offers a much gentler alternative to the really brutal and toxic treatments that are usually necessary today.

So what does “niche” mean, in this context? Is it a physical slot into which the tab of a hematopoietic stem cell is tucked? Is it a conceptual niche, a constraint based on available levels of some soluble factor, or on rates of contact with some supporting cell type? I think all three are possible, and2 have parallels in other aspects of the immune system.

For example, growth in the thymus (the figure at top left) probably requires physical niches, cells into which developing thymocytes cuddle up and receive nourishment and advice as they mature. (See, especially, the videos taken by Bousso et al, 3 of thymocytes interacting with thymic stromal cells.) Although I admit I find that the most attractive concept, I don’t really have a good reason for it, and there are probably good examples of non-physical “niches” as well. Survival of naïve lymphocytes outside of the periphery requires intermittent contact with MHC class I molecules — potentially a limiting factor, if they have to compete with others of their kind. There are also several examples of regulation by limiting amounts of certain cytokines, such as IL-7. 4 Still, the various two-photon microscopy videos of in-situ interactions that have been coming out over the past few years have really made me appreciate the importance of physical location and direct interactions in the immune system, which might explain my bias toward physical niches.


  1. As an experiment in aggregation, I am including a second version of the reference here, thus: Czechowicz, A., Kraft, D., Weissman, I.L., Bhattacharya, D. (2007). Efficient Transplantation via Antibody-Based Clearance of Hematopoietic Stem Cell Niches. Science, 318, 1296-1299. DOI: 10.1126/science.1149726[]
  2. According to current understanding, anyway[]
  3. Bousso, P., Bhakta, N. R., Lewis, R. S., and Robey, E. (2002). Dynamics of thymocyte-stromal cell interactions visualized by two-photon microscopy. Science 296, 1876-1880. []
  4. Purton, J. F., Tan, J. T., Rubinstein, M. P., Kim, D. M., Sprent, J., and Surh, C. D. (2007). Antiviral CD4+ memory T cells are IL-15 dependent. J Exp Med 204, 951-961. []
November 20th, 2007

“Social immunity” followup

Rowley & Powell: I should have waited a day before commenting on the “social immunity in ants” paper.1, 2 , 3 I referred to a review in BioEssays,4 but the latest issue of the Journal of Immunology has a review with a very similar theme. 5

My comment on the original paper was basically that they refer to “immunity” and “immune priming” without actually examining any immunological functions. Quoting Hauton and Smith:

The failure to make assessment of immunological parameters is a consistent weakness in most papers purporting to demonstrate priming, memory or adaptivity in the invertebrate innate immune system. In some cases, only single-end points are taken and the role of the immune system is inferred but not actually tested.

ResearchBlogging.org

The J Immunol review from Rowley and Powell surveys the recent literature on invertebrate immune responses. As with Hauton and Smith, they’re not much impressed by most of the claims (“Whether these observations prove the existence of an analogous adaptive immune system with levels of specificity and memory with equivalent status to that in jawed vertebrates is still very much unanswered”). They are a little more convinced, though, especially by a recent paper that Hauton and Smith didn’t specifically mention6 although even here they’re clearly not swept off their feet:

Although such specific protection could also be found for other pathogens such as the entomopathogenic fungus Beauveria bassiana, rather surprisingly (and perhaps worryingly) the other bacteria tested yielded no enhancement in protection against later challenge.

They also review possible mechanisms for immune memory in invertebrates (assuming it does exist) and propose methods to test these mechanisms (as well as explaining what isn’t acceptable): “What is surely needed is the ability to unequivocally prove the existence of immune mechanisms in selected invertebrates that both yield a memory component and have specificity in their mode of action.” This is exactly what Hauton and Smith call for, as well.


  1. Social Prophylaxis: Group Interaction Promotes Collective Immunity in Ant Colonies. Line V. Ugelvig and Sylvia Cremer. Current Biology 17:1967-1971 (20 November 2007) []
  2. I am experimenting with a citation aggregator; the next footnote should include the same reference formatted for the aggregator.[]
  3. Ugelvig, L.V., Cremer, .S. (2007). Social Prophylaxis: Group Interaction Promotes Collective Immunity in Ant Colonies. Current Biology, 17, 1967-1971.[]
  4. Hauton, C., and Smith, V. J. (2007). Adaptive immunity in invertebrates: A straw house without a mechanistic foundation. Bioessays 29, 1138-1146. []
  5. Rowley, A. F., and Powell, A. (2007). Invertebrate Immune Systems Specific, Quasi-Specific, or Nonspecific? J Immunol 179, 7209-7214. []
  6. Sadd, B. M., P. Schmid-Hempel. 2006. Insect immunity shows specificity in protection upon secondary pathogen exposure. Curr. Biol. 16: 1206-1210. []
November 19th, 2007

“Social immunity” in ants?

Lasius neglectusThe review article1 I wrote about last month has sensitized me to some of the issues with research on invertebrate immunity. Unfortunately for me, that made an otherwise-fascinating article on parasite resistance in ants a rather painful read.

The article is Social Prophylaxis: Group Interaction Promotes Collective Immunity in Ant Colonies. Line V. Ugelvig and Sylvia Cremer. Current Biology 17:1967-1971 (20 November 2007) (hat tip to Not Exactly Rocket Science, which drew my attention to it before publication). The fundamental observation in this paper is that

Social contact with individual workers, which were experimentally exposed to a fungal parasite, provided a clear survival benefit to nontreated, naive group members upon later challenge with the same parasite.

This is indeed very interesting — of course, you’d expect that contact with an infected peer would raise your risk of infection, rather than benefiting you, so it had been hard to explain why social insects do sometimes perform “meticulous care by the performance of hygienic behaviors” on infected individuals. Ugelvig and Cremer found that in fact exposure to the infected ant conferred resistance to the detrimental effect of the pathogen (the fungus Metarhizium anisopliae; see the figure to the right) on later exposure. They propose that

either parasites might be transferred between individuals eliciting an immune response potentially followed by immune priming in the naive group members or that the exposed individual might directly transfer immunity by passing on immune compounds to its nestmates.

Metarhizium anisopliae Of course, it’s the use of the term “immunity”, and especially “immune priming”, that makes me uncomfortable. “Immunity” and “immune priming” have specific meanings; in particular, “priming” very strongly implies immune memory and an adaptive immune system, which has not been previously demonstrated2 in insects. Yet Line and Cremer did nothing to test immunity per se; they looked at ant survival after exposure, and assumed that the differences are due to immunity. This is exactly the practice that Hauton and Smith specifically criticized:

The failure to make assessment of immunological parameters is a consistent weakness in most papers purporting to demonstrate priming, memory or adaptivity in the invertebrate innate immune system. In some cases, only single-end points are taken and the role of the immune system is inferred but not actually tested.

Blogging on Peer-Reviewed ResearchI realize that actually testing the role of the immune system in the ant system would be an enormous task, and that at least part of the importance of the paper has nothing to do with the terminology used. In fact, for the most part the word “immunity” could have been entirely metaphorical throughout the paper (except that they do cite a previous paper that attempted to identify a non-metaphorical immunity in insects.3 ) Is there anything wrong with using the term “immune priming” loosely? It certainly raises the interest factor for the paper. As Hauton and Smith say:

Hypotheses erected from these observations appear revelatory because the terminology adopted draws analogy to processes that have been characterized in the adaptive immune responses of jawed vertebrates.

Is there any harm in speculating that this is immunity? Perhaps not, but given that there’s no case made for actual immunity here, I think the paper really is somewhat misleading; it will certainly reinforce the concept that insects have some form of adaptive memory. I don’t know whether insects do or not, frankly, but I do think the question is important enough that it should be tested — not taken as given, or treated as a metaphor. And I think Ugelvig and Cremer’s paper is interesting enough to stand on its own, even without the loaded terminology.


  1. Hauton, C., and Smith, V. J. (2007). Adaptive immunity in invertebrates: A straw house without a mechanistic foundation. Bioessays 29, 1138-1146. []
  2. Convincingly[]
  3. B.M. Sadd and P. Schmid-Hempel, Insect immunity shows specificity upon secondary pathogen exposure, Curr. Biol. 16 (2006), pp. 1206-1210. []
November 16th, 2007

AIC

I’m going to the Autumn Immunology Conference in Chicago this weekend. It’s a fairly small, but well-organized and friendly, conference that’s within an easy 3-hour drive,1 and it gives me a chance to meet other immunologists from the area. 2 I went last year and enjoyed it.

One of my students will be presenting; it’s really earlier in the project than I’m really enthusiastic about a presentation for, but the AIC really encourages grad student presentations, and I think students should give as many talks as much as possible, so it’s a good opportunity for him.

Should be a good time.


  1. Plus an hour or two of sitting motionless in Chicago traffic[]
  2. “The area” being the Midwest, I guess, which is a pretty large area.[]
November 15th, 2007

Storms and natural killers

Lightning storm NOAA We usually expect that our immune system will protect us against disease. But it’s not unusual for diseases (especially viral diseases) to cause their damage through the immune system. One of the popular concepts for this is the “cytokine storm” idea — cytokines being the soluble proteins produced by immune responses that drive inflammation, and a “cytokine storm” being a massive release of these inflammatory mediators, leading to immune-mediated damage to blood vessels, leakage from the vascular system, shock, and eventually death. This is a death caused by a hyperreactive immune system.

It’s important to point out that cytokine storms are far from the only cause of immune-mediated disease, even in the context of infection; and in fact, cytokine storms are probably pretty rare. For example, although it’s often stated as fact that avian influenza and the 1918 flu cause death through cytokine storms, especially in the wake of a paper by Chan et al,1 I think the evidence for this is pretty weak — and for avian flu in particular, it’s been shown that cytokines are probably not the culprits at all. 2

However, I don’t question that in some cases — for example, Dengue virus,3 some poxviruses,4 and other viruses– cytokine storms are the underlying problem. It would seem, then, that one way to protect against this would be to inhibit the T cell response, right? — thereby reducing cytokine production. Well, not necessarily so.

Traditionally, innate and adaptive immune responses are taught separately. I do this too, but at least I always preface the split with the explanation that this is an artificial division. The immune response is a tightly integrated system,5 and the innate and adaptive immune systems talk back and forth, modulate each other, help each other and suppress one another.

Natural killer cells are traditionally considered as parts of the innate immune response. They are early responders, ramping up very fast, and then fading away around the time the adaptive immune response (in the form of T cells) kicks in (a few days after an infection, for example). Because of the time course, it’s been easy to understand how effectively NK cells can modulate the adaptive immune response — NK cells release cytokines that talk to T cells and help activate, attract, and guide the subsequent T cell response.

Blogging on Peer-Reviewed ResearchRecently we learned that the reverse is also true. 6 T cells also regulate the NK cell response — and without adult supervision, NK cells can trigger a lethal cytokine storm.

Nude mice — mice lacking any T cells — are very susceptible to some virus infections, as you’d expect; they have essentially no adaptive immune system. But Kim et al (looking at infection with mouse hepatitis virus) found that the mice do not die because the virus is out of control. On the contrary, there really was no more virus in the nude mice (which have no T cells, remember) than in wild-type mice with a fully functional immune system. Instead, the deaths are apparently because of a cytokine storm.

Nude mice do have highly active NK cells, and it further turned out that these uncontrolled NK cells explode with huge amounts of interferon when they’re stimulated. Interferon is generally a useful antiviral cytokine, but it is well known to be highly toxic when overproduced — and blocking interferon in these mice protected them from death when their NK cells were stimulated.

This is interesting for a couple of reasons. For one, it’s generally been assumed that mice without T cells are susceptible to virus infections because they can’t effectively control the virus. In fact, it may be that they die because they can’t control the immune response. Are NK cells contributers to cytokine storms even in normal people? Could this offer a tool to control some of these viral diseases? 7

The concept of an unleashed innate response in the absence of adaptive modulation may also lead to new diagnosis and treatment for individuals with congenital or acquired immune deficiency.

For another, while it’s been obvious that NK cells can regulate T cell responses, the reverse hasn’t been as obvious — the timing, for example, didn’t seem to fit. But now it’s clear that the conversation goes both ways:8

Because the innate immune response precedes the adaptive immune response to infection by several days, one would assume that adaptive immunity should not affect the early innate response, but the findings of Kim et al. show that even the earliest innate response requires adaptive regulation.


  1. Chan, M. C., Cheung, C. Y., Chui, W. H., Tsao, S. W., Nicholls, J. M., Chan, Y. O., Chan, R. W., Long, H. T., Poon, L. L., Guan, Y., and Peiris, J. S. (2005). Proinflammatory cytokine responses induced by influenza A (H5N1) viruses in primary human alveolar and bronchial epithelial cells. Respir Res 6, 135. []
  2. Salomon, R., Hoffmann, E., and Webster, R. G. (2007). Inhibition of the cytokine response does not protect against lethal H5N1 influenza infection. Proc Natl Acad Sci U S A 104, 12479-12481. []
  3. Pang, T., Cardosa, M. J., and Guzman, M. G. (2007). Of cascades and perfect storms: the immunopathogenesis of dengue haemorrhagic fever-dengue shock syndrome (DHF/DSS). Immunol Cell Biol 85, 43-45. []
  4. Stanford, M. M., McFadden, G., Karupiah, G., and Chaudhri, G. (2007). Immunopathogenesis of poxvirus infections: forecasting the impending storm. Immunol Cell Biol 85, 93-102. []
  5. For that matter, there’s no such thing as an “immune system” that exists in glorious isolation somewhere — the whole body is one integrated network. But our tiny little human brains have to start somewhere.[]
  6. Kim, K. D., Zhao, J., Auh, S., Yang, X., Du, P., Tang, H., and Fu, Y. X. (2007). Adaptive immune cells temper initial innate responses. Nat Med 13, 1248-1252. Also see the commentary on this paper: Palm, N. W., and Medzhitov, R. (2007). Not so fast: adaptive suppression of innate immunity. Nat Med 13, 1142-1144. []
  7. Kim, K. D., Zhao, J., Auh, S., Yang, X., Du, P., Tang, H., and Fu, Y. X. (2007). Adaptive immune cells temper initial innate responses. Nat Med 13, 1248-1252.[]
  8. Palm, N. W., and Medzhitov, R. (2007). Not so fast: adaptive suppression of innate immunity. Nat Med 13, 1142-1144. []
November 12th, 2007

Anti-tumor immunity

Breast cancer cellsIt’s pretty much an article of faith for me, as an immunologist, that our immune system normally protects us against cancer. The question is, then, why do we see so much cancer? And why, when we see them, does the immune system pretty much leave them alone, instead of, you know, protecting us?

This is actually a long-running controversy that has gone back and forth over the years. There’s too much history to treat all in one post,1 and indeed there’s circumstantial evidence arguing that in fact immune systems are not major players in cancer resistance. For example, immune deficient mice and humans don’t have huge increases in the frequency of common cancers (though they do, often, develop cancers that are otherwise rare). However, the pendulum swing at the moment has it that the immune system does represent a major barrier to cancer progression.

Our current understanding of tumor development is that it’s a multi-step process. 2 A normal cell undergoes sequential changes in its genome and epigenome that eventually turns it into a pre-cancerous cell, then an overtly cancerous cell, and finally into a malignant cell. Each step in the process represents a checkpoint that blocks progression of most of the cells that reach it. Checkpoints include things like cell-cycle deregulation, independence from growth factors, and so on. As each step is overcome, the new clone of proto-cancerous cells proliferates and expands until it reaches the next checkpoint. At that point, almost all the clones are stopped from progressing further, but if a fortuitous mutation is present in one of the individual cells, it escapes that selection event, proliferates and expands, and moves on to the next point.

Galone Fig 3
Cancer survival and appropriate immune response

The present model is that the immune system is just one checkpoint (though probably a fairly significant barrier) that the developing cancer cell must overcome. That means that by the time we can detect a cancer, it’s already been selected to be immune resistant. The cancers that were susceptible to the immune system were killed off when they were just a little cluster of cells, long before there was anything we could identify. The surprising thing, then, is not that the immune system doesn’t eliminate cancers; it’s that the immune system sometimes actually does contribute to cancer survival. Tumors escape from immune recognition in several ways, and the immune escape is not necessarily irreversible.

Blogging on Peer-Reviewed ResearchFor example, I’ve previously mentioned the recent suggestion that it’s actually the immune system that mediates tumor clearance after chemotherapy, and that the main role of the chemotherapeutic agent is to make the cancer cells recognizable to the immune cells. In other cases, tumor vaccines3 or artificially enhanced T cells4 have been able to break through the tumor’s cloak of invisibility.

Even more encouragingly, it seems that immune responses may actually be ongoing even within a tumor, though perhaps at a level that’s inadequate to keep up with the tumor, and this immune response may be enough to prevent recurrence after surgery. In fact, it was shown last year that spontaneous, appropriate anti-tumor immune responses in colo-rectal tumors correlate well with a good clinical response:5

Our results suggest that once human CRCs6 become clinically detectable, the adaptive immune response plays a role in preventing tumor recurrence. … We found a positive correlation between the presence of markers for TH1 polarization and of cytotoxic and memory T cells and a low incidence of tumor recurrence. This argues for immune-mediated rejection of persistent tumor cells after surgery. We hypothesize that the trafficking properties and long-lasting anti-tumor capacity of memory T cells play a central role in the control of tumor recurrence. … This suggests that time to recurrence and overall survival time are governed in large part by the state of the local adaptive immune response.


  1. Note the cunning way I escape having to work out the details of the history[]
  2. For example, Land, H., Parada, L. F., and Weinberg, R. A. (1983). Cellular oncogenes and multistep carcinogenesis. Science 222, 771-778. []
  3. E.g. Slingluff, C. L. J., Petroni, G. R., Chianese-Bullock, K. A., Smolkin, M. E., Hibbitts, S., Murphy, C., Johansen, N., Grosh, W. W., Yamshchikov, G. V., Neese, P. Y., Patterson, J. W., Fink, R., and Rehm, P. K. (2007). Immunologic and Clinical Outcomes of a Randomized Phase II Trial of Two Multipeptide Vaccines for Melanoma in the Adjuvant Setting. Clin Cancer Res 13, 6386-6395. []
  4. Morgan, R. A., Dudley, M. E., Wunderlich, J. R., Hughes, M. S., Yang, J. C., Sherry, R. M., Royal, R. E., Topalian, S. L., Kammula, U. S., Restifo, N. P., Zheng, Z., Nahvi, A., de Vries, C. R., Rogers-Freezer, L. J., Mavroukakis, S. A., and Rosenberg, S. A. (2006). Cancer regression in patients after transfer of genetically engineered lymphocytes. Science 314, 126-129. []
  5. Galon, J., Costes, A., Sanchez-Cabo, F., Kirilovsky, A., Mlecnik, B., Lagorce-Pages, C., Tosolini, M., Camus, M., Berger, A., Wind, P., Zinzindohoue, F., Bruneval, P., Cugnenc, P. H., Trajanoski, Z., Fridman, W. H., and Pages, F. (2006). Type, density, and location of immune cells within human colorectal tumors predict clinical outcome. Science 313, 1960-1964. []
  6. Colo-Rectal Cancers[]
November 9th, 2007

Ephemera

Ephemeroptera (Mayfly)
Ephemeroptera

One of the questions in antigen processing is what happens to peptides between the time they’re generated, and the time the they bind to MHC class I.

(The reason we care about peptides and MHC is that antiviral lymphocytes react with a complex of peptides and MHC class I, so this is a central point for antiviral immunity. Peptides are formed as a byproduct of normal protein degradation; an outline of the process, should you care, can be found here.)

In general, the peptides we’re interested in are produced by proteasomes. A protein (say, 500 amino acids long) enters the proteasome, the protein is chopped up, and peptides (between 3 and 30 amino acids long) come out. Almost all of those peptides are further chopped up, to produce amino acids – recycling and replenishing the amino acid pool for new protein synthesis. A small fraction of the peptides (perhaps between 0.01% and 1%), though, escape destruction and manage to bind to MHC class I. We would like to know more about that fraction of peptides, because they drive the lymphocyte attack on virus-infected cells. Why are they not destroyed — is it pure chance, or is there something special about the peptides that are not destroyed? How do they reach the MHC — is it chance again, just random diffusion, or is there some kind of specialized shuttle system that ferries the peptides to the proper subcellular location? Is there any active process modifying the peptides, to make them more (or less) suitable for binding MHC? And so on.

The problem is that it’s really hard to look at those peptides. Ideally, we’d like to grab samples of peptides at every point in the process: Exiting the proteasome, in transit, being degraded and processed, and so on. Then we could analyze what they’re like at each step, and develop a time course of modifications, interactions, and so on. But we can’t do that (yet), because it’s really difficult to measure peptides within a living cell.

A couple of years ago Jacques Neefjes (who always turns out cool papers) put some numbers on just how difficult is is.1

Blogging on Peer-Reviewed ResearchThere were a whole bunch of really cool things about this paper, but just focusing on one: Neefjes’ group came up with a way of measuring the rate of peptide destruction in living cells. They added a fluorescent tag to peptides in such a way that it would only fluoresce when the peptide was degraded; injected the tagged peptides into single cells; and measured (again in single cells) the rate at which the fluorescence appeared.

The injected peptides were destroyed with a half-life of 7 seconds. That is, a single cell can destroy hundreds of thousands, or millions, of peptides within a few seconds. (Most of this destruction, by the way, is performed by aminopeptidases, which are very abundant in cytosol.)

That’s not a long time, and it doesn’t give any individual peptide much chance to find its potential MHC binding partner. “A peptide will thus diffuse through the entire cell in 6 s and has to find TAP within this short period for translocation into the ER lumen.”

Why so fast? Why is the cell so worried about letting peptides hang about? Well, we presume this is because peptides are potentially very toxic. These peptides are generated, pretty much randomly, from active proteins. The peptides will therefore include short chunks of active protein domains, separated from any regulatory context; they could conceivably have biological activities by themselves. Also, you’d get hydrophobic chunks that could cluster into degradation-resistant clumps, if you let them accumulate, and it’s believed that such degradation-resistant complexes are themselves toxic. So you need to get rid of peptides fast, before they accumulate to form dangerous side-effects.

As a result, we antigen processing guys have to pretty much guess and use roundabout, indirect methods to measure peptides. Keeps us off the streets, I guess.


  1. Reits, E., Griekspoor, A., Neijssen, J., Groothuis, T., Jalink, K., van Veelen, P., Janssen, H., Calafat, J., Drijfhout, J. W., and Neefjes, J. (2003). Peptide diffusion, protection, and degradation in nuclear and cytoplasmic compartments before antigen presentation by MHC class I. Immunity 18, 97-108 .[]