I’m off for a week’s vacation with the family – camping, etc., and with limited internet access. I’ll be back in the first week of August some time. Talk amongst yourselves.
I’m off for a week’s vacation with the family – camping, etc., and with limited internet access. I’ll be back in the first week of August some time. Talk amongst yourselves.
Today’s issue of Science1 has a number of letters that refer to things I’ve previously talked about here on Mystery Rays.
More plausible than a “RAG transposon” is the insertion of an infectious DNA virus resembling a herpes virus adjacent to the RAG2 protein in a primordial deuterostome.
–David H. Dreyfus
Immune memory, supposedly a characteristic of adaptive immunity and therefore of higher vertebrates, does in fact exist in invertebrates … The adaptive immune system never works on its own [a little-known fact first revealed 20 years ago (4) but subsequently neglected].
I heartily disagree with most of this letter. First, the existence of immunological memory in invertebrates is at best debatable:
Second, far from being “neglected”, the essay that he claims is a “little-known fact” is probably the most famous in immunology; the claim he thinks is neglected, is one of the most basic tenets of modern immunology:
We do not know precisely when the change from Epimethean (reacting) to Promethean (anticipating) took place, and there are no satisfactory intermediate forms (“missing links”) to indicate the steps along the way. But absence of proof is not proof of absence. We may with confidence recognize the Promethean “Big Bang” in immunology as one of the high points in the workings of Darwinian evolution.
—Arthur M. Silverstein
Everyone knows that the MHC is in the MHC, right? Well, it’s not necessarily so.
That’s not as tautological as it sounds. MHC (major histocompatibility complex) can refer to either the protein complex, or to the genomic region. In most species the genes encoding MHC proteins are clustered together into a distinct region of the genome that usually contains a bunch of genes that are functionally, and in some cases structurally, linked. For example, the human MHC genomic region contains not only many MHC class I genes, but also the TAP genes that are required for their function (outline of function here); MHC class II genes, and a number of genes required for their function; some proteasome subunits that are also involved in the antiviral MHC function; and so on. There’s a crude map here, and a somewhat more detailed one here; in humans and many other species the MHC genomic region is densely packed with genes, many of which are immunologically important.
Although the details are different the same concept applies to many vertebrates — chickens 1, Xenopus (frogs),2 and sharks,3 for example, have only one classical MHC class I gene, but it’s recognizably in the MHC genomic region, tightly linked to TAP and not quite as tightly linked to MHC class II genes.
Why are these functionally-related genes clustered together? There are probably a bunch of reasons, and the reasons may actually be different for different species. A recent paper,4 showing a partial exception to the rule, makes some interesting suggestions. Siddle et al5 have looked at wallaby MHC genes and find that their classical MHC class I genes are actually scattered throughout the genome, and are not in the MHC region.
First of all, what’s the advantage of having a single MHC class I gene tightly linked to TAP (probably the primordial organization)? TAP transports peptides to the MHC (again, cartoons of MHC class I function here), and the MHC then presents the peptides to T cells for antiviral surveillance. That means that TAP needs to handle the same kinds6 of peptides that the MHC class I does. By linking the genes for TAP and the MHC class I, the two can evolve in tandem — if a particular MHC class I gene likes to bind peptides ending with, say, arginine, then it can co-evolve along with a TAP that likes to transport peptides ending in arg. MHC class I genes are extremely variable, and in non-mammalian species, TAP genes are also relatively variable, 7 arguing for this kind of co-evolution.
The problem with this organization is that it only really allows one MHC class I specificity. If the TAP has a certain, strong, specificity (ending with Arg, say), and you had several different MHC class I proteins each with different peptide preferences (one that wants peptides ending with Arg, but another that wants peptides ending in tyrosine), then some of them wouldn’t match the TAP peptides and would go wanting.
(By the way, this makes a start at explaining a paper that puzzled me some time ago [post is here]. The chicken B21 MHC class I allele was said to have very weak peptide preferences — allowing “promiscuous peptide binding”. But if TAP has strong peptide preferences, then the MHC is only going to bind to a limited subset of peptides, no matter how promiscuous the MHC is itself. That doesn’t explain everything, but it makes a start. I should mention, though, that a different group looking at B21 did, in fact, identify peptide binding preferences,8 suggesting that binding isn’t actually promiscuous; but now I wonder if they were detecting TAP preferences rather than MHC.)
Although it’s not a hundred percent clear why MHC class I is so diverse,9 according to the most plausible explanations the advantages of diversity are going to be increased if you have several different MHC class I genes, with different peptide-binding properties. If you can hoick the MHC away from TAP, then, you’d allow the MHC to start diversifying independent of TAP. You’d probably need TAP to now be fairly peptide-promiscuous (which it is, in most mammals), and shift the peptide specificity over to the MHC class I molecules themselves.
Humans, mice, and most mammals that have been looked at do this (separate MHC class I from TAP, and have multiple MHC class I alleles) by sliding the MHC class I genes over to the side, remaining within the MHC genomic region but becoming far enough separated from TAP that the genes can evolve more or less independently. Wallabies apparently have done the same thing functionally, but instead of sliding over and keeping the genes in the MHC genomic region, they’re scattered throughout the rest of the genome, apparently via retrotranspon-mediated transposition.
The classical class I have moved away from antigen processing genes in eutherian mammals and the wallaby independently, but both lineages appear to have benefited from this loss of linkage by increasing the number of classical genes, perhaps enabling response to a wider range of pathogens.4
Incidentally, it occurs to me that there is an extra cost to this increased diversity. By un-linking TAP specificity from MHC class I peptide preferences, mammals force TAP to be highly promiscuous, and to transport a wide range of peptides — unlike in chickens, TAP no longer “knows” what MHC allele it’s dealing with and has to offer every possible peptide sequence that any of the thousands of MHC class I alleles could bind. That means that there must be a vast amount of wasted peptides transported into the endoplasmic reticulum; in contrast, I would expect chickens, for example, to predominately only transport peptides that can bind to their MHC class I. If you suspect, as I do, that peptides are intrinsically toxic at high doses, then mammals must have developed (or enhanced) some mechanisms for destroying the extra peptides, that non-mammalian vertebrates don’t have to worry about. I have a guess as to what the mechanism might be, but I’m not sure exactly how to test it right now.
Here we estimated the evolutionary history and inferred date of introduction to humans of each of the genes for all 20th century pandemic influenza strains. Our results indicate that genetic components of the 1918 H1N1 pandemic virus circulated in mammalian hosts, i.e., swine and humans, as early as 1911 and was not likely to be a recently introduced avian virus …. The possible generation of pandemic strains through a series of reassortment events in mammals over a period of years before pandemic recognition suggests that appropriate surveillance strategies for detection of precursor viruses may abort future pandemics.
—Smith, G., Bahl, J., Vijaykrishna, D., Zhang, J., Poon, L., Chen, H., Webster, R., Peiris, J., & Guan, Y. (2009). From the Cover: Dating the emergence of pandemic influenza viruses Proceedings of the National Academy of Sciences, 106 (28), 11709-11712 DOI: 10.1073/pnas.0904991106
Further reading: 1
A year or so ago, the first time I mentioned transmissible tumors, I dismissed Tasmanian Devil Facial Tumor disease as not particularly surprising. As I said more recently, I’ve changed my mind about that, almost entirely because of a chat with Elizabeth Murchison at the Origins of Cancer symposium last month, who told me a couple of things I hadn’t known about the situation.
TDFT is a transmissible tumor, a cancer that arose in one Tasmanian Devil some time ago (at least a decade ago, and maybe much longer) and that is now spreading throughout the Tasmanian Devil population — killing a vast number of them. It’s a tumor that’s spread when these highly territorial animals1 bite each other on the face; the tumor then grows on the bitten animal’s face and eventually makes it unable to eat properly. Nearly 90% of Tasmanian Devils, in affected areas, have died. This is a catastrophe.
(The good news, such as it is, may be that the Devils as a population are adapting to the tumor to some extent — not by resisting the tumor, though, but through rapid selection for much earlier breeding. 2 By reproducing earlier, the population may be maintained even though the Devils are dying as adults. Of course, the population that “survives” won’t be the same as those the existed earlier — they’ll be younger, they’ll have all kinds of different characteristics because they’re no longer being selected for adult survival — but at least it might open a window to save the species.)
Cancers are not, in general, transmissible. Each new cancer is a new event, that arises from normal cells of the affected individual. A transmissible cancer would be like an organ transplant — it would be rapidly rejected, because individuals in a population have different MHC molecules, and the immune system rapidly and aggressively rejects cells with the wrong MHC. So there are two possible reasons why a tumor could, in fact, become transmissible. Either the individuals in a population do not have different MHC molecules on their cells, or the tumor can transmit between individual in spite of different MHC molecules.
The explanation for the spread of TDFT seemed to be the former: It was claimed that Tasmanian Devils have very little MHC diversity, so that they can’t reject the tumors3. Even though MHC is normally highly diverse in a population, there are certainly populations — especially small, island, threatened populations, like Tasmanian Devils — that have very limited MHC diversity, so this seemed reasonably plausible. 4 This would be a fairly well-understood mechanism of tumor spread, which is why I said it wasn’t that interesting.
The other possibility is that the tumor could spread between individuals in spite of them having different MHC molecules. This is not supposed to happen, according to our understanding of MHC and organ transplants; but in fact, it’s the way the only other extant transmissible tumor (Canine Transmissible Venereal Tumor) spreads. We have no idea why that happens, which makes it interesting. (A number of ways have been proposed by which CTVT avoids rejection. I won’t go into them in any detail here: none of them, as far as I can see, are unique to CTVT, but rather are very common molecular changes in tumors of all kinds, and yet other tumors are not transmissible; so I don’t consider any of these suggestions to explain the unique feature of CTVT.)
Anyway, as I say, the explanation for TDFT was simple enough: The tumor spread because Tasmanian Devils aren’t genetically diverse. But there are three major arguments, I’ve learned, that say that explanation is wrong.
First: Tasmanian Devils are not, in fact, spectacularly genetically homogenous. 5 They’re not as diverse as you’d like to see, but they’re not completely homogenous. In particular, there are two clear, genetically distinct, populations of Devils in Tasmania, one in the East, and another in the Northwest.
Second: Murchison told me that Tasmanian Devils — even those in the same sub-population — vigorously reject each others’ skin grafts. This is what’s supposed to happen with skin grafts, of course. It implies that the Devils do not, in fact, have the same MHC; and in my opinion it’s a much stronger experiment than those in the original homogenous-MHC paper. 3 If Devils reject skin grafts from each other, then they ought to reject tumors from each other — in other words, even if the tumor can take in one individual, then it should be rejected in another, so the tumor should not spread throughout the population. The skin graft finding hasn’t, as far as I know, been published, but if it holds up, it’s a strong argument against homogenous MHC.
Third: Murchison also told me that the tumor is spreading into Devils in the Northwest. 6 As I said, the Northwestern and Eastern Tasmanian Devils are clearly distinct populations, with different genetic characteristics. 7 If the tumor can spread between them, then the tumor isn’t relying on genetic homogeneity for its transmission.
So the evidence for MHC homogeneity is not good, the evidence that the tumor requires MHC homogeneity is not good, and the only precedent we know of, CTVT, does not require MHC homogeneity for its transmission.
It seems that the two transmissible tumors we know of may be much more similar than I had thought.
As the overwhelming majority of the mutations in cancer cells are unrelated to malignancy, the mutation-generated epitopes shall be specific for each individual tumor, and constitute the antigenic fingerprint of each tumor. These calculations highlight the benefits for personalization of immunotherapy of human cancer, and in view of the substantial pre-existing antigenic repertoire of tumors, emphasize the enormous potential of therapies that modulate the anti-cancer immune response by liberating it from inhibitory influences.
–Srivastava N, Srivastava PK (2009)
Modeling the Repertoire of True Tumor-Specific MHC I Epitopes in a Human Tumor.
PLoS ONE 4(7): e6094. doi:10.1371/journal.pone.0006094
(See many of my previous posts here for more information)
|Dogs & Wolf (Gotthilf Heinrich von Schubert, 1872)
Naturgeschichte der Säugethiere: mit colorirten
Abbildungen zum Anschauugs-Unterricht für die
Jugend. (Esslingen : Schreiber, 1872)
Cancer is a creepy disease. Your own cells turn on you, mindlessly and blindly destroying themselves — because the only way a cancer can survive is for its host to survive; unlike viruses, cancers don’t spread from their original carrier to new hosts. Each cancer is a new and unique event, and each cancer is a terminal event, with no future, no children, no transmission. 1 Cancers don’t spread between individuals, because they would essentially be tissue transplants; if you try to transplant skin (or whatever) between two animals, the skin will be rapidly rejected because of mismatched MHC alleles, and the same is true for tumors.
In theory, tumors could spread from one identical twin to another (I don’t know of cases where this has occurred, though). Tumors might also theoretically spread within a population that has little MHC diversity. Cheetahs, for example, notoriously don’t have much MHC diversity,2 probably due to a genetic bottleneck some 10,000 years ago,3 and tolerate random skin grafts very well;4 it’s conceivable that a tumor that arose in one cheetah could spread throughout the population. But MHC is generally diverse, and becomes diverse very rapidly, so these sort of low-diversity populations are unusual (though they may be more common than generally realized). And so, as I say, tumors are dead ends and don’t spread from their original host.
But there are always exceptions, and we know of a couple exceptions for this principle as well. Tasmanian Devil Facial Tumor is one; canine transmissible venereal tumor (CTVT) is the other. The last time I talked about this, I said that there wasn’t anything particularly surprising about TDFT. I’ve changed my mind about that, for reasons I’ll talk about later. Here I want to give a quick update on CTVT, which is still even more interesting than TDFT.
CTVT is just what it sounds like: an infectious tumor of dogs. It can be transmitted from one dog to the next, mainly during sex. There’s no sign of a viral agent, and in fact the tumor cells are distinct from the host — that is, the tumor cells are not host cells that have been transformed by, say, a virus, but are foreign agents altogether, cells from an ancient animal that have been passed along in this way, generation after generation, spreading throughout the world. Cells from a CTVT on a German Shepherd in Italy are virtually identical to those from a CTVT on a poodle in Brazil, but the tumor’s cells are very different from their hosts': “… the differences in genome content between dog and CTVT are substantially greater than those between different CTVT samples.” 5
The last time I talked about this I cited a paper6 that showed that the original host of CTVT was actually very ancient: “Our analysis of divergence of microsatellites indicates that the tumor arose between 200 and 2500 years ago.” 6 Amazingly enough, it seemed that the tumor had been passed between dogs perhaps for a couple of thousand years.
But it turns out that it’s even more amazing than that: The 2500 year estimate turns out to be an underestimate. “The estimated time of origin of CTVT is 6500–65,000 years ago. … The cycle of infection currently takes about six months; if this has been true for, say, 15,000 years, then there have been 30,000 transmission events.”5 That spans the age where dogs were domesticated and diverged from wolves , about 10,000-15,000 years ago; and in fact, based on genome analysis of the tumors, the tumors did arise in wolves, not dogs. 7
This raises a fascinating scenario (which I didn’t see spelled out in Reddeck et al, though I think they were hinting at it). It’s still mysterious how CTVT spreads between hosts. As I said, tumors should act like tissue grafts, which are very rapidly rejected if they’re not MHC matched (as is the case with the CTVT and modern dogs). But tumors could, theoretically, spread within a population that has minimal MHC diversity — that is, an inbred population, that has recently undergone a genetic bottleneck. Such a bottleneck very likely happened during the domestication of dogs, as they evolved from wolves. Was the original CTVT a tumor of one of the very first domesticated proto-dogs — an inbred proto-dog,8 a member of a small and inbred population — a spontaneous, fairly ordinary tumor that then spread to the first host’s MHC-matched neighbours in the small and inbred population? That would not be so mysterious; we know tumors can be transplanted between genetically identical hosts, that’s done with lab mice all the time. Then, as the domestic dog population expanded and spread over the world, the tumor would expand and spread along with it, and would have the opportunity to undergo natural selection, adapting to the newly-diverse MHC and to the immune responses that arose after the tumor did. We don’t know, in molecular terms, how the tumor has adapted — we don’t know why it’s able to spread in grow in spite of host immune responses. But at least we can now imagine how the tumor could have reached this point. Thirty thousand transmission events — a couple of million cell divisions — is a long time for a cancer to adapt.
It was suggested at the time, and is widely believed, that cheetahs are particularly susceptible to infectious diseases for this reason, but I think the evidence for this is very weak. Cheetahs have high mortality when infected with feline infectious peritonitis virus, but it’s not unusual for viruses infecting new species to have a high mortality — think SARS and avian influenza in hunans, canine distemper in seals, and feline (or something) parvovirus in dogs, all of which had high mortality in their new, MHC-diverse, host[↩]
|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
|Tb family trees
Life & Death, pre-vaccination
In 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.